A Software Toolkit to Study Systematic Uncertainties of the Physics Models of the Geant4 Simulation Package

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

Genser, Krzysztof; Hatcher, Robert; Perdue, Gabriel

2016-11-10

The Geant4 toolkit is used to model interactions between particles and matter. Geant4 employs a set of validated physics models that span a wide range of interaction energies. These models are tuned to cover a large variety of possible applications. This raises the critical question of what uncertainties are associated with the Geant4 physics model, or group of models, involved in a simulation project. To address the challenge, we have designed and implemented a comprehen- sive, modular, user-friendly software toolkit that allows the variation of one or more parameters of one or more Geant4 physics models involved in simulation studies.more » It also enables analysis of multiple variants of the resulting physics observables of interest in order to estimate the uncertain- ties associated with the simulation model choices. Key functionalities of the toolkit are presented in this paper and are illustrated with selected results.« less

SIGMA Release v1.2 - Capabilities, Enhancements and Fixes

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

Mahadevan, Vijay; Grindeanu, Iulian R.; Ray, Navamita

In this report, we present details on SIGMA toolkit along with its component structure, capabilities, and feature additions in FY15, release cycles, and continuous integration process. These software processes along with updated documentation are imperative to successfully integrate and utilize in several applications including the SHARP coupled analysis toolkit for reactor core systems funded under the NEAMS DOE-NE program.

Integrated Systems Health Management (ISHM) Toolkit

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

PubMed Central

Rampp, Markus; Soddemann, Thomas; Lederer, Hermann

2006-01-01

We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Currently, supported tasks comprise sequence similarity searches in public or user-supplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein–structure prediction. Individual tools can be seamlessly chained into pipelines allowing the user to conveniently process complex workflows without the necessity to take care of any format conversions or tedious parsing of intermediate results. The toolkit is part of the Max-Planck Integrated Gene Analysis System (MIGenAS) of the Max Planck Society available at (click ‘Start Toolkit’). PMID:16844980

The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

PubMed

Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

2013-07-01

The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

Cancer Imaging Phenomics Toolkit (CaPTk) | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

CaPTk is a software toolkit to facilitate translation of quantitative image analysis methods that help us obtain rich imaging phenotypic signatures of oncologic images and relate them to precision diagnostics and prediction of clinical outcomes, as well as to underlying molecular characteristics of cancer. The stand-alone graphical user interface of CaPTk brings analysis methods from the realm of medical imaging research to the clinic, and will be extended to use web-based services for computationally-demanding pipelines.

Toolkit for testing scientific CCD cameras

NASA Astrophysics Data System (ADS)

Uzycki, Janusz; Mankiewicz, Lech; Molak, Marcin; Wrochna, Grzegorz

2006-03-01

The CCD Toolkit (1) is a software tool for testing CCD cameras which allows to measure important characteristics of a camera like readout noise, total gain, dark current, 'hot' pixels, useful area, etc. The application makes a statistical analysis of images saved in files with FITS format, commonly used in astronomy. A graphical interface is based on the ROOT package, which offers high functionality and flexibility. The program was developed in a way to ensure future compatibility with different operating systems: Windows and Linux. The CCD Toolkit was created for the "Pie of the Sky" project collaboration (2).

Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis

PubMed Central

2015-01-01

Efficiently and accurately analyzing big protein tandem mass spectrometry data sets requires robust software that incorporates state-of-the-art computational, machine learning, and statistical methods. The Crux mass spectrometry analysis software toolkit (http://cruxtoolkit.sourceforge.net) is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data. PMID:25182276

Desensitized Optimal Filtering and Sensor Fusion Toolkit

NASA Technical Reports Server (NTRS)

Karlgaard, Christopher D.

2015-01-01

Analytical Mechanics Associates, Inc., has developed a software toolkit that filters and processes navigational data from multiple sensor sources. A key component of the toolkit is a trajectory optimization technique that reduces the sensitivity of Kalman filters with respect to model parameter uncertainties. The sensor fusion toolkit also integrates recent advances in adaptive Kalman and sigma-point filters for non-Gaussian problems with error statistics. This Phase II effort provides new filtering and sensor fusion techniques in a convenient package that can be used as a stand-alone application for ground support and/or onboard use. Its modular architecture enables ready integration with existing tools. A suite of sensor models and noise distribution as well as Monte Carlo analysis capability are included to enable statistical performance evaluations.

"Handy Manny" and the Emergent Literacy Technology Toolkit

ERIC Educational Resources Information Center

Hourcade, Jack J.; Parette, Howard P., Jr.; Boeckmann, Nichole; Blum, Craig

2010-01-01

This paper outlines the use of a technology toolkit to support emergent literacy curriculum and instruction in early childhood education settings. Components of the toolkit include hardware and software that can facilitate key emergent literacy skills. Implementation of the comprehensive technology toolkit enhances the development of these…

The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite.

PubMed

Adolf-Bryfogle, Jared; Dunbrack, Roland L

2013-01-01

The Rosetta Molecular Modeling suite is a command-line-only collection of applications that enable high-resolution modeling and design of proteins and other molecules. Although extremely useful, Rosetta can be difficult to learn for scientists with little computational or programming experience. To that end, we have created a Graphical User Interface (GUI) for Rosetta, called the PyRosetta Toolkit, for creating and running protocols in Rosetta for common molecular modeling and protein design tasks and for analyzing the results of Rosetta calculations. The program is highly extensible so that developers can add new protocols and analysis tools to the PyRosetta Toolkit GUI.

QALMA: A computational toolkit for the analysis of quality protocols for medical linear accelerators in radiation therapy

NASA Astrophysics Data System (ADS)

Rahman, Md Mushfiqur; Lei, Yu; Kalantzis, Georgios

2018-01-01

Quality Assurance (QA) for medical linear accelerator (linac) is one of the primary concerns in external beam radiation Therapy. Continued advancements in clinical accelerators and computer control technology make the QA procedures more complex and time consuming which often, adequate software accompanied with specific phantoms is required. To ameliorate that matter, we introduce QALMA (Quality Assurance for Linac with MATLAB), a MALAB toolkit which aims to simplify the quantitative analysis of QA for linac which includes Star-Shot analysis, Picket Fence test, Winston-Lutz test, Multileaf Collimator (MLC) log file analysis and verification of light & radiation field coincidence test.

The image-guided surgery toolkit IGSTK: an open source C++ software toolkit.

PubMed

Enquobahrie, Andinet; Cheng, Patrick; Gary, Kevin; Ibanez, Luis; Gobbi, David; Lindseth, Frank; Yaniv, Ziv; Aylward, Stephen; Jomier, Julien; Cleary, Kevin

2007-11-01

This paper presents an overview of the image-guided surgery toolkit (IGSTK). IGSTK is an open source C++ software library that provides the basic components needed to develop image-guided surgery applications. It is intended for fast prototyping and development of image-guided surgery applications. The toolkit was developed through a collaboration between academic and industry partners. Because IGSTK was designed for safety-critical applications, the development team has adopted lightweight software processes that emphasizes safety and robustness while, at the same time, supporting geographically separated developers. A software process that is philosophically similar to agile software methods was adopted emphasizing iterative, incremental, and test-driven development principles. The guiding principle in the architecture design of IGSTK is patient safety. The IGSTK team implemented a component-based architecture and used state machine software design methodologies to improve the reliability and safety of the components. Every IGSTK component has a well-defined set of features that are governed by state machines. The state machine ensures that the component is always in a valid state and that all state transitions are valid and meaningful. Realizing that the continued success and viability of an open source toolkit depends on a strong user community, the IGSTK team is following several key strategies to build an active user community. These include maintaining a users and developers' mailing list, providing documentation (application programming interface reference document and book), presenting demonstration applications, and delivering tutorial sessions at relevant scientific conferences.

Basic Internet Software Toolkit.

ERIC Educational Resources Information Center

Buchanan, Larry

1998-01-01

Once schools are connected to the Internet, the next step is getting network workstations configured for Internet access. This article describes a basic toolkit comprising software currently available on the Internet for free or modest cost. Lists URLs for Web browser, Telnet, FTP, file decompression, portable document format (PDF) reader,…

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis :

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

Adams, Brian M.; Ebeida, Mohamed Salah; Eldred, Michael S.

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components requiredmore » for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a user's manual for the Dakota software and provides capability overviews and procedures for software execution, as well as a variety of example studies.« less

A Toolkit to Study Sensitivity of the Geant4 Predictions to the Variations of the Physics Model Parameters

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

Fields, Laura; Genser, Krzysztof; Hatcher, Robert

Geant4 is the leading detector simulation toolkit used in high energy physics to design detectors and to optimize calibration and reconstruction software. It employs a set of carefully validated physics models to simulate interactions of particles with matter across a wide range of interaction energies. These models, especially the hadronic ones, rely largely on directly measured cross-sections and phenomenological predictions with physically motivated parameters estimated by theoretical calculation or measurement. Because these models are tuned to cover a very wide range of possible simulation tasks, they may not always be optimized for a given process or a given material. Thismore » raises several critical questions, e.g. how sensitive Geant4 predictions are to the variations of the model parameters, or what uncertainties are associated with a particular tune of a Geant4 physics model, or a group of models, or how to consistently derive guidance for Geant4 model development and improvement from a wide range of available experimental data. We have designed and implemented a comprehensive, modular, user-friendly software toolkit to study and address such questions. It allows one to easily modify parameters of one or several Geant4 physics models involved in the simulation, and to perform collective analysis of multiple variants of the resulting physics observables of interest and comparison against a variety of corresponding experimental data. Based on modern event-processing infrastructure software, the toolkit offers a variety of attractive features, e.g. flexible run-time configurable workflow, comprehensive bookkeeping, easy to expand collection of analytical components. Design, implementation technology, and key functionalities of the toolkit are presented and illustrated with results obtained with Geant4 key hadronic models.« less

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

PubMed

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

2002-01-01

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

A Scalable Analysis Toolkit

NASA Technical Reports Server (NTRS)

Aiken, Alexander

2001-01-01

The Scalable Analysis Toolkit (SAT) project aimed to demonstrate that it is feasible and useful to statically detect software bugs in very large systems. The technical focus of the project was on a relatively new class of constraint-based techniques for analysis software, where the desired facts about programs (e.g., the presence of a particular bug) are phrased as constraint problems to be solved. At the beginning of this project, the most successful forms of formal software analysis were limited forms of automatic theorem proving (as exemplified by the analyses used in language type systems and optimizing compilers), semi-automatic theorem proving for full verification, and model checking. With a few notable exceptions these approaches had not been demonstrated to scale to software systems of even 50,000 lines of code. Realistic approaches to large-scale software analysis cannot hope to make every conceivable formal method scale. Thus, the SAT approach is to mix different methods in one application by using coarse and fast but still adequate methods at the largest scales, and reserving the use of more precise but also more expensive methods at smaller scales for critical aspects (that is, aspects critical to the analysis problem under consideration) of a software system. The principled method proposed for combining a heterogeneous collection of formal systems with different scalability characteristics is mixed constraints. This idea had been used previously in small-scale applications with encouraging results: using mostly coarse methods and narrowly targeted precise methods, useful information (meaning the discovery of bugs in real programs) was obtained with excellent scalability.

The Visible Human Data Sets (VHD) and Insight Toolkit (ITk): Experiments in Open Source Software

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

From its inception in 1989, the Visible Human Project was designed as an experiment in open source software. In 1994 and 1995 the male and female Visible Human data sets were released by the National Library of Medicine (NLM) as open source data sets. In 2002 the NLM released the first version of the Insight Toolkit (ITk) as open source software. PMID:14728278

Technical note: DIRART--A software suite for deformable image registration and adaptive radiotherapy research.

PubMed

Yang, Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu, Yu; Goddu, S Murty; Mutic, Sasa; Deasy, Joseph O; Low, Daniel A

2011-01-01

Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. DIRART provides a set of image processing/registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research. 0 2011 Ameri-

The development of an artificial organic networks toolkit for LabVIEW.

PubMed

Ponce, Hiram; Ponce, Pedro; Molina, Arturo

2015-03-15

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

The Bio-Community Perl toolkit for microbial ecology.

PubMed

Angly, Florent E; Fields, Christopher J; Tyson, Gene W

2014-07-01

The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software. Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute. © The Author 2014. Published by Oxford University Press.

Toolkit of Available EPA Green Infrastructure Modeling Software. National Stormwater Calculator

EPA Science Inventory

This webinar will present a toolkit consisting of five EPA green infrastructure models and tools, along with communication material. This toolkit can be used as a teaching and quick reference resource for use by planners and developers when making green infrastructure implementat...

The 2006 NESCent Phyloinformatics Hackathon: A Field Report

PubMed Central

Lapp, Hilmar; Bala, Sendu; Balhoff, James P.; Bouck, Amy; Goto, Naohisa; Holder, Mark; Holland, Richard; Holloway, Alisha; Katayama, Toshiaki; Lewis, Paul O.; Mackey, Aaron J.; Osborne, Brian I.; Piel, William H.; Kosakovsky Pond, Sergei L.; Poon, Art F.Y.; Qiu, Wei-Gang; Stajich, Jason E.; Stoltzfus, Arlin; Thierer, Tobias; Vilella, Albert J.; Vos, Rutger A.; Zmasek, Christian M.; Zwickl, Derrick J.; Vision, Todd J.

2007-01-01

In December, 2006, a group of 26 software developers from some of the most widely used life science programming toolkits and phylogenetic software projects converged on Durham, North Carolina, for a Phyloinformatics Hackathon, an intense five-day collaborative software coding event sponsored by the National Evolutionary Synthesis Center (NESCent). The goal was to help researchers to integrate multiple phylogenetic software tools into automated workflows. Participants addressed deficiencies in interoperability between programs by implementing “glue code” and improving support for phylogenetic data exchange standards (particularly NEXUS) across the toolkits. The work was guided by use-cases compiled in advance by both developers and users, and the code was documented as it was developed. The resulting software is freely available for both users and developers through incorporation into the distributions of several widely-used open-source toolkits. We explain the motivation for the hackathon, how it was organized, and discuss some of the outcomes and lessons learned. We conclude that hackathons are an effective mode of solving problems in software interoperability and usability, and are underutilized in scientific software development.

EduSpeak[R]: A Speech Recognition and Pronunciation Scoring Toolkit for Computer-Aided Language Learning Applications

ERIC Educational Resources Information Center

Franco, Horacio; Bratt, Harry; Rossier, Romain; Rao Gadde, Venkata; Shriberg, Elizabeth; Abrash, Victor; Precoda, Kristin

2010-01-01

SRI International's EduSpeak[R] system is a software development toolkit that enables developers of interactive language education software to use state-of-the-art speech recognition and pronunciation scoring technology. Automatic pronunciation scoring allows the computer to provide feedback on the overall quality of pronunciation and to point to…

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

NASA Technical Reports Server (NTRS)

Bancroft, Gordon V.; Kelaita, Paul G.; Mccabe, R. Kevin; Merritt, Fergus J.; Plessel, Todd C.; Sandstrom, Timothy A.; West, John T.

1993-01-01

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described.

pyPcazip: A PCA-based toolkit for compression and analysis of molecular simulation data

NASA Astrophysics Data System (ADS)

Shkurti, Ardita; Goni, Ramon; Andrio, Pau; Breitmoser, Elena; Bethune, Iain; Orozco, Modesto; Laughton, Charles A.

The biomolecular simulation community is currently in need of novel and optimised software tools that can analyse and process, in reasonable timescales, the large generated amounts of molecular simulation data. In light of this, we have developed and present here pyPcazip: a suite of software tools for compression and analysis of molecular dynamics (MD) simulation data. The software is compatible with trajectory file formats generated by most contemporary MD engines such as AMBER, CHARMM, GROMACS and NAMD, and is MPI parallelised to permit the efficient processing of very large datasets. pyPcazip is a Unix based open-source software (BSD licenced) written in Python.

Technical Note: DIRART – A software suite for deformable image registration and adaptive radiotherapy research

PubMed Central

Yang, Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu, Yu; Murty Goddu, S.; Mutic, Sasa; Deasy, Joseph O.; Low, Daniel A.

2011-01-01

Purpose: Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). Methods:DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. Results: DIRART provides a set of image processing∕registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. Conclusions: By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research. PMID:21361176

Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field.

PubMed

Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

2015-01-01

There has been huge progress in the open cheminformatics field in both methods and software development. Unfortunately, there has been little effort to unite those methods and software into one package. We here describe the Open Drug Discovery Toolkit (ODDT), which aims to fulfill the need for comprehensive and open source drug discovery software. The Open Drug Discovery Toolkit was developed as a free and open source tool for both computer aided drug discovery (CADD) developers and researchers. ODDT reimplements many state-of-the-art methods, such as machine learning scoring functions (RF-Score and NNScore) and wraps other external software to ease the process of developing CADD pipelines. ODDT is an out-of-the-box solution designed to be easily customizable and extensible. Therefore, users are strongly encouraged to extend it and develop new methods. We here present three use cases for ODDT in common tasks in computer-aided drug discovery. Open Drug Discovery Toolkit is released on a permissive 3-clause BSD license for both academic and industrial use. ODDT's source code, additional examples and documentation are available on GitHub (https://github.com/oddt/oddt).

Design Optimization Toolkit: Users' Manual

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

Aguilo Valentin, Miguel Alejandro

The Design Optimization Toolkit (DOTk) is a stand-alone C++ software package intended to solve complex design optimization problems. DOTk software package provides a range of solution methods that are suited for gradient/nongradient-based optimization, large scale constrained optimization, and topology optimization. DOTk was design to have a flexible user interface to allow easy access to DOTk solution methods from external engineering software packages. This inherent flexibility makes DOTk barely intrusive to other engineering software packages. As part of this inherent flexibility, DOTk software package provides an easy-to-use MATLAB interface that enables users to call DOTk solution methods directly from the MATLABmore » command window.« less

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

PubMed

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

2010-12-21

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

Matlab based Toolkits used to Interface with Optical Design Software for NASA's James Webb Space Telescope

NASA Technical Reports Server (NTRS)

Howard, Joseph

2007-01-01

The viewgraph presentation provides an introduction to the James Webb Space Telescope (JWST). The first part provides a brief overview of Matlab toolkits including CodeV, OSLO, and Zemax Toolkits. The toolkit overview examines purpose, layout, how Matlab gets data from CodeV, function layout, and using cvHELP. The second part provides examples of use with JWST, including wavefront sensitivities and alignment simulations.

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

PubMed

Klemm, Martin; Kirchner, Thomas; Gröhl, Janek; Cheray, Dominique; Nolden, Marco; Seitel, Alexander; Hoppe, Harald; Maier-Hein, Lena; Franz, Alfred M

2017-03-01

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000 Hz and a latency of 2.81 ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128 Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

Fragment Impact Toolkit (FIT)

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

Shevitz, Daniel Wolf; Key, Brian P.; Garcia, Daniel B.

2017-09-05

The Fragment Impact Toolkit (FIT) is a software package used for probabilistic consequence evaluation of fragmenting sources. The typical use case for FIT is to simulate an exploding shell and evaluate the consequence on nearby objects. FIT is written in the programming language Python and is designed as a collection of interacting software modules. Each module has a function that interacts with the other modules to produce desired results.

WIRM: An Open Source Toolkit for Building Biomedical Web Applications

PubMed Central

Jakobovits, Rex M.; Rosse, Cornelius; Brinkley, James F.

2002-01-01

This article describes an innovative software toolkit that allows the creation of web applications that facilitate the acquisition, integration, and dissemination of multimedia biomedical data over the web, thereby reducing the cost of knowledge sharing. There is a lack of high-level web application development tools suitable for use by researchers, clinicians, and educators who are not skilled programmers. Our Web Interfacing Repository Manager (WIRM) is a software toolkit that reduces the complexity of building custom biomedical web applications. WIRM’s visual modeling tools enable domain experts to describe the structure of their knowledge, from which WIRM automatically generates full-featured, customizable content management systems. PMID:12386108

NeuroMatic: An Integrated Open-Source Software Toolkit for Acquisition, Analysis and Simulation of Electrophysiological Data

PubMed Central

Rothman, Jason S.; Silver, R. Angus

2018-01-01

Acquisition, analysis and simulation of electrophysiological properties of the nervous system require multiple software packages. This makes it difficult to conserve experimental metadata and track the analysis performed. It also complicates certain experimental approaches such as online analysis. To address this, we developed NeuroMatic, an open-source software toolkit that performs data acquisition (episodic, continuous and triggered recordings), data analysis (spike rasters, spontaneous event detection, curve fitting, stationarity) and simulations (stochastic synaptic transmission, synaptic short-term plasticity, integrate-and-fire and Hodgkin-Huxley-like single-compartment models). The merging of a wide range of tools into a single package facilitates a more integrated style of research, from the development of online analysis functions during data acquisition, to the simulation of synaptic conductance trains during dynamic-clamp experiments. Moreover, NeuroMatic has the advantage of working within Igor Pro, a platform-independent environment that includes an extensive library of built-in functions, a history window for reviewing the user's workflow and the ability to produce publication-quality graphics. Since its original release, NeuroMatic has been used in a wide range of scientific studies and its user base has grown considerably. NeuroMatic version 3.0 can be found at http://www.neuromatic.thinkrandom.com and https://github.com/SilverLabUCL/NeuroMatic. PMID:29670519

SHARP pre-release v1.0 - Current Status and Documentation

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

Mahadevan, Vijay S.; Rahaman, Ronald O.

The NEAMS Reactor Product Line effort aims to develop an integrated multiphysics simulation capability for the design and analysis of future generations of nuclear power plants. The Reactor Product Line code suite’s multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. In this report, building on a several previous report issued in September 2014, we describe our continued efforts to integrate thermal/hydraulics, neutronics, and structural mechanics modeling codes to perform coupled analysis of a representativemore » fast sodium-cooled reactor core in preparation for a unified release of the toolkit. The work reported in the current document covers the software engineering aspects of managing the entire stack of components in the SHARP toolkit and the continuous integration efforts ongoing to prepare a release candidate for interested reactor analysis users. Here we report on the continued integration effort of PROTEUS/Nek5000 and Diablo into the NEAMS framework and the software processes that enable users to utilize the capabilities without losing scientific productivity. Due to the complexity of the individual modules and their necessary/optional dependency library chain, we focus on the configuration and build aspects for the SHARP toolkit, which includes capability to autodownload dependencies and configure/install with optimal flags in an architecture-aware fashion. Such complexity is untenable without strong software engineering processes such as source management, source control, change reviews, unit tests, integration tests and continuous test suites. Details on these processes are provided in the report as a building step for a SHARP user guide that will accompany the first release, expected by Mar 2016.« less

Monitoring Areal Snow Cover Using NASA Satellite Imagery

NASA Technical Reports Server (NTRS)

Harshburger, Brian J.; Blandford, Troy; Moore, Brandon

2011-01-01

The objective of this project is to develop products and tools to assist in the hydrologic modeling process, including tools to help prepare inputs for hydrologic models and improved methods for the visualization of streamflow forecasts. In addition, this project will facilitate the use of NASA satellite imagery (primarily snow cover imagery) by other federal and state agencies with operational streamflow forecasting responsibilities. A GIS software toolkit for monitoring areal snow cover extent and producing streamflow forecasts is being developed. This toolkit will be packaged as multiple extensions for ArcGIS 9.x and an opensource GIS software package. The toolkit will provide users with a means for ingesting NASA EOS satellite imagery (snow cover analysis), preparing hydrologic model inputs, and visualizing streamflow forecasts. Primary products include a software tool for predicting the presence of snow under clouds in satellite images; a software tool for producing gridded temperature and precipitation forecasts; and a suite of tools for visualizing hydrologic model forecasting results. The toolkit will be an expert system designed for operational users that need to generate accurate streamflow forecasts in a timely manner. The Remote Sensing of Snow Cover Toolbar will ingest snow cover imagery from multiple sources, including the MODIS Operational Snowcover Data and convert them to gridded datasets that can be readily used. Statistical techniques will then be applied to the gridded snow cover data to predict the presence of snow under cloud cover. The toolbar has the ability to ingest both binary and fractional snow cover data. Binary mapping techniques use a set of thresholds to determine whether a pixel contains snow or no snow. Fractional mapping techniques provide information regarding the percentage of each pixel that is covered with snow. After the imagery has been ingested, physiographic data is attached to each cell in the snow cover image. This data can be obtained from a digital elevation model (DEM) for the area of interest.

Implementing Project Based Survey Research Skills to Grade Six ELP Students with "The Survey Toolkit" and "TinkerPlots"[R

ERIC Educational Resources Information Center

Walsh, Thomas, Jr.

2011-01-01

"Survey Toolkit Collecting Information, Analyzing Data and Writing Reports" (Walsh, 2009a) is discussed as a survey research curriculum used by the author's sixth grade students. The report describes the implementation of "The Survey Toolkit" curriculum and "TinkerPlots"[R] software to provide instruction to students learning a project based…

An Automated Method for Identifying Inconsistencies within Diagrammatic Software Requirements Specifications

NASA Technical Reports Server (NTRS)

Zhang, Zhong

1997-01-01

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

VoroTop: Voronoi cell topology visualization and analysis toolkit

NASA Astrophysics Data System (ADS)

Lazar, Emanuel A.

2018-01-01

This paper introduces a new open-source software program called VoroTop, which uses Voronoi topology to analyze local structure in atomic systems. Strengths of this approach include its abilities to analyze high-temperature systems and to characterize complex structure such as grain boundaries. This approach enables the automated analysis of systems and mechanisms previously not possible.

Integrating existing software toolkits into VO system

NASA Astrophysics Data System (ADS)

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

2004-09-01

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

Telescience Resource Kit (TReK)

NASA Technical Reports Server (NTRS)

Lippincott, Jeff

2015-01-01

Telescience Resource Kit (TReK) is one of the Huntsville Operations Support Center (HOSC) remote operations solutions. It can be used to monitor and control International Space Station (ISS) payloads from anywhere in the world. It is comprised of a suite of software applications and libraries that provide generic data system capabilities and access to HOSC services. The TReK Software has been operational since 2000. A new cross-platform version of TReK is under development. The new software is being released in phases during the 2014-2016 timeframe. The TReK Release 3.x series of software is the original TReK software that has been operational since 2000. This software runs on Windows. It contains capabilities to support traditional telemetry and commanding using CCSDS (Consultative Committee for Space Data Systems) packets. The TReK Release 4.x series of software is the new cross platform software. It runs on Windows and Linux. The new TReK software will support communication using standard IP protocols and traditional telemetry and commanding. All the software listed above is compatible and can be installed and run together on Windows. The new TReK software contains a suite of software that can be used by payload developers on the ground and onboard (TReK Toolkit). TReK Toolkit is a suite of lightweight libraries and utility applications for use onboard and on the ground. TReK Desktop is the full suite of TReK software -most useful on the ground. When TReK Desktop is released, the TReK installation program will provide the option to choose just the TReK Toolkit portion of the software or the full TReK Desktop suite. The ISS program is providing the TReK Toolkit software as a generic flight software capability offered as a standard service to payloads. TReK Software Verification was conducted during the April/May 2015 timeframe. Payload teams using the TReK software onboard can reference the TReK software verification. TReK will be demonstrated on-orbit running on an ISS provided T61p laptop. Target Timeframe: September 2015 -2016. The on-orbit demonstration will collect benchmark metrics, and will be used in the future to provide live demonstrations during ISS Payload Conferences. Benchmark metrics and demonstrations will address the protocols described in SSP 52050-0047 Ku Forward section 3.3.7. (Associated term: CCSDS File Delivery Protocol (CFDP)).

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.

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications.

PubMed

Incarnato, Danny; Morandi, Edoardo; Simon, Lisa Marie; Oliviero, Salvatore

2018-06-09

RNA is emerging as a key regulator of a plethora of biological processes. While its study has remained elusive for decades, the recent advent of high-throughput sequencing technologies provided the unique opportunity to develop novel techniques for the study of RNA structure and post-transcriptional modifications. Nonetheless, most of the required downstream bioinformatics analyses steps are not easily reproducible, thus making the application of these techniques a prerogative of few laboratories. Here we introduce RNA Framework, an all-in-one toolkit for the analysis of most NGS-based RNA structure probing and post-transcriptional modification mapping experiments. To prove the extreme versatility of RNA Framework, we applied it to both an in-house generated DMS-MaPseq dataset, and to a series of literature available experiments. Notably, when starting from publicly available datasets, our software easily allows replicating authors' findings. Collectively, RNA Framework provides the most complete and versatile toolkit to date for a rapid and streamlined analysis of the RNA epistructurome. RNA Framework is available for download at: http://www.rnaframework.com.

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

PubMed Central

2010-01-01

Background There is a huge demand on bioinformaticians to provide their biologists with user friendly and scalable software infrastructures to capture, exchange, and exploit the unprecedented amounts of new *omics data. We here present MOLGENIS, a generic, open source, software toolkit to quickly produce the bespoke MOLecular GENetics Information Systems needed. Methods The MOLGENIS toolkit provides bioinformaticians with a simple language to model biological data structures and user interfaces. At the push of a button, MOLGENIS’ generator suite automatically translates these models into a feature-rich, ready-to-use web application including database, user interfaces, exchange formats, and scriptable interfaces. Each generator is a template of SQL, JAVA, R, or HTML code that would require much effort to write by hand. This ‘model-driven’ method ensures reuse of best practices and improves quality because the modeling language and generators are shared between all MOLGENIS applications, so that errors are found quickly and improvements are shared easily by a re-generation. A plug-in mechanism ensures that both the generator suite and generated product can be customized just as much as hand-written software. Results In recent years we have successfully evaluated the MOLGENIS toolkit for the rapid prototyping of many types of biomedical applications, including next-generation sequencing, GWAS, QTL, proteomics and biobanking. Writing 500 lines of model XML typically replaces 15,000 lines of hand-written programming code, which allows for quick adaptation if the information system is not yet to the biologist’s satisfaction. Each application generated with MOLGENIS comes with an optimized database back-end, user interfaces for biologists to manage and exploit their data, programming interfaces for bioinformaticians to script analysis tools in R, Java, SOAP, REST/JSON and RDF, a tab-delimited file format to ease upload and exchange of data, and detailed technical documentation. Existing databases can be quickly enhanced with MOLGENIS generated interfaces using the ‘ExtractModel’ procedure. Conclusions The MOLGENIS toolkit provides bioinformaticians with a simple model to quickly generate flexible web platforms for all possible genomic, molecular and phenotypic experiments with a richness of interfaces not provided by other tools. All the software and manuals are available free as LGPLv3 open source at http://www.molgenis.org. PMID:21210979

Flightspeed Integral Image Analysis Toolkit

NASA Technical Reports Server (NTRS)

Thompson, David R.

2009-01-01

The Flightspeed Integral Image Analysis Toolkit (FIIAT) is a C library that provides image analysis functions in a single, portable package. It provides basic low-level filtering, texture analysis, and subwindow descriptor for applications dealing with image interpretation and object recognition. Designed with spaceflight in mind, it addresses: Ease of integration (minimal external dependencies) Fast, real-time operation using integer arithmetic where possible (useful for platforms lacking a dedicated floatingpoint processor) Written entirely in C (easily modified) Mostly static memory allocation 8-bit image data The basic goal of the FIIAT library is to compute meaningful numerical descriptors for images or rectangular image regions. These n-vectors can then be used directly for novelty detection or pattern recognition, or as a feature space for higher-level pattern recognition tasks. The library provides routines for leveraging training data to derive descriptors that are most useful for a specific data set. Its runtime algorithms exploit a structure known as the "integral image." This is a caching method that permits fast summation of values within rectangular regions of an image. This integral frame facilitates a wide range of fast image-processing functions. This toolkit has applicability to a wide range of autonomous image analysis tasks in the space-flight domain, including novelty detection, object and scene classification, target detection for autonomous instrument placement, and science analysis of geomorphology. It makes real-time texture and pattern recognition possible for platforms with severe computational restraints. The software provides an order of magnitude speed increase over alternative software libraries currently in use by the research community. FIIAT can commercially support intelligent video cameras used in intelligent surveillance. It is also useful for object recognition by robots or other autonomous vehicles

SIGKit: a New Data-based Software for Learning Introductory Geophysics

NASA Astrophysics Data System (ADS)

Zhang, Y.; Kruse, S.; George, O.; Esmaeili, S.; Papadimitrios, K. S.; Bank, C. G.; Cadmus, A.; Kenneally, N.; Patton, K.; Brusher, J.

2016-12-01

Students of diverse academic backgrounds take introductory geophysics courses to learn the theory of a variety of measurement and analysis methods with the expectation to be able to apply their basic knowledge to real data. Ideally, such data is collected in field courses and also used in lecture-based courses because they provide a critical context for better learning and understanding of geophysical methods. Each method requires a separate software package for the data processing steps, and the complexity and variety of professional software makes the path through data processing to data interpretation a strenuous learning process for students and a challenging teaching task for instructors. SIGKit (Student Investigation of Geophysics Toolkit) being developed as a collaboration between the University of South Florida, the University of Toronto, and MathWorks intends to address these shortcomings by showing the most essential processing steps and allowing students to visualize the underlying physics of the various methods. It is based on MATLAB software and offered as an easy-to-use graphical user interface and packaged so it can run as an executable in the classroom and the field even on computers without MATLAB licenses. An evaluation of the software based on student feedback from focus-group interviews and think-aloud observations helps drive its development and refinement. The toolkit provides a logical gateway into the more sophisticated and costly software students will encounter later in their training and careers by combining essential visualization, modeling, processing, and analysis steps for seismic, GPR, magnetics, gravity, resistivity, and electromagnetic data.

A Toolkit to assess health needs for congenital disorders in low- and middle-income countries: an instrument for public health action.

PubMed

Nacul, L C; Stewart, A; Alberg, C; Chowdhury, S; Darlison, M W; Grollman, C; Hall, A; Modell, B; Moorthie, S; Sagoo, G S; Burton, H

2014-06-01

In 2010 the World Health Assembly called for action to improve the care and prevention of congenital disorders, noting that technical guidance would be required for this task, especially in low- and middle-income countries. Responding to this call, we have developed a freely available web-accessible Toolkit for assessing health needs for congenital disorders. Materials for the Toolkit website (http://toolkit.phgfoundation.org) were prepared by an iterative process of writing, discussion and modification by the project team, with advice from external experts. A customized database was developed using epidemiological, demographic, socio-economic and health-services data from a range of validated sources. Document-processing and data integration software combines data from the database with a template to generate topic- and country-specific Calculator documents for quantitative analysis. The Toolkit guides users through selection of topics (including both clinical conditions and relevant health services), assembly and evaluation of qualitative and quantitative information, assessment of the potential effects of selected interventions, and planning and prioritization of actions to reduce the risk or prevalence of congenital disorders. The Toolkit enables users without epidemiological or public health expertise to undertake health needs assessment as a prerequisite for strategic planning in relation to congenital disorders in their country or region. © The Author 2013. Published by Oxford University Press on behalf of Faculty of Public Health.

The Seismic Tool-Kit (STK): an open source software for seismology and signal processing.

NASA Astrophysics Data System (ADS)

Reymond, Dominique

2016-04-01

We present an open source software project (GNU public license), named STK: Seismic ToolKit, that is dedicated mainly for seismology and signal processing. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 19 500 downloads at the date of writing. The STK project is composed of two main branches: First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The estimation of spectral density of the signal are performed via the Fourier transform, with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noize), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. A MINimum library of Linear AlGebra (MIN-LINAG) is also provided for computing the main matrix process like: QR/QL decomposition, Cholesky solve of linear system, finding eigen value/eigen vectors, QR-solve/Eigen-solve of linear equations systems ... etc. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. Usefull links: http://sourceforge.net/projects/seismic-toolkit/ http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

PubMed

Moody, George B; Mark, Roger G; Goldberger, Ary L

2011-01-01

PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

Designing Tracking Software for Image-Guided Surgery Applications: IGSTK Experience

PubMed Central

Enquobahrie, Andinet; Gobbi, David; Turek, Matt; Cheng, Patrick; Yaniv, Ziv; Lindseth, Frank; Cleary, Kevin

2009-01-01

Objective Many image-guided surgery applications require tracking devices as part of their core functionality. The Image-Guided Surgery Toolkit (IGSTK) was designed and developed to interface tracking devices with software applications incorporating medical images. Methods IGSTK was designed as an open source C++ library that provides the basic components needed for fast prototyping and development of image-guided surgery applications. This library follows a component-based architecture with several components designed for specific sets of image-guided surgery functions. At the core of the toolkit is the tracker component that handles communication between a control computer and navigation device to gather pose measurements of surgical instruments present in the surgical scene. The representations of the tracked instruments are superimposed on anatomical images to provide visual feedback to the clinician during surgical procedures. Results The initial version of the IGSTK toolkit has been released in the public domain and several trackers are supported. The toolkit and related information are available at www.igstk.org. Conclusion With the increased popularity of minimally invasive procedures in health care, several tracking devices have been developed for medical applications. Designing and implementing high-quality and safe software to handle these different types of trackers in a common framework is a challenging task. It requires establishing key software design principles that emphasize abstraction, extensibility, reusability, fault-tolerance, and portability. IGSTK is an open source library that satisfies these needs for the image-guided surgery community. PMID:20037671

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

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

BamTools: a C++ API and toolkit for analyzing and managing BAM files.

PubMed

Barnett, Derek W; Garrison, Erik K; Quinlan, Aaron R; Strömberg, Michael P; Marth, Gabor T

2011-06-15

Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.

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

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

The Archivists' Toolkit: Another Step toward Streamlined Archival Processing

ERIC Educational Resources Information Center

Westbrook, Bradley D.; Mandell, Lee; Shepherd, Kelcy; Stevens, Brian; Varghese, Jason

2006-01-01

The Archivists' Toolkit is a software application currently in development and designed to support the creation and management of archival information. This article summarizes the development of the application, including some of the problems the application is designed to resolve. Primary emphasis is placed on describing the application's…

GABBs: Cyberinfrastructure for Self-Service Geospatial Data Exploration, Computation, and Sharing

NASA Astrophysics Data System (ADS)

Song, C. X.; Zhao, L.; Biehl, L. L.; Merwade, V.; Villoria, N.

2016-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. In addressing these needs, the Geospatial data Analysis Building Blocks (GABBs) project aims at building geospatial modeling, data analysis and visualization capabilities in an open source web platform, HUBzero. Funded by NSF's Data Infrastructure Building Blocks initiative, GABBs is creating a geospatial data architecture that integrates spatial data management, mapping and visualization, and interfaces in the HUBzero platform for scientific collaborations. The geo-rendering enabled Rappture toolkit, a generic Python mapping library, geospatial data exploration and publication tools, and an integrated online geospatial data management solution are among the software building blocks from the project. The GABBS software will be available through Amazon's AWS Marketplace VM images and open source. Hosting services are also available to the user community. The outcome of the project will enable researchers and educators to self-manage their scientific data, rapidly create GIS-enable tools, share geospatial data and tools on the web, and build dynamic workflows connecting data and tools, all without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the GABBs architecture, toolkits and libraries, and showcase the scientific use cases that utilize GABBs capabilities, as well as the challenges and solutions for GABBs to interoperate with other cyberinfrastructure platforms.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

Open cyberGIS software for geospatial research and education in the big data era

NASA Astrophysics Data System (ADS)

Wang, Shaowen; Liu, Yan; Padmanabhan, Anand

CyberGIS represents an interdisciplinary field combining advanced cyberinfrastructure, geographic information science and systems (GIS), spatial analysis and modeling, and a number of geospatial domains to improve research productivity and enable scientific breakthroughs. It has emerged as new-generation GIS that enable unprecedented advances in data-driven knowledge discovery, visualization and visual analytics, and collaborative problem solving and decision-making. This paper describes three open software strategies-open access, source, and integration-to serve various research and education purposes of diverse geospatial communities. These strategies have been implemented in a leading-edge cyberGIS software environment through three corresponding software modalities: CyberGIS Gateway, Toolkit, and Middleware, and achieved broad and significant impacts.

Microgrid Design Toolkit (MDT) User Guide Software v1.2.

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

Eddy, John P.

2017-08-01

The Microgrid Design Toolkit (MDT) supports decision analysis for new ("greenfield") microgrid designs as well as microgrids with existing infrastructure. The current version of MDT includes two main capabilities. The first capability, the Microgrid Sizing Capability (MSC), is used to determine the size and composition of a new, grid connected microgrid in the early stages of the design process. MSC is focused on developing a microgrid that is economically viable when connected to the grid. The second capability is focused on designing a microgrid for operation in islanded mode. This second capability relies on two models: the Technology Management Optimizationmore » (TMO) model and Performance Reliability Model (PRM).« less

Data visualization and analysis tools for the MAVEN mission

NASA Astrophysics Data System (ADS)

Harter, B.; De Wolfe, A. W.; Putnam, B.; Brain, D.; Chaffin, M.

2016-12-01

The Mars Atmospheric and Volatile Evolution (MAVEN) mission has been collecting data at Mars since September 2014. We have developed new software tools for exploring and analyzing the science data. Our open-source Python toolkit for working with data from MAVEN and other missions is based on the widely-used "tplot" IDL toolkit. We have replicated all of the basic tplot functionality in Python, and use the bokeh and matplotlib libraries to generate interactive line plots and spectrograms, providing additional functionality beyond the capabilities of IDL graphics. These Python tools are generalized to work with missions beyond MAVEN, and our software is available on Github. We have also been exploring 3D graphics as a way to better visualize the MAVEN science data and models. We have constructed a 3D visualization of MAVEN's orbit using the CesiumJS library, which not only allows viewing of MAVEN's orientation and position, but also allows the display of selected science data sets and their variation over time.

ImTK: an open source multi-center information management toolkit

NASA Astrophysics Data System (ADS)

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

2008-03-01

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

IBiSA_Tools: A Computational Toolkit for Ion-Binding State Analysis in Molecular Dynamics Trajectories of Ion Channels.

PubMed

Kasahara, Kota; Kinoshita, Kengo

2016-01-01

Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering. This approach effectively revealed the ion conduction mechanisms and their dependence on the conditions, i.e., ion concentration and membrane voltage. Here, we present an easy-to-use computational toolkit for ion-binding state analysis, called IBiSA_tools. This toolkit consists of a C++ program and a series of Python and R scripts. From the trajectory file of MD simulations and a structure file, users can generate several images and statistics of ion conduction processes. A complex network named ion-binding state graph is generated in a standard graph format (graph modeling language; GML), which can be visualized by standard network analyzers such as Cytoscape. As a tutorial, a trajectory of a 50 ns MD simulation of the Kv1.2 channel is also distributed with the toolkit. Users can trace the entire process of ion-binding state analysis step by step. The novel method for analysis of ion conduction mechanisms of ion channels can be easily used by means of IBiSA_tools. This software is distributed under an open source license at the following URL: http://www.ritsumei.ac.jp/~ktkshr/ibisa_tools/.

BamTools: a C++ API and toolkit for analyzing and managing BAM files

PubMed Central

Barnett, Derek W.; Garrison, Erik K.; Quinlan, Aaron R.; Strömberg, Michael P.; Marth, Gabor T.

2011-01-01

Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research. Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit. Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools. Contact: barnetde@bc.edu PMID:21493652

The Exoplanet Characterization ToolKit (ExoCTK)

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

Use of the MATRIXx Integrated Toolkit on the Microwave Anisotropy Probe Attitude Control System

NASA Technical Reports Server (NTRS)

Ward, David K.; Andrews, Stephen F.; McComas, David C.; ODonnell, James R., Jr.

1999-01-01

Recent advances in analytical software tools allow the analysis, simulation, flight code, and documentation of an algorithm to be generated from a single source, all within one integrated analytical design package. NASA's Microwave Anisotropy Probe project has used one such package, Integrated Systems' MATRIXx suite, in the design of the spacecraft's Attitude Control System. The project's experience with the linear analysis, simulation, code generation, and documentation tools will be presented and compared with more traditional development tools. In particular, the quality of the flight software generated will be examined in detail. Finally, lessons learned on each of the tools will be shared.

Ground Operations Autonomous Control and Integrated Health Management

NASA Technical Reports Server (NTRS)

Daniels, James

2014-01-01

The Ground Operations Autonomous Control and Integrated Health Management plays a key role for future ground operations at NASA. The software that is integrated into this system is called G2 2011 Gensym. The purpose of this report is to describe the Ground Operations Autonomous Control and Integrated Health Management with the use of the G2 Gensym software and the G2 NASA toolkit for Integrated System Health Management (ISHM) which is a Computer Software Configuration Item (CSCI). The decision rationale for the use of the G2 platform is to develop a modular capability for ISHM and AC. Toolkit modules include knowledge bases that are generic and can be applied in any application domain module. That way, there's a maximization of reusability, maintainability, and systematic evolution, portability, and scalability. Engine modules are generic, while application modules represent the domain model of a specific application. Furthermore, the NASA toolkit, developed since 2006 (a set of modules), makes it possible to create application domain models quickly, using pre-defined objects that include sensors and components libraries for typical fluid, electrical, and mechanical systems.

Software Reviews.

ERIC Educational Resources Information Center

Bitter, Gary G., Ed.

1989-01-01

Describes three software packages: (1) "MacMendeleev"--database/graphic display for chemistry, grades 10-12, Macintosh; (2) "Geometry One: Foundations"--geometry tutorial, grades 7-12, IBM; (3) "Mathematics Exploration Toolkit"--algebra and calculus tutorial, grades 8-12, IBM. (MVL)

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.

Application development environment for advanced digital workstations

NASA Astrophysics Data System (ADS)

Valentino, Daniel J.; Harreld, Michael R.; Liu, Brent J.; Brown, Matthew S.; Huang, Lu J.

1998-06-01

One remaining barrier to the clinical acceptance of electronic imaging and information systems is the difficulty in providing intuitive access to the information needed for a specific clinical task (such as reaching a diagnosis or tracking clinical progress). The purpose of this research was to create a development environment that enables the design and implementation of advanced digital imaging workstations. We used formal data and process modeling to identify the diagnostic and quantitative data that radiologists use and the tasks that they typically perform to make clinical decisions. We studied a diverse range of radiology applications, including diagnostic neuroradiology in an academic medical center, pediatric radiology in a children's hospital, screening mammography in a breast cancer center, and thoracic radiology consultation for an oncology clinic. We used object- oriented analysis to develop software toolkits that enable a programmer to rapidly implement applications that closely match clinical tasks. The toolkits support browsing patient information, integrating patient images and reports, manipulating images, and making quantitative measurements on images. Collectively, we refer to these toolkits as the UCLA Digital ViewBox toolkit (ViewBox/Tk). We used the ViewBox/Tk to rapidly prototype and develop a number of diverse medical imaging applications. Our task-based toolkit approach enabled rapid and iterative prototyping of workstations that matched clinical tasks. The toolkit functionality and performance provided a 'hands-on' feeling for manipulating images, and for accessing textual information and reports. The toolkits directly support a new concept for protocol based-reading of diagnostic studies. The design supports the implementation of network-based application services (e.g., prefetching, workflow management, and post-processing) that will facilitate the development of future clinical applications.

Phase 1 Development Report for the SESSA Toolkit

DTIC Science & Technology

2014-09-01

data acquisition, data management, and data analysis. SESSA was designed to meet forensic crime scene needs as defined by the DoD’s Military Criminal...on the design , functional attributes, algorithm development, system architecture, and software programming include: Robert Knowlton, Brad Melton...Building Restoration Operations Optimization Model (BROOM). BROOM (Knowlton et al., 2012) was designed for consequence management activities (e.g

The TeleEngineering Toolkit Software Reference Manual

DTIC Science & Technology

2007-08-01

arrangement of windows. ................................................................. 74 Figure 6.26. Tile arrangement of windows...Level 1, and Commercial Satellite Imagery (CSIL). The Toolkit also supports USGS Digital Orthophoto Quadrangle, scanned georectified maps, and various...in a cascading manner as shown in Figure 6.25. Tile The Tile tool in the Window menu will arrange the windows in a tiled manner as shown in

Integrated System Health Management Development Toolkit

NASA Technical Reports Server (NTRS)

Figueroa, Jorge; Smith, Harvey; Morris, Jon

2009-01-01

This software toolkit is designed to model complex systems for the implementation of embedded Integrated System Health Management (ISHM) capability, which focuses on determining the condition (health) of every element in a complex system (detect anomalies, diagnose causes, and predict future anomalies), and to provide data, information, and knowledge (DIaK) to control systems for safe and effective operation.

MAKER-P: a tool-kit for the creation, management, and quality control of plant genome annotations

USDA-ARS?s Scientific Manuscript database

We have optimized and extended the widely used annotation-engine MAKER for use on plant genomes. We have benchmarked the resulting software, MAKER-P, using the A. thaliana genome and the TAIR10 gene models. Here we demonstrate the ability of the MAKER-P toolkit to generate de novo repeat databases, ...

C-CAT: a computer software used to analyze and select Chinese characters and character components for psychological research.

PubMed

Lo, Ming; Hue, Chih-Wei

2008-11-01

The Character-Component Analysis Toolkit (C-CAT) software was designed to assist researchers in constructing experimental materials using traditional Chinese characters. The software package contains two sets of character stocks: one suitable for research using literate adults as subjects and one suitable for research using schoolchildren as subjects. The software can identify linguistic properties, such as the number of strokes contained, the character-component pronunciation regularity, and the arrangement of character components within a character. Moreover, it can compute a character's linguistic frequency, neighborhood size, and phonetic validity with respect to a user-selected character stock. It can also search the selected character stock for similar characters or for character components with user-specified linguistic properties.

The Seismic Tool-Kit (STK): An Open Source Software For Learning the Basis of Signal Processing and Seismology.

NASA Astrophysics Data System (ADS)

Reymond, D.

2016-12-01

We present an open source software project (GNU public license), named STK: Seismic Tool-Kit, that is dedicated mainly for learning signal processing and seismology. The STK project that started in 2007, is hosted by SourceForge.net, and count more than 20000 downloads at the date of writing.The STK project is composed of two main branches:First, a graphical interface dedicated to signal processing (in the SAC format (SAC_ASCII and SAC_BIN): where the signal can be plotted, zoomed, filtered, integrated, derivated, ... etc. (a large variety of IFR and FIR filter is proposed). The passage in the frequency domain via the Fourier transform is used to introduce the estimation of spectral density of the signal , with visualization of the Power Spectral Density (PSD) in linear or log scale, and also the evolutive time-frequency representation (or sonagram). The 3-components signals can be also processed for estimating their polarization properties, either for a given window, or either for evolutive windows along the time. This polarization analysis is useful for extracting the polarized noises, differentiating P waves, Rayleigh waves, Love waves, ... etc. Secondly, a panel of Utilities-Program are proposed for working in a terminal mode, with basic programs for computing azimuth and distance in spherical geometry, inter/auto-correlation, spectral density, time-frequency for an entire directory of signals, focal planes, and main components axis, radiation pattern of P waves, Polarization analysis of different waves (including noise), under/over-sampling the signals, cubic-spline smoothing, and linear/non linear regression analysis of data set. STK is developed in C/C++, mainly under Linux OS, and it has been also partially implemented under MS-Windows. STK has been used in some schools for viewing and plotting seismic records provided by IRIS, and it has been used as a practical support for teaching the basis of signal processing. Useful links:http://sourceforge.net/projects/seismic-toolkit/http://sourceforge.net/p/seismic-toolkit/wiki/browse_pages/

A prototype forensic toolkit for industrial-control-systems incident response

NASA Astrophysics Data System (ADS)

Carr, Nickolas B.; Rowe, Neil C.

2015-05-01

Industrial control systems (ICSs) are an important part of critical infrastructure in cyberspace. They are especially vulnerable to cyber-attacks because of their legacy hardware and software and the difficulty of changing it. We first survey the history of intrusions into ICSs, the more serious of which involved a continuing adversary presence on an ICS network. We discuss some common vulnerabilities and the categories of possible attacks, noting the frequent use of software written a long time ago. We propose a framework for designing ICS incident response under the constraints that no new software must be required and that interventions cannot impede the continuous processing that is the norm for such systems. We then discuss a prototype toolkit we built using the Windows Management Instrumentation Command-Line tool for host-based analysis and the Bro intrusion-detection software for network-based analysis. Particularly useful techniques we used were learning the historical range of parameters of numeric quantities so as to recognize anomalies, learning the usual addresses of connections to a node, observing Internet addresses (usually rare), observing anomalous network protocols such as unencrypted data transfers, observing unusual scheduled tasks, and comparing key files through registry entries and hash values to find malicious modifications. We tested our methods on actual data from ICSs including publicly-available data, voluntarily-submitted data, and researcher-provided "advanced persistent threat" data. We found instances of interesting behavior in our experiments. Intrusions were generally easy to see because of the repetitive nature of most processing on ICSs, but operators need to be motivated to look.

KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies.

PubMed

Mapleson, Daniel; Garcia Accinelli, Gonzalo; Kettleborough, George; Wright, Jonathan; Clavijo, Bernardo J

2017-02-15

De novo assembly of whole genome shotgun (WGS) next-generation sequencing (NGS) data benefits from high-quality input with high coverage. However, in practice, determining the quality and quantity of useful reads quickly and in a reference-free manner is not trivial. Gaining a better understanding of the WGS data, and how that data is utilized by assemblers, provides useful insights that can inform the assembly process and result in better assemblies. We present the K-mer Analysis Toolkit (KAT): a multi-purpose software toolkit for reference-free quality control (QC) of WGS reads and de novo genome assemblies, primarily via their k-mer frequencies and GC composition. KAT enables users to assess levels of errors, bias and contamination at various stages of the assembly process. In this paper we highlight KAT's ability to provide valuable insights into assembly composition and quality of genome assemblies through pairwise comparison of k-mers present in both input reads and the assemblies. KAT is available under the GPLv3 license at: https://github.com/TGAC/KAT . bernardo.clavijo@earlham.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

phylo-node: A molecular phylogenetic toolkit using Node.js.

PubMed

O'Halloran, Damien M

2017-01-01

Node.js is an open-source and cross-platform environment that provides a JavaScript codebase for back-end server-side applications. JavaScript has been used to develop very fast and user-friendly front-end tools for bioinformatic and phylogenetic analyses. However, no such toolkits are available using Node.js to conduct comprehensive molecular phylogenetic analysis. To address this problem, I have developed, phylo-node, which was developed using Node.js and provides a stable and scalable toolkit that allows the user to perform diverse molecular and phylogenetic tasks. phylo-node can execute the analysis and process the resulting outputs from a suite of software options that provides tools for read processing and genome alignment, sequence retrieval, multiple sequence alignment, primer design, evolutionary modeling, and phylogeny reconstruction. Furthermore, phylo-node enables the user to deploy server dependent applications, and also provides simple integration and interoperation with other Node modules and languages using Node inheritance patterns, and a customized piping module to support the production of diverse pipelines. phylo-node is open-source and freely available to all users without sign-up or login requirements. All source code and user guidelines are openly available at the GitHub repository: https://github.com/dohalloran/phylo-node.

A software architecture for automating operations processes

NASA Technical Reports Server (NTRS)

Miller, Kevin J.

1994-01-01

The Operations Engineering Lab (OEL) at JPL has developed a software architecture based on an integrated toolkit approach for simplifying and automating mission operations tasks. The toolkit approach is based on building adaptable, reusable graphical tools that are integrated through a combination of libraries, scripts, and system-level user interface shells. The graphical interface shells are designed to integrate and visually guide a user through the complex steps in an operations process. They provide a user with an integrated system-level picture of an overall process, defining the required inputs and possible output through interactive on-screen graphics. The OEL has developed the software for building these process-oriented graphical user interface (GUI) shells. The OEL Shell development system (OEL Shell) is an extension of JPL's Widget Creation Library (WCL). The OEL Shell system can be used to easily build user interfaces for running complex processes, applications with extensive command-line interfaces, and tool-integration tasks. The interface shells display a logical process flow using arrows and box graphics. They also allow a user to select which output products are desired and which input sources are needed, eliminating the need to know which program and its associated command-line parameters must be executed in each case. The shells have also proved valuable for use as operations training tools because of the OEL Shell hypertext help environment. The OEL toolkit approach is guided by several principles, including the use of ASCII text file interfaces with a multimission format, Perl scripts for mission-specific adaptation code, and programs that include a simple command-line interface for batch mode processing. Projects can adapt the interface shells by simple changes to the resources configuration file. This approach has allowed the development of sophisticated, automated software systems that are easy, cheap, and fast to build. This paper will discuss our toolkit approach and the OEL Shell interface builder in the context of a real operations process example. The paper will discuss the design and implementation of a Ulysses toolkit for generating the mission sequence of events. The Sequence of Events Generation (SEG) system provides an adaptable multimission toolkit for producing a time-ordered listing and timeline display of spacecraft commands, state changes, and required ground activities.

Software Reviews.

ERIC Educational Resources Information Center

Science and Children, 1988

1988-01-01

Reviews five software packages for use with school age children. Includes "Science Toolkit Module 2: Earthquake Lab"; "Adaptations and Identification"; "Geoworld"; "Body Systems II Series: The Blood System: A Liquid of Life," all for Apple II, and "Science Courseware: Life Science/Biology" for…

Health Equity Assessment Toolkit (HEAT): software for exploring and comparing health inequalities in countries.

PubMed

Hosseinpoor, Ahmad Reza; Nambiar, Devaki; Schlotheuber, Anne; Reidpath, Daniel; Ross, Zev

2016-10-19

It is widely recognised that the pursuit of sustainable development cannot be accomplished without addressing inequality, or observed differences between subgroups of a population. Monitoring health inequalities allows for the identification of health topics where major group differences exist, dimensions of inequality that must be prioritised to effect improvements in multiple health domains, and also population subgroups that are multiply disadvantaged. While availability of data to monitor health inequalities is gradually improving, there is a commensurate need to increase, within countries, the technical capacity for analysis of these data and interpretation of results for decision-making. Prior efforts to build capacity have yielded demand for a toolkit with the computational ability to display disaggregated data and summary measures of inequality in an interactive and customisable fashion that would facilitate interpretation and reporting of health inequality in a given country. To answer this demand, the Health Equity Assessment Toolkit (HEAT), was developed between 2014 and 2016. The software, which contains the World Health Organization's Health Equity Monitor database, allows the assessment of inequalities within a country using over 30 reproductive, maternal, newborn and child health indicators and five dimensions of inequality (economic status, education, place of residence, subnational region and child's sex, where applicable). HEAT was beta-tested in 2015 as part of ongoing capacity building workshops on health inequality monitoring. This is the first and only application of its kind; further developments are proposed to introduce an upload data feature, translate it into different languages and increase interactivity of the software. This article will present the main features and functionalities of HEAT and discuss its relevance and use for health inequality monitoring.

bioWidgets: data interaction components for genomics.

PubMed

Fischer, S; Crabtree, J; Brunk, B; Gibson, M; Overton, G C

1999-10-01

The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components. We have designed the bioWidget toolkit as a set of JavaBean components. It includes a wide array of user interface components and defines an architecture for assembling applications. The toolkit is founded on established software engineering design patterns and principles, including componentry, Model-View-Controller, factored models and schema neutrality. As a proof of concept, we have used the bioWidget toolkit to create three extendible applications: AnnotView, BlastView and AlignView.

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

PubMed Central

Wang, Yupeng; Tang, Haibao; DeBarry, Jeremy D.; Tan, Xu; Li, Jingping; Wang, Xiyin; Lee, Tae-ho; Jin, Huizhe; Marler, Barry; Guo, Hui; Kissinger, Jessica C.; Paterson, Andrew H.

2012-01-01

MCScan is an algorithm able to scan multiple genomes or subgenomes in order to identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX toolkit implements an adjusted MCScan algorithm for detection of synteny and collinearity that extends the original software by incorporating 14 utility programs for visualization of results and additional downstream analyses. Applications of MCScanX to several sequenced plant genomes and gene families are shown as examples. MCScanX can be used to effectively analyze chromosome structural changes, and reveal the history of gene family expansions that might contribute to the adaptation of lineages and taxa. An integrated view of various modes of gene duplication can supplement the traditional gene tree analysis in specific families. The source code and documentation of MCScanX are freely available at http://chibba.pgml.uga.edu/mcscan2/. PMID:22217600

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

DTIC Science & Technology

1994-07-29

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

A basic analysis toolkit for biological sequences

PubMed Central

Giancarlo, Raffaele; Siragusa, Alessandro; Siragusa, Enrico; Utro, Filippo

2007-01-01

This paper presents a software library, nicknamed BATS, for some basic sequence analysis tasks. Namely, local alignments, via approximate string matching, and global alignments, via longest common subsequence and alignments with affine and concave gap cost functions. Moreover, it also supports filtering operations to select strings from a set and establish their statistical significance, via z-score computation. None of the algorithms is new, but although they are generally regarded as fundamental for sequence analysis, they have not been implemented in a single and consistent software package, as we do here. Therefore, our main contribution is to fill this gap between algorithmic theory and practice by providing an extensible and easy to use software library that includes algorithms for the mentioned string matching and alignment problems. The library consists of C/C++ library functions as well as Perl library functions. It can be interfaced with Bioperl and can also be used as a stand-alone system with a GUI. The software is available at under the GNU GPL. PMID:17877802

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

Goto, Naohisa; Prins, Pjotr; Nakao, Mitsuteru; Bonnal, Raoul; Aerts, Jan; Katayama, Toshiaki

2010-10-15

The BioRuby software toolkit contains a comprehensive set of free development tools and libraries for bioinformatics and molecular biology, written in the Ruby programming language. BioRuby has components for sequence analysis, pathway analysis, protein modelling and phylogenetic analysis; it supports many widely used data formats and provides easy access to databases, external programs and public web services, including BLAST, KEGG, GenBank, MEDLINE and GO. BioRuby comes with a tutorial, documentation and an interactive environment, which can be used in the shell, and in the web browser. BioRuby is free and open source software, made available under the Ruby license. BioRuby runs on all platforms that support Ruby, including Linux, Mac OS X and Windows. And, with JRuby, BioRuby runs on the Java Virtual Machine. The source code is available from http://www.bioruby.org/. katayama@bioruby.org

TRSkit: A Simple Digital Library Toolkit

NASA Technical Reports Server (NTRS)

Nelson, Michael L.; Esler, Sandra L.

1997-01-01

This paper introduces TRSkit, a simple and effective toolkit for building digital libraries on the World Wide Web. The toolkit was developed for the creation of the Langley Technical Report Server and the NASA Technical Report Server, but is applicable to most simple distribution paradigms. TRSkit contains a handful of freely available software components designed to be run under the UNIX operating system and served via the World Wide Web. The intended customer is the person that must continuously and synchronously distribute anywhere from 100 - 100,000's of information units and does not have extensive resources to devote to the problem.

RAVE—a Detector-independent vertex reconstruction toolkit

NASA Astrophysics Data System (ADS)

Waltenberger, Wolfgang; Mitaroff, Winfried; Moser, Fabian

2007-10-01

A detector-independent toolkit for vertex reconstruction (RAVE ) is being developed, along with a standalone framework (VERTIGO ) for testing, analyzing and debugging. The core algorithms represent state of the art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available. VERTIGO = "vertex reconstruction toolkit and interface to generic objects".

Astronomy Data Visualization with Blender

NASA Astrophysics Data System (ADS)

Kent, Brian R.

2015-08-01

We present innovative methods and techniques for using Blender, a 3D software package, in the visualization of astronomical data. N-body simulations, data cubes, galaxy and stellar catalogs, and planetary surface maps can be rendered in high quality videos for exploratory data analysis. Blender's API is Python based, making it advantageous for use in astronomy with flexible libraries like astroPy. Examples will be exhibited that showcase the features of the software in astronomical visualization paradigms. 2D and 3D voxel texture applications, animations, camera movement, and composite renders are introduced to the astronomer's toolkit and how they mesh with different forms of data.

HyRAM V1.0 User Guide

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

Groth, Katrina M.; Zumwalt, Hannah Ruth; Clark, Andrew Jordan

2016-03-01

Hydrogen Risk Assessment Models (HyRAM) is a prototype software toolkit that integrates data and methods relevant to assessing the safety of hydrogen fueling and storage infrastructure. The HyRAM toolkit integrates deterministic and probabilistic models for quantifying accident scenarios, predicting physical effects, and characterizing the impact of hydrogen hazards, including thermal effects from jet fires and thermal pressure effects from deflagration. HyRAM version 1.0 incorporates generic probabilities for equipment failures for nine types of components, and probabilistic models for the impact of heat flux on humans and structures, with computationally and experimentally validated models of various aspects of gaseous hydrogen releasemore » and flame physics. This document provides an example of how to use HyRAM to conduct analysis of a fueling facility. This document will guide users through the software and how to enter and edit certain inputs that are specific to the user-defined facility. Description of the methodology and models contained in HyRAM is provided in [1]. This User’s Guide is intended to capture the main features of HyRAM version 1.0 (any HyRAM version numbered as 1.0.X.XXX). This user guide was created with HyRAM 1.0.1.798. Due to ongoing software development activities, newer versions of HyRAM may have differences from this guide.« less

Effectiveness and feasibility of a software tool to help patients communicate with doctors about problems they face with their medication regimen (EMPATHy): study protocol for a randomized controlled trial.

PubMed

Billimek, John; Guzman, Herlinda; Angulo, Marco A

2015-04-10

Low-income, Mexican-American patients with diabetes exhibit high rates of medication nonadherence, poor blood sugar control and serious complications, and often have difficulty communicating their concerns about the medication regimen to physicians. Interventions led by community health workers, non-professional community members who are trained to work with patients to improve engagement and communication during the medical visit, have had mixed success in improving outcomes. The primary objective of this project is to pilot test a prototype software toolkit called "EMPATHy" that a community health worker can administer to help patients identify the most important barriers to adherence that they face and discuss these barriers with their doctor. The EMPATHy toolkit will be piloted in an ongoing intervention (Coached Care) in which community health workers are trained to be "coaches" to meet with patients before the medical visit and help them prepare a list of important questions for the doctor. A total of 190 Mexican-American patients with poorly controlled type 2 diabetes will be recruited from December 2014 through June 2015 and will be randomly assigned to complete either a single Coached Care intervention visit with no software tools or a Coached Care visit incorporating the EMPATHy software toolkit. The primary endpoints are (1) the development of a "contextualized plan of care" (i.e., a plan of care that addresses a barrier to medication adherence in the patient's daily life) with the doctor, determined from an audio recording of the medical visit, and (2) attainment of a concrete behavioral goal set during the intervention session, assessed in a 2-week follow-up phone call to the patient. The statistical analysis will include logistic regression models and is powered to detect a 50% increase in the primary endpoints. The study will provide evidence regarding the effectiveness and feasibility of a software tool to help patients communicate with doctors about problems they face with their medications. ClinicalTrials.gov NCT02324036 Registered 16 December 2014.

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

NASA Astrophysics Data System (ADS)

Diglio, A.; Nicolodi, B.

2002-07-01

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

Automatic Commercial Permit Sets

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

Grana, Paul

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

‘Survival’: a simulation toolkit introducing a modular approach for radiobiological evaluations in ion beam therapy

NASA Astrophysics Data System (ADS)

Manganaro, L.; Russo, G.; Bourhaleb, F.; Fausti, F.; Giordanengo, S.; Monaco, V.; Sacchi, R.; Vignati, A.; Cirio, R.; Attili, A.

2018-04-01

One major rationale for the application of heavy ion beams in tumour therapy is their increased relative biological effectiveness (RBE). The complex dependencies of the RBE on dose, biological endpoint, position in the field etc require the use of biophysical models in treatment planning and clinical analysis. This study aims to introduce a new software, named ‘Survival’, to facilitate the radiobiological computations needed in ion therapy. The simulation toolkit was written in C++ and it was developed with a modular architecture in order to easily incorporate different radiobiological models. The following models were successfully implemented: the local effect model (LEM, version I, II and III) and variants of the microdosimetric-kinetic model (MKM). Different numerical evaluation approaches were also implemented: Monte Carlo (MC) numerical methods and a set of faster analytical approximations. Among the possible applications, the toolkit was used to reproduce the RBE versus LET for different ions (proton, He, C, O, Ne) and different cell lines (CHO, HSG). Intercomparison between different models (LEM and MKM) and computational approaches (MC and fast approximations) were performed. The developed software could represent an important tool for the evaluation of the biological effectiveness of charged particles in ion beam therapy, in particular when coupled with treatment simulations. Its modular architecture facilitates benchmarking and inter-comparison between different models and evaluation approaches. The code is open source (GPL2 license) and available at https://github.com/batuff/Survival.

JAVA Stereo Display Toolkit

NASA Technical Reports Server (NTRS)

Edmonds, Karina

2008-01-01

This toolkit provides a common interface for displaying graphical user interface (GUI) components in stereo using either specialized stereo display hardware (e.g., liquid crystal shutter or polarized glasses) or anaglyph display (red/blue glasses) on standard workstation displays. An application using this toolkit will work without modification in either environment, allowing stereo software to reach a wider audience without sacrificing high-quality display on dedicated hardware. The toolkit is written in Java for use with the Swing GUI Toolkit and has cross-platform compatibility. It hooks into the graphics system, allowing any standard Swing component to be displayed in stereo. It uses the OpenGL graphics library to control the stereo hardware and to perform the rendering. It also supports anaglyph and special stereo hardware using the same API (application-program interface), and has the ability to simulate color stereo in anaglyph mode by combining the red band of the left image with the green/blue bands of the right image. This is a low-level toolkit that accomplishes simply the display of components (including the JadeDisplay image display component). It does not include higher-level functions such as disparity adjustment, 3D cursor, or overlays all of which can be built using this toolkit.

ParCAT: A Parallel Climate Analysis Toolkit

NASA Astrophysics Data System (ADS)

Haugen, B.; Smith, B.; Steed, C.; Ricciuto, D. M.; Thornton, P. E.; Shipman, G.

2012-12-01

Climate science has employed increasingly complex models and simulations to analyze the past and predict the future of our climate. The size and dimensionality of climate simulation data has been growing with the complexity of the models. This growth in data is creating a widening gap between the data being produced and the tools necessary to analyze large, high dimensional data sets. With single run data sets increasing into 10's, 100's and even 1000's of gigabytes, parallel computing tools are becoming a necessity in order to analyze and compare climate simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools that efficiently use parallel computing techniques to narrow the gap between data set size and analysis tools. ParCAT was created as a collaborative effort between climate scientists and computer scientists in order to provide efficient parallel implementations of the computing tools that are of use to climate scientists. Some of the basic functionalities included in the toolkit are the ability to compute spatio-temporal means and variances, differences between two runs and histograms of the values in a data set. ParCAT is designed to facilitate the "heavy lifting" that is required for large, multidimensional data sets. The toolkit does not focus on performing the final visualizations and presentation of results but rather, reducing large data sets to smaller, more manageable summaries. The output from ParCAT is provided in commonly used file formats (NetCDF, CSV, ASCII) to allow for simple integration with other tools. The toolkit is currently implemented as a command line utility, but will likely also provide a C library for developers interested in tighter software integration. Elements of the toolkit are already being incorporated into projects such as UV-CDAT and CMDX. There is also an effort underway to implement portions of the CCSM Land Model Diagnostics package using ParCAT in conjunction with Python and gnuplot. ParCAT is implemented in C to provide efficient file IO. The file IO operations in the toolkit use the parallel-netcdf library; this enables the code to use the parallel IO capabilities of modern HPC systems. Analysis that currently requires an estimated 12+ hours with the traditional CCSM Land Model Diagnostics Package can now be performed in as little as 30 minutes on a single desktop workstation and a few minutes for relatively small jobs completed on modern HPC systems such as ORNL's Jaguar.

DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research.

PubMed

Fedorov, Andriy; Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R

2016-01-01

Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM(®)) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard.

BIO::Phylo-phyloinformatic analysis using perl.

PubMed

Vos, Rutger A; Caravas, Jason; Hartmann, Klaas; Jensen, Mark A; Miller, Chase

2011-02-27

Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo.

BIO::Phylo-phyloinformatic analysis using perl

PubMed Central

2011-01-01

Background Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. Results This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. Conclusions Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo PMID:21352572

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...

An Aerodynamic Simulation Process for Iced Lifting Surfaces and Associated Issues

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Vickerman, Mary B.; Hackenberg, Anthony W.; Rigby, David L.

2003-01-01

This paper discusses technologies and software tools that are being implemented in a software toolkit currently under development at NASA Glenn Research Center. Its purpose is to help study the effects of icing on airfoil performance and assist with the aerodynamic simulation process which consists of characterization and modeling of ice geometry, application of block topology and grid generation, and flow simulation. Tools and technologies for each task have been carefully chosen based on their contribution to the overall process. For the geometry characterization and modeling, we have chosen an interactive rather than automatic process in order to handle numerous ice shapes. An Appendix presents features of a software toolkit developed to support the interactive process. Approaches taken for the generation of block topology and grids, and flow simulation, though not yet implemented in the software, are discussed with reasons for why particular methods are chosen. Some of the issues that need to be addressed and discussed by the icing community are also included.

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectropscopy using IFEFFIT

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

Ravel, B.; Newville, M.; UC)

2010-07-20

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demandsmore » of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.« less

DeepInfer: open-source deep learning deployment toolkit for image-guided therapy

NASA Astrophysics Data System (ADS)

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A.; Kapur, Tina; Wells, William M.; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-03-01

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research work ows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy.

PubMed

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A; Kapur, Tina; Wells, William M; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-02-11

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose "DeepInfer" - an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections.

DeepInfer: Open-Source Deep Learning Deployment Toolkit for Image-Guided Therapy

PubMed Central

Mehrtash, Alireza; Pesteie, Mehran; Hetherington, Jorden; Behringer, Peter A.; Kapur, Tina; Wells, William M.; Rohling, Robert; Fedorov, Andriy; Abolmaesumi, Purang

2017-01-01

Deep learning models have outperformed some of the previous state-of-the-art approaches in medical image analysis. Instead of using hand-engineered features, deep models attempt to automatically extract hierarchical representations at multiple levels of abstraction from the data. Therefore, deep models are usually considered to be more flexible and robust solutions for image analysis problems compared to conventional computer vision models. They have demonstrated significant improvements in computer-aided diagnosis and automatic medical image analysis applied to such tasks as image segmentation, classification and registration. However, deploying deep learning models often has a steep learning curve and requires detailed knowledge of various software packages. Thus, many deep models have not been integrated into the clinical research workflows causing a gap between the state-of-the-art machine learning in medical applications and evaluation in clinical research procedures. In this paper, we propose “DeepInfer” – an open-source toolkit for developing and deploying deep learning models within the 3D Slicer medical image analysis platform. Utilizing a repository of task-specific models, DeepInfer allows clinical researchers and biomedical engineers to deploy a trained model selected from the public registry, and apply it to new data without the need for software development or configuration. As two practical use cases, we demonstrate the application of DeepInfer in prostate segmentation for targeted MRI-guided biopsy and identification of the target plane in 3D ultrasound for spinal injections. PMID:28615794

Tools for 3D scientific visualization in computational aerodynamics at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

Hardware, software, and techniques used by the Fluid Dynamics Division (NASA) for performing visualization of computational aerodynamics, which can be applied to the visualization of flow fields from computer simulations of fluid dynamics about the Space Shuttle, are discussed. Three visualization techniques applied, post-processing, tracking, and steering, are described, as well as the post-processing software packages used, PLOT3D, SURF (Surface Modeller), GAS (Graphical Animation System), and FAST (Flow Analysis software Toolkit). Using post-processing methods a flow simulation was executed on a supercomputer and, after the simulation was complete, the results were processed for viewing. It is shown that the high-resolution, high-performance three-dimensional workstation combined with specially developed display and animation software provides a good tool for analyzing flow field solutions obtained from supercomputers.

OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging

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

de Raad, Markus; de Rond, Tristan; Rübel, Oliver

Mass spectrometry imaging (MSI) has primarily been applied in localizing biomolecules within biological matrices. Although well-suited, the application of MSI for comparing thousands of spatially defined spotted samples has been limited. One reason for this is a lack of suitable and accessible data processing tools for the analysis of large arrayed MSI sample sets. In this paper, the OpenMSI Arrayed Analysis Toolkit (OMAAT) is a software package that addresses the challenges of analyzing spatially defined samples in MSI data sets. OMAAT is written in Python and is integrated with OpenMSI (http://openmsi.nersc.gov), a platform for storing, sharing, and analyzing MSI data.more » By using a web-based python notebook (Jupyter), OMAAT is accessible to anyone without programming experience yet allows experienced users to leverage all features. OMAAT was evaluated by analyzing an MSI data set of a high-throughput glycoside hydrolase activity screen comprising 384 samples arrayed onto a NIMS surface at a 450 μm spacing, decreasing analysis time >100-fold while maintaining robust spot-finding. The utility of OMAAT was demonstrated for screening metabolic activities of different sized soil particles, including hydrolysis of sugars, revealing a pattern of size dependent activities. Finally, these results introduce OMAAT as an effective toolkit for analyzing spatially defined samples in MSI. OMAAT runs on all major operating systems, and the source code can be obtained from the following GitHub repository: https://github.com/biorack/omaat.« less

Modular modeling system for building distributed hydrologic models with a user-friendly software package

NASA Astrophysics Data System (ADS)

Wi, S.; Ray, P. A.; Brown, C.

2015-12-01

A software package developed to facilitate building distributed hydrologic models in a modular modeling system is presented. The software package provides a user-friendly graphical user interface that eases its practical use in water resources-related research and practice. The modular modeling system organizes the options available to users when assembling models according to the stages of hydrological cycle, such as potential evapotranspiration, soil moisture accounting, and snow/glacier melting processes. The software is intended to be a comprehensive tool that simplifies the task of developing, calibrating, validating, and using hydrologic models through the inclusion of intelligent automation to minimize user effort, and reduce opportunities for error. Processes so far automated include the definition of system boundaries (i.e., watershed delineation), climate and geographical input generation, and parameter calibration. Built-in post-processing toolkits greatly improve the functionality of the software as a decision support tool for water resources system management and planning. Example post-processing toolkits enable streamflow simulation at ungauged sites with predefined model parameters, and perform climate change risk assessment by means of the decision scaling approach. The software is validated through application to watersheds representing a variety of hydrologic regimes.

KinLinks: Software Toolkit for Kinship Analysis and Pedigree Generation from NGS Datasets

DTIC Science & Technology

2015-04-21

Retinitis pigmentosa families 2110 and 2111 of 52 individuals across 6 generations (Figure 5a), and 54 geographically diverse samples (Supplementary Table...relationships within the Retinitis pigmentosa family. Machine Learning Classifier for pairwise kinship prediction Ten features were identified for training...family (Figure 4b), and the Retinitis pigmentosa family (Figure 5b). The auto-generated pedigrees were graphed as well as in family-tree format using

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data.

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X). Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

The Reconstruction Toolkit (RTK), an open-source cone-beam CT reconstruction toolkit based on the Insight Toolkit (ITK)

NASA Astrophysics Data System (ADS)

Rit, S.; Vila Oliva, M.; Brousmiche, S.; Labarbe, R.; Sarrut, D.; Sharp, G. C.

2014-03-01

We propose the Reconstruction Toolkit (RTK, http://www.openrtk.org), an open-source toolkit for fast cone-beam CT reconstruction, based on the Insight Toolkit (ITK) and using GPU code extracted from Plastimatch. RTK is developed by an open consortium (see affiliations) under the non-contaminating Apache 2.0 license. The quality of the platform is daily checked with regression tests in partnership with Kitware, the company supporting ITK. Several features are already available: Elekta, Varian and IBA inputs, multi-threaded Feldkamp-David-Kress reconstruction on CPU and GPU, Parker short scan weighting, multi-threaded CPU and GPU forward projectors, etc. Each feature is either accessible through command line tools or C++ classes that can be included in independent software. A MIDAS community has been opened to share CatPhan datasets of several vendors (Elekta, Varian and IBA). RTK will be used in the upcoming cone-beam CT scanner developed by IBA for proton therapy rooms. Many features are under development: new input format support, iterative reconstruction, hybrid Monte Carlo / deterministic CBCT simulation, etc. RTK has been built to freely share tomographic reconstruction developments between researchers and is open for new contributions.

Citizen Observatories: A Standards Based Architecture

NASA Astrophysics Data System (ADS)

Simonis, Ingo

2015-04-01

A number of large-scale research projects are currently under way exploring the various components of citizen observatories, e.g. CITI-SENSE (http://www.citi-sense.eu), Citclops (http://citclops.eu), COBWEB (http://cobwebproject.eu), OMNISCIENTIS (http://www.omniscientis.eu), and WeSenseIt (http://www.wesenseit.eu). Common to all projects is the motivation to develop a platform enabling effective participation by citizens in environmental projects, while considering important aspects such as security, privacy, long-term storage and availability, accessibility of raw and processed data and its proper integration into catalogues and international exchange and collaboration systems such as GEOSS or INSPIRE. This paper describes the software architecture implemented for setting up crowdsourcing campaigns using standardized components, interfaces, security features, and distribution capabilities. It illustrates the Citizen Observatory Toolkit, a software suite that allows defining crowdsourcing campaigns, to invite registered and unregistered participants to participate in crowdsourcing campaigns, and to analyze, process, and visualize raw and quality enhanced crowd sourcing data and derived products. The Citizen Observatory Toolkit is not a single software product. Instead, it is a framework of components that are built using internationally adopted standards wherever possible (e.g. OGC standards from Sensor Web Enablement, GeoPackage, and Web Mapping and Processing Services, as well as security and metadata/cataloguing standards), defines profiles of those standards where necessary (e.g. SWE O&M profile, SensorML profile), and implements design decisions based on the motivation to maximize interoperability and reusability of all components. The toolkit contains tools to set up, manage and maintain crowdsourcing campaigns, allows building on-demand apps optimized for the specific sampling focus, supports offline and online sampling modes using modern cell phones with built-in sensing technologies, automates the upload of the raw data, and handles conflation services to match quality requirements and analysis challenges. The strict implementation of all components using internationally adopted standards ensures maximal interoperability and reusability of all components. The Citizen Observatory Toolkit is currently developed as part of the COBWEB research project. COBWEB is partially funded by the European Programme FP7/2007-2013 under grant agreement n° 308513; part of the topic ENV.2012.6.5-1 "Developing community based environmental monitoring and information systems using innovative and novel earth observation applications.

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

PubMed

Thijssen, Bram; Dijkstra, Tjeerd M H; Heskes, Tom; Wessels, Lodewyk F A

2016-10-21

Computational models in biology are characterized by a large degree of uncertainty. This uncertainty can be analyzed with Bayesian statistics, however, the sampling algorithms that are frequently used for calculating Bayesian statistical estimates are computationally demanding, and each algorithm has unique advantages and disadvantages. It is typically unclear, before starting an analysis, which algorithm will perform well on a given computational model. We present BCM, a toolkit for the Bayesian analysis of Computational Models using samplers. It provides efficient, multithreaded implementations of eleven algorithms for sampling from posterior probability distributions and for calculating marginal likelihoods. BCM includes tools to simplify the process of model specification and scripts for visualizing the results. The flexible architecture allows it to be used on diverse types of biological computational models. In an example inference task using a model of the cell cycle based on ordinary differential equations, BCM is significantly more efficient than existing software packages, allowing more challenging inference problems to be solved. BCM represents an efficient one-stop-shop for computational modelers wishing to use sampler-based Bayesian statistics.

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data.

PubMed

Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

2011-12-15

High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein-DNA and protein-RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy eduardo.eyras@upf.edu Supplementary data are available at Bioinformatics online.

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

Hart, David; Klise, Katherine A.

The PyEPANET package is a set of commands for the Python programming language that are built to wrap the EPANET toolkit library commands, without requiring the end user to program using the ctypes package. This package does not contain the EPANET code, nor does it implement the functions within the EPANET software, and it requires the separately downloaded or compiled EPANET2 toolkit dynamic library (epanet.dll, libepanent.so, or epanet.dylib) and/or the EPANET-MSX dynamic library in order to function.

Gpufit: An open-source toolkit for GPU-accelerated curve fitting.

PubMed

Przybylski, Adrian; Thiel, Björn; Keller-Findeisen, Jan; Stock, Bernd; Bates, Mark

2017-11-16

We present a general purpose, open-source software library for estimation of non-linear parameters by the Levenberg-Marquardt algorithm. The software, Gpufit, runs on a Graphics Processing Unit (GPU) and executes computations in parallel, resulting in a significant gain in performance. We measured a speed increase of up to 42 times when comparing Gpufit with an identical CPU-based algorithm, with no loss of precision or accuracy. Gpufit is designed such that it is easily incorporated into existing applications or adapted for new ones. Multiple software interfaces, including to C, Python, and Matlab, ensure that Gpufit is accessible from most programming environments. The full source code is published as an open source software repository, making its function transparent to the user and facilitating future improvements and extensions. As a demonstration, we used Gpufit to accelerate an existing scientific image analysis package, yielding significantly improved processing times for super-resolution fluorescence microscopy datasets.

The component-based architecture of the HELIOS medical software engineering environment.

PubMed

Degoulet, P; Jean, F C; Engelmann, U; Meinzer, H P; Baud, R; Sandblad, B; Wigertz, O; Le Meur, R; Jagermann, C

1994-12-01

The constitution of highly integrated health information networks and the growth of multimedia technologies raise new challenges for the development of medical applications. We describe in this paper the general architecture of the HELIOS medical software engineering environment devoted to the development and maintenance of multimedia distributed medical applications. HELIOS is made of a set of software components, federated by a communication channel called the HELIOS Unification Bus. The HELIOS kernel includes three main components, the Analysis-Design and Environment, the Object Information System and the Interface Manager. HELIOS services consist in a collection of toolkits providing the necessary facilities to medical application developers. They include Image Related services, a Natural Language Processor, a Decision Support System and Connection services. The project gives special attention to both object-oriented approaches and software re-usability that are considered crucial steps towards the development of more reliable, coherent and integrated applications.

CRISPR-Cas9 Toolkit for Actinomycete Genome Editing.

PubMed

Tong, Yaojun; Robertsen, Helene Lunde; Blin, Kai; Weber, Tilmann; Lee, Sang Yup

2018-01-01

Bacteria of the order Actinomycetales are one of the most important sources of bioactive natural products, which are the source of many drugs. However, many of them still lack efficient genome editing methods, some strains even cannot be manipulated at all. This restricts systematic metabolic engineering approaches for boosting known and discovering novel natural products. In order to facilitate the genome editing for actinomycetes, we developed a CRISPR-Cas9 toolkit with high efficiency for actinomyces genome editing. This basic toolkit includes a software for spacer (sgRNA) identification, a system for in-frame gene/gene cluster knockout, a system for gene loss-of-function study, a system for generating a random size deletion library, and a system for gene knockdown. For the latter, a uracil-specific excision reagent (USER) cloning technology was adapted to simplify the CRISPR vector construction process. The application of this toolkit was successfully demonstrated by perturbation of genomes of Streptomyces coelicolor A3(2) and Streptomyces collinus Tü 365. The CRISPR-Cas9 toolkit and related protocol described here can be widely used for metabolic engineering of actinomycetes.

PDB@: an offline toolkit for exploration and analysis of PDB files.

PubMed

Mani, Udayakumar; Ravisankar, Sadhana; Ramakrishnan, Sai Mukund

2013-12-01

Protein Data Bank (PDB) is a freely accessible archive of the 3-D structural data of biological molecules. Structure based studies offers a unique vantage point in inferring the properties of a protein molecule from structural data. This is too big a task to be done manually. Moreover, there is no single tool, software or server that comprehensively analyses all structure-based properties. The objective of the present work is to develop an offline computational toolkit, PDB@ containing in-built algorithms that help categorizing the structural properties of a protein molecule. The user has the facility to view and edit the PDB file to his need. Some features of the present work are unique in itself and others are an improvement over existing tools. Also, the representation of protein properties in both graphical and textual formats helps in predicting all the necessary details of a protein molecule on a single platform.

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research

PubMed Central

Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R.

2016-01-01

Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM®) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions. Conversion and visualization tools utilizing this toolkit were developed. The encoded objects were validated for consistency and interoperability. The resulting dataset was deposited in the QIN-HEADNECK collection of The Cancer Imaging Archive (TCIA). Supporting tools for data analysis and DICOM conversion were made available as free open-source software. Discussion. We presented a detailed investigation of the development and application of the DICOM model, as well as the supporting open-source tools and toolkits, to accommodate representation of the research data in QI biomarker development. We demonstrated that the DICOM standard can be used to represent the types of data relevant in HNC QI biomarker development, and encode their complex relationships. The resulting annotated objects are amenable to data mining applications, and are interoperable with a variety of systems that support the DICOM standard. PMID:27257542

CheMentor Software System by H. A. Peoples

NASA Astrophysics Data System (ADS)

Reid, Brian P.

1997-09-01

CheMentor Software System H. A. Peoples. Computerized Learning Enhancements: http://www.ecis.com/~clehap; email: clehap@ecis.com; 1996 - 1997. CheMentor is a series of software packages for introductory-level chemistry, which includes Practice Items (I), Stoichiometry (I), Calculating Chemical Formulae, and the CheMentor Toolkit. The first three packages provide practice problems for students and various types of help to solve them; the Toolkit includes "calculators" for determining chemical quantities as well as the Practice Items (I) set of problems. The set of software packages is designed so that each individual product acts as a module of a common CheMentor program. As the name CheMentor implies, the software is designed as a "mentor" for students learning introductory chemistry concepts and problems. The typical use of the software would be by individual students (or perhaps small groups) as an adjunct to lectures. CheMentor is a HyperCard application and the modules are HyperCard stacks. The requirements to run the packages include a Macintosh computer with at least 1 MB of RAM, a hard drive with several MB of available space depending upon the packages selected (10 MB were required for all the packages reviewed here), and the Mac operating system 6.0.5 or later.

Recent developments in Geant4

DOE PAGES

Allison, J.; Amako, K.; Apostolakis, J.; ...

2016-07-01

Geant4 is a software toolkit for the simulation of the passage of particles through matter. It is used by a large number of experiments and projects in a variety of application domains, including high energy physics, astrophysics and space science, medical physics and radiation protection. Over the past several years, major changes have been made to the toolkit in order to accommodate the needs of these user communities, and to efficiently exploit the growth of computing power made available by advances in technology. In conclusion, the adaptation of Geant4 to multithreading, advances in physics, detector modeling and visualization, extensions tomore » the toolkit, including biasing and reverse Monte Carlo, and tools for physics and release validation are discussed here.« less

Tracker Toolkit

NASA Technical Reports Server (NTRS)

Lewis, Steven J.; Palacios, David M.

2013-01-01

This software can track multiple moving objects within a video stream simultaneously, use visual features to aid in the tracking, and initiate tracks based on object detection in a subregion. A simple programmatic interface allows plugging into larger image chain modeling suites. It extracts unique visual features for aid in tracking and later analysis, and includes sub-functionality for extracting visual features about an object identified within an image frame. Tracker Toolkit utilizes a feature extraction algorithm to tag each object with metadata features about its size, shape, color, and movement. Its functionality is independent of the scale of objects within a scene. The only assumption made on the tracked objects is that they move. There are no constraints on size within the scene, shape, or type of movement. The Tracker Toolkit is also capable of following an arbitrary number of objects in the same scene, identifying and propagating the track of each object from frame to frame. Target objects may be specified for tracking beforehand, or may be dynamically discovered within a tripwire region. Initialization of the Tracker Toolkit algorithm includes two steps: Initializing the data structures for tracked target objects, including targets preselected for tracking; and initializing the tripwire region. If no tripwire region is desired, this step is skipped. The tripwire region is an area within the frames that is always checked for new objects, and all new objects discovered within the region will be tracked until lost (by leaving the frame, stopping, or blending in to the background).

Validation and Verification of Operational Land Analysis Activities at the Air Force Weather Agency

NASA Technical Reports Server (NTRS)

Shaw, Michael; Kumar, Sujay V.; Peters-Lidard, Christa D.; Cetola, Jeffrey

2012-01-01

The NASA developed Land Information System (LIS) is the Air Force Weather Agency's (AFWA) operational Land Data Assimilation System (LDAS) combining real time precipitation observations and analyses, global forecast model data, vegetation, terrain, and soil parameters with the community Noah land surface model, along with other hydrology module options, to generate profile analyses of global soil moisture, soil temperature, and other important land surface characteristics. (1) A range of satellite data products and surface observations used to generate the land analysis products (2) Global, 1/4 deg spatial resolution (3) Model analysis generated at 3 hours. AFWA recognizes the importance of operational benchmarking and uncertainty characterization for land surface modeling and is developing standard methods, software, and metrics to verify and/or validate LIS output products. To facilitate this and other needs for land analysis activities at AFWA, the Model Evaluation Toolkit (MET) -- a joint product of the National Center for Atmospheric Research Developmental Testbed Center (NCAR DTC), AFWA, and the user community -- and the Land surface Verification Toolkit (LVT), developed at the Goddard Space Flight Center (GSFC), have been adapted to operational benchmarking needs of AFWA's land characterization activities.

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

NASA Technical Reports Server (NTRS)

Choo, Yung K.; Vickerman, Mary B.

2005-01-01

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

Provenance tracking for scientific software toolchains through on-demand release and archiving

NASA Astrophysics Data System (ADS)

Ham, David

2017-04-01

There is an emerging consensus that published computational science results must be backed by a provenance chain tying results to the exact versions of input data and the code which generated them. There is also now an impressive range of web services devoted to revision control of software, and the archiving in citeable form of both software and input data. However, much scientific software itself builds on libraries and toolkits, and these themselves have dependencies. Further, it is common for cutting edge research to depend on the latest version of software in online repositories, rather than the official release version. This creates a situation in which an author who wishes to follow best practice in recording the provenance chain of their results must archive and cite unreleased versions of a series of dependencies. Here, we present an alternative which toolkit authors can easily implement to provide a semi-automatic mechanism for creating and archiving custom software releases of the precise version of a package used in a particular simulation. This approach leverages the excellent services provided by GitHub and Zenodo to generate a connected set of citeable DOIs for the archived software. We present the integration of this workflow into the Firedrake automated finite element framework as a practical example of this approach in use on a complex geoscientific tool chain in practical use.

Software Aids Visualization of Computed Unsteady Flow

NASA Technical Reports Server (NTRS)

Kao, David; Kenwright, David

2003-01-01

Unsteady Flow Analysis Toolkit (UFAT) is a computer program that synthesizes motions of time-dependent flows represented by very large sets of data generated in computational fluid dynamics simulations. Prior to the development of UFAT, it was necessary to rely on static, single-snapshot depictions of time-dependent flows generated by flow-visualization software designed for steady flows. Whereas it typically takes weeks to analyze the results of a largescale unsteady-flow simulation by use of steady-flow visualization software, the analysis time is reduced to hours when UFAT is used. UFAT can be used to generate graphical objects of flow visualization results using multi-block curvilinear grids in the format of a previously developed NASA data-visualization program, PLOT3D. These graphical objects can be rendered using FAST, another popular flow visualization software developed at NASA. Flow-visualization techniques that can be exploited by use of UFAT include time-dependent tracking of particles, detection of vortex cores, extractions of stream ribbons and surfaces, and tetrahedral decomposition for optimal particle tracking. Unique computational features of UFAT include capabilities for automatic (batch) processing, restart, memory mapping, and parallel processing. These capabilities significantly reduce analysis time and storage requirements, relative to those of prior flow-visualization software. UFAT can be executed on a variety of supercomputers.

X-Ray Toolkit

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

2015-10-20

Radiographic Image Acquisition & Processing Software for Security Markets. Used in operation of commercial x-ray scanners and manipulation of x-ray images for emergency responders including State, Local, Federal, and US Military bomb technicians and analysts.

BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees.

PubMed

Bond, Stephen R; Keat, Karl E; Barreira, Sofia N; Baxevanis, Andreas D

2017-06-01

The ability to manipulate sequence, alignment, and phylogenetic tree files has become an increasingly important skill in the life sciences, whether to generate summary information or to prepare data for further downstream analysis. The command line can be an extremely powerful environment for interacting with these resources, but only if the user has the appropriate general-purpose tools on hand. BuddySuite is a collection of four independent yet interrelated command-line toolkits that facilitate each step in the workflow of sequence discovery, curation, alignment, and phylogenetic reconstruction. Most common sequence, alignment, and tree file formats are automatically detected and parsed, and over 100 tools have been implemented for manipulating these data. The project has been engineered to easily accommodate the addition of new tools, is written in the popular programming language Python, and is hosted on the Python Package Index and GitHub to maximize accessibility. Documentation for each BuddySuite tool, including usage examples, is available at http://tiny.cc/buddysuite_wiki. All software is open source and freely available through http://research.nhgri.nih.gov/software/BuddySuite. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution 2017. This work is written by US Government employees and is in the public domain in the US.

Simulink/PARS Integration Support

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

Vacaliuc, B.; Nakhaee, N.

2013-12-18

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

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

NASA Astrophysics Data System (ADS)

Snider, E. L.; Petrillo, G.

2017-10-01

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

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

PubMed Central

Althammer, Sonja; González-Vallinas, Juan; Ballaré, Cecilia; Beato, Miguel; Eyras, Eduardo

2011-01-01

Motivation: High-throughput sequencing (HTS) has revolutionized gene regulation studies and is now fundamental for the detection of protein–DNA and protein–RNA binding, as well as for measuring RNA expression. With increasing variety and sequencing depth of HTS datasets, the need for more flexible and memory-efficient tools to analyse them is growing. Results: We describe Pyicos, a powerful toolkit for the analysis of mapped reads from diverse HTS experiments: ChIP-Seq, either punctuated or broad signals, CLIP-Seq and RNA-Seq. We prove the effectiveness of Pyicos to select for significant signals and show that its accuracy is comparable and sometimes superior to that of methods specifically designed for each particular type of experiment. Pyicos facilitates the analysis of a variety of HTS datatypes through its flexibility and memory efficiency, providing a useful framework for data integration into models of regulatory genomics. Availability: Open-source software, with tutorials and protocol files, is available at http://regulatorygenomics.upf.edu/pyicos or as a Galaxy server at http://regulatorygenomics.upf.edu/galaxy Contact: eduardo.eyras@upf.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21994224

The RAVE/VERTIGO vertex reconstruction toolkit and framework

NASA Astrophysics Data System (ADS)

Waltenberger, W.; Mitaroff, W.; Moser, F.; Pflugfelder, B.; Riedel, H. V.

2008-07-01

A detector-independent toolkit for vertex reconstruction (RAVE1) is being developed, along with a standalone framework (VERTIGO2) for testing, analyzing and debugging. The core algorithms represent state-of-the-art for geometric vertex finding and fitting by both linear (Kalman filter) and robust estimation methods. Main design goals are ease of use, flexibility for embedding into existing software frameworks, extensibility, and openness. The implementation is based on modern object-oriented techniques, is coded in C++ with interfaces for Java and Python, and follows an open-source approach. A beta release is available.

The MUSOS (MUsic SOftware System) Toolkit: A computer-based, open source application for testing memory for melodies.

PubMed

Rainsford, M; Palmer, M A; Paine, G

2018-04-01

Despite numerous innovative studies, rates of replication in the field of music psychology are extremely low (Frieler et al., 2013). Two key methodological challenges affecting researchers wishing to administer and reproduce studies in music cognition are the difficulty of measuring musical responses, particularly when conducting free-recall studies, and access to a reliable set of novel stimuli unrestricted by copyright or licensing issues. In this article, we propose a solution for these challenges in computer-based administration. We present a computer-based application for testing memory for melodies. Created using the software Max/MSP (Cycling '74, 2014a), the MUSOS (Music Software System) Toolkit uses a simple modular framework configurable for testing common paradigms such as recall, old-new recognition, and stem completion. The program is accompanied by a stimulus set of 156 novel, copyright-free melodies, in audio and Max/MSP file formats. Two pilot tests were conducted to establish the properties of the accompanying stimulus set that are relevant to music cognition and general memory research. By using this software, a researcher without specialist musical training may administer and accurately measure responses from common paradigms used in the study of memory for music.

Pcetk: A pDynamo-based Toolkit for Protonation State Calculations in Proteins.

PubMed

Feliks, Mikolaj; Field, Martin J

2015-10-26

Pcetk (a pDynamo-based continuum electrostatic toolkit) is an open-source, object-oriented toolkit for the calculation of proton binding energetics in proteins. The toolkit is a module of the pDynamo software library, combining the versatility of the Python scripting language and the efficiency of the compiled languages, C and Cython. In the toolkit, we have connected pDynamo to the external Poisson-Boltzmann solver, extended-MEAD. Our goal was to provide a modern and extensible environment for the calculation of protonation states, electrostatic energies, titration curves, and other electrostatic-dependent properties of proteins. Pcetk is freely available under the CeCILL license, which is compatible with the GNU General Public License. The toolkit can be found on the Web at the address http://github.com/mfx9/pcetk. The calculation of protonation states in proteins requires a knowledge of pKa values of protonatable groups in aqueous solution. However, for some groups, such as protonatable ligands bound to protein, the pKa aq values are often difficult to obtain from experiment. As a complement to Pcetk, we revisit an earlier computational method for the estimation of pKa aq values that has an accuracy of ± 0.5 pKa-units or better. Finally, we verify the Pcetk module and the method for estimating pKa aq values with different model cases.

Comparison of GEANT4 very low energy cross section models with experimental data in water.

PubMed

Incerti, S; Ivanchenko, A; Karamitros, M; Mantero, A; Moretto, P; Tran, H N; Mascialino, B; Champion, C; Ivanchenko, V N; Bernal, M A; Francis, Z; Villagrasa, C; Baldacchin, G; Guèye, P; Capra, R; Nieminen, P; Zacharatou, C

2010-09-01

The GEANT4 general-purpose Monte Carlo simulation toolkit is able to simulate physical interaction processes of electrons, hydrogen and helium atoms with charge states (H0, H+) and (He0, He+, He2+), respectively, in liquid water, the main component of biological systems, down to the electron volt regime and the submicrometer scale, providing GEANT4 users with the so-called "GEANT4-DNA" physics models suitable for microdosimetry simulation applications. The corresponding software has been recently re-engineered in order to provide GEANT4 users with a coherent and unique approach to the simulation of electromagnetic interactions within the GEANT4 toolkit framework (since GEANT4 version 9.3 beta). This work presents a quantitative comparison of these physics models with a collection of experimental data in water collected from the literature. An evaluation of the closeness between the total and differential cross section models available in the GEANT4 toolkit for microdosimetry and experimental reference data is performed using a dedicated statistical toolkit that includes the Kolmogorov-Smirnov statistical test. The authors used experimental data acquired in water vapor as direct measurements in the liquid phase are not yet available in the literature. Comparisons with several recommendations are also presented. The authors have assessed the compatibility of experimental data with GEANT4 microdosimetry models by means of quantitative methods. The results show that microdosimetric measurements in liquid water are necessary to assess quantitatively the validity of the software implementation for the liquid water phase. Nevertheless, a comparison with existing experimental data in water vapor provides a qualitative appreciation of the plausibility of the simulation models. The existing reference data themselves should undergo a critical interpretation and selection, as some of the series exhibit significant deviations from each other. The GEANT4-DNA physics models available in the GEANT4 toolkit have been compared in this article to available experimental data in the water vapor phase as well as to several published recommendations on the mass stopping power. These models represent a first step in the extension of the GEANT4 Monte Carlo toolkit to the simulation of biological effects of ionizing radiation.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

Yamamoto, Y.; Ishihara, Y.; Otake, H.; Imai, K.; Masuda, K.

2015-12-01

Scientific data obtained by Japanese scientific satellites and lunar and planetary explorations are archived in DARTS (Data ARchives and Transmission System). DARTS provides the data with a simple method such as HTTP directory listing for long-term preservation while DARTS tries to provide rich web applications for ease of access with modern web technologies based on open source software. This presentation showcases availability of open source software through our services. KADIAS is a web-based application to search, analyze, and obtain scientific data measured by SELENE(Kaguya), a Japanese lunar orbiter. KADIAS uses OpenLayers to display maps distributed from Web Map Service (WMS). As a WMS server, open source software MapServer is adopted. KAGUYA 3D GIS (KAGUYA 3D Moon NAVI) provides a virtual globe for the SELENE's data. The main purpose of this application is public outreach. NASA World Wind Java SDK is used to develop. C3 (Cross-Cutting Comparisons) is a tool to compare data from various observations and simulations. It uses Highcharts to draw graphs on web browsers. Flow is a tool to simulate a Field-Of-View of an instrument onboard a spacecraft. This tool itself is open source software developed by JAXA/ISAS, and the license is BSD 3-Caluse License. SPICE Toolkit is essential to compile FLOW. SPICE Toolkit is also open source software developed by NASA/JPL, and the website distributes many spacecrafts' data. Nowadays, open source software is an indispensable tool to integrate DARTS services.

Integration of XNAT/PACS, DICOM, and Research Software for Automated Multi-modal Image Analysis.

PubMed

Gao, Yurui; Burns, Scott S; Lauzon, Carolyn B; Fong, Andrew E; James, Terry A; Lubar, Joel F; Thatcher, Robert W; Twillie, David A; Wirt, Michael D; Zola, Marc A; Logan, Bret W; Anderson, Adam W; Landman, Bennett A

2013-03-29

Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software.

Integration of XNAT/PACS, DICOM, and research software for automated multi-modal image analysis

NASA Astrophysics Data System (ADS)

Gao, Yurui; Burns, Scott S.; Lauzon, Carolyn B.; Fong, Andrew E.; James, Terry A.; Lubar, Joel F.; Thatcher, Robert W.; Twillie, David A.; Wirt, Michael D.; Zola, Marc A.; Logan, Bret W.; Anderson, Adam W.; Landman, Bennett A.

2013-03-01

Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software.

Integration of XNAT/PACS, DICOM, and Research Software for Automated Multi-modal Image Analysis

PubMed Central

Gao, Yurui; Burns, Scott S.; Lauzon, Carolyn B.; Fong, Andrew E.; James, Terry A.; Lubar, Joel F.; Thatcher, Robert W.; Twillie, David A.; Wirt, Michael D.; Zola, Marc A.; Logan, Bret W.; Anderson, Adam W.; Landman, Bennett A.

2013-01-01

Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software. PMID:24386548

A MATLAB Library for Rapid Prototyping of Wireless Communications Algorithms with the Universal Software Radio Peripheral (USRP) Radio Family

DTIC Science & Technology

2013-06-01

Radio is a software development toolkit that provides signal processing blocks to drive the SDR. GNU Radio has many strong points – it is actively...maintained with a large user base, new capabilities are constantly being added, and compiled C code is fast for many real-time applications such as...programming interface (API) makes learning the architecture a daunting task, even for the experienced software developer. This requirement poses many

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

PubMed

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

2004-11-01

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

Designing a ticket to ride with the Cognitive Work Analysis Design Toolkit.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G; Jenkins, Daniel P

2015-01-01

Cognitive work analysis has been applied in the design of numerous sociotechnical systems. The process used to translate analysis outputs into design concepts, however, is not always clear. Moreover, structured processes for translating the outputs of ergonomics methods into concrete designs are lacking. This paper introduces the Cognitive Work Analysis Design Toolkit (CWA-DT), a design approach which has been developed specifically to provide a structured means of incorporating cognitive work analysis outputs in design using design principles and values derived from sociotechnical systems theory. This paper outlines the CWA-DT and describes its application in a public transport ticketing design case study. Qualitative and quantitative evaluations of the process provide promising early evidence that the toolkit fulfils the evaluation criteria identified for its success, with opportunities for improvement also highlighted. The Cognitive Work Analysis Design Toolkit has been developed to provide ergonomics practitioners with a structured approach for translating the outputs of cognitive work analysis into design solutions. This paper demonstrates an application of the toolkit and provides evaluation findings.

The Microsoft Biology Foundation Applications for High-Throughput Sequencing

PubMed Central

Mercer, S.

2010-01-01

w9-2 The need for reusable libraries of bioinformatics functions has been recognized for many years and a number of language-specific toolkits have been constructed. Such toolkits have served as valuable nucleation points for the community, promoting the sharing of code and establishing standards. The majority of DNA sequencing machines and many other standard pieces of lab equipment are controlled by PCs using Windows, and a Microsoft genomics toolkit would enable initial processing and quality control to happen closer to the instrumentation and provide opportunities for added-value services within core facilities. The Microsoft Biology Foundation (MBF) is an open source software library, freely available for both commercial and academic use, available as an early-stage betafrom mbf.codeplex.com. This presentation will describe the structure and goals of MBF and demonstrate some of its uses.

The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences

PubMed Central

Portales-Casamar, Elodie; Arenillas, David; Lim, Jonathan; Swanson, Magdalena I.; Jiang, Steven; McCallum, Anthony; Kirov, Stefan; Wasserman, Wyeth W.

2009-01-01

The PAZAR database unites independently created and maintained data collections of transcription factor and regulatory sequence annotation. The flexible PAZAR schema permits the representation of diverse information derived from experiments ranging from biochemical protein–DNA binding to cellular reporter gene assays. Data collections can be made available to the public, or restricted to specific system users. The data ‘boutiques’ within the shopping-mall-inspired system facilitate the analysis of genomics data and the creation of predictive models of gene regulation. Since its initial release, PAZAR has grown in terms of data, features and through the addition of an associated package of software tools called the ORCA toolkit (ORCAtk). ORCAtk allows users to rapidly develop analyses based on the information stored in the PAZAR system. PAZAR is available at http://www.pazar.info. ORCAtk can be accessed through convenient buttons located in the PAZAR pages or via our website at http://www.cisreg.ca/ORCAtk. PMID:18971253

Estimation of water quality parameters of inland and coastal waters with the use of a toolkit for processing of remote sensing data

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

Dekker, A.G.; Hoogenboom, H.J.; Rijkeboer, M.

1997-06-01

Deriving thematic maps of water quality parameters from a remote sensing image requires a number of processing steps, such as calibration, atmospheric correction, air/water interface correction, and application of water quality algorithms. A prototype software environment has recently been developed that enables the user to perform and control these processing steps. Main parts of this environment are: (i) access to the MODTRAN 3 radiative transfer code for removing atmospheric and air-water interface influences, (ii) a tool for analyzing of algorithms for estimating water quality and (iii) a spectral database, containing apparent and inherent optical properties and associated water quality parameters.more » The use of the software is illustrated by applying implemented algorithms for estimating chlorophyll to data from a spectral library of Dutch inland waters with CHL ranging from 1 to 500 pg 1{sup -1}. The algorithms currently implemented in the Toolkit software are recommended for optically simple waters, but for optically complex waters development of more advanced retrieval methods is required.« less

OSCAR4: a flexible architecture for chemical text-mining.

PubMed

Jessop, David M; Adams, Sam E; Willighagen, Egon L; Hawizy, Lezan; Murray-Rust, Peter

2011-10-14

The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed.

THE AUTOMATED GEOSPATIAL WATERSHED ASSESSMENT TOOL

EPA Science Inventory

A toolkit for distributed hydrologic modeling at multiple scales using a geographic information system is presented. This open-source, freely available software was developed through a collaborative endeavor involving two Universities and two government agencies. Called the Auto...

Dakota, a multilevel parallel object-oriented framework for design optimization, parameter estimation, uncertainty quantification, and sensitivity analysis version 6.0 theory manual

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

Adams, Brian M.; Ebeida, Mohamed Salah; Eldred, Michael S

The Dakota (Design Analysis Kit for Optimization and Terascale Applications) toolkit provides a exible and extensible interface between simulation codes and iterative analysis methods. Dakota contains algorithms for optimization with gradient and nongradient-based methods; uncertainty quanti cation with sampling, reliability, and stochastic expansion methods; parameter estimation with nonlinear least squares methods; and sensitivity/variance analysis with design of experiments and parameter study methods. These capabilities may be used on their own or as components within advanced strategies such as surrogate-based optimization, mixed integer nonlinear programming, or optimization under uncertainty. By employing object-oriented design to implement abstractions of the key components requiredmore » for iterative systems analyses, the Dakota toolkit provides a exible and extensible problem-solving environment for design and performance analysis of computational models on high performance computers. This report serves as a theoretical manual for selected algorithms implemented within the Dakota software. It is not intended as a comprehensive theoretical treatment, since a number of existing texts cover general optimization theory, statistical analysis, and other introductory topics. Rather, this manual is intended to summarize a set of Dakota-related research publications in the areas of surrogate-based optimization, uncertainty quanti cation, and optimization under uncertainty that provide the foundation for many of Dakota's iterative analysis capabilities.« less

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

PubMed

Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel

2011-08-01

Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Water Security Toolkit User Manual: Version 1.3 | Science ...

EPA Pesticide Factsheets

User manual: Data Product/Software The Water Security Toolkit (WST) is a suite of tools that help provide the information necessary to make good decisions resulting in the minimization of further human exposure to contaminants, and the maximization of the effectiveness of intervention strategies. WST assists in the evaluation of multiple response actions in order to select the most beneficial consequence management strategy. It includes hydraulic and water quality modeling software and optimization methodologies to identify: (1) sensor locations to detect contamination, (2) locations in the network in which the contamination was introduced, (3) hydrants to remove contaminated water from the distribution system, (4) locations in the network to inject decontamination agents to inactivate, remove or destroy contaminants, (5) locations in the network to take grab sample to confirm contamination or cleanup and (6) valves to close in order to isolate contaminated areas of the network.

An open-source framework for testing tracking devices using Lego Mindstorms

NASA Astrophysics Data System (ADS)

Jomier, Julien; Ibanez, Luis; Enquobahrie, Andinet; Pace, Danielle; Cleary, Kevin

2009-02-01

In this paper, we present an open-source framework for testing tracking devices in surgical navigation applications. At the core of image-guided intervention systems is the tracking interface that handles communication with the tracking device and gathers tracking information. Given that the correctness of tracking information is critical for protecting patient safety and for ensuring the successful execution of an intervention, the tracking software component needs to be thoroughly tested on a regular basis. Furthermore, with widespread use of extreme programming methodology that emphasizes continuous and incremental testing of application components, testing design becomes critical. While it is easy to automate most of the testing process, it is often more difficult to test components that require manual intervention such as tracking device. Our framework consists of a robotic arm built from a set of Lego Mindstorms and an open-source toolkit written in C++ to control the robot movements and assess the accuracy of the tracking devices. The application program interface (API) is cross-platform and runs on Windows, Linux and MacOS. We applied this framework for the continuous testing of the Image-Guided Surgery Toolkit (IGSTK), an open-source toolkit for image-guided surgery and shown that regression testing on tracking devices can be performed at low cost and improve significantly the quality of the software.

A fast - Monte Carlo toolkit on GPU for treatment plan dose recalculation in proton therapy

NASA Astrophysics Data System (ADS)

Senzacqua, M.; Schiavi, A.; Patera, V.; Pioli, S.; Battistoni, G.; Ciocca, M.; Mairani, A.; Magro, G.; Molinelli, S.

2017-10-01

In the context of the particle therapy a crucial role is played by Treatment Planning Systems (TPSs), tools aimed to compute and optimize the tratment plan. Nowadays one of the major issues related to the TPS in particle therapy is the large CPU time needed. We developed a software toolkit (FRED) for reducing dose recalculation time by exploiting Graphics Processing Units (GPU) hardware. Thanks to their high parallelization capability, GPUs significantly reduce the computation time, up to factor 100 respect to a standard CPU running software. The transport of proton beams in the patient is accurately described through Monte Carlo methods. Physical processes reproduced are: Multiple Coulomb Scattering, energy straggling and nuclear interactions of protons with the main nuclei composing the biological tissues. FRED toolkit does not rely on the water equivalent translation of tissues, but exploits the Computed Tomography anatomical information by reconstructing and simulating the atomic composition of each crossed tissue. FRED can be used as an efficient tool for dose recalculation, on the day of the treatment. In fact it can provide in about one minute on standard hardware the dose map obtained combining the treatment plan, earlier computed by the TPS, and the current patient anatomic arrangement.

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

PubMed Central

2008-01-01

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

PLUS: open-source toolkit for ultrasound-guided intervention systems.

PubMed

Lasso, Andras; Heffter, Tamas; Rankin, Adam; Pinter, Csaba; Ungi, Tamas; Fichtinger, Gabor

2014-10-01

A variety of advanced image analysis methods have been under the development for ultrasound-guided interventions. Unfortunately, the transition from an image analysis algorithm to clinical feasibility trials as part of an intervention system requires integration of many components, such as imaging and tracking devices, data processing algorithms, and visualization software. The objective of our paper is to provide a freely available open-source software platform-PLUS: Public software Library for Ultrasound-to facilitate rapid prototyping of ultrasound-guided intervention systems for translational clinical research. PLUS provides a variety of methods for interventional tool pose and ultrasound image acquisition from a wide range of tracking and imaging devices, spatial and temporal calibration, volume reconstruction, simulated image generation, and recording and live streaming of the acquired data. This paper introduces PLUS, explains its functionality and architecture, and presents typical uses and performance in ultrasound-guided intervention systems. PLUS fulfills the essential requirements for the development of ultrasound-guided intervention systems and it aspires to become a widely used translational research prototyping platform. PLUS is freely available as open source software under BSD license and can be downloaded from http://www.plustoolkit.org.

Tailored prevention of inpatient falls: development and usability testing of the fall TIPS toolkit.

PubMed

Zuyev, Lyubov; Benoit, Angela N; Chang, Frank Y; Dykes, Patricia C

2011-02-01

Patient falls and fall-related injuries are serious problems in hospitals. The Fall TIPS application aims to prevent patient falls by translating routine nursing fall risk assessment into a decision support intervention that communicates fall risk status and creates a tailored evidence-based plan of care that is accessible to the care team, patients, and family members. In our design and implementation of the Fall TIPS toolkit, we used the Spiral Software Development Life Cycle model. Three output tools available to be generated from the toolkit are bed poster, plan of care, and patient education handout. A preliminary design of the application was based on initial requirements defined by project leaders and informed by focus groups with end users. Preliminary design partially simulated the paper version of the Morse Fall Scale currently used in hospitals involved in the research study. Strengths and weaknesses of the first prototype were identified by heuristic evaluation. Usability testing was performed at sites where research study is implemented. Suggestions mentioned by end users participating in usability studies were either directly incorporated into the toolkit and output tools, were slightly modified, or will be addressed during training. The next step is implementation of the fall prevention toolkit on the pilot testing units.

Distribution of a Generic Mission Planning and Scheduling Toolkit for Astronomical Spacecraft

NASA Technical Reports Server (NTRS)

Kleiner, Steven C.

1996-01-01

Work is progressing as outlined in the proposal for this contract. A working planning and scheduling system has been documented and packaged and made available to the WIRE Small Explorer group at JPL, the FUSE group at JHU, the NASA/GSFC Laboratory for Astronomy and Solar Physics and the Advanced Planning and Scheduling Branch at STScI. The package is running successfully on the WIRE computer system. It is expected that the WIRE will reuse significant portions of the SWAS code in its system. This scheduling system itself was tested successfully against the spacecraft hardware in December 1995. A fully automatic scheduling module has been developed and is being added to the toolkit. In order to maximize reuse, the code is being reorganized during the current build into object-oriented class libraries. A paper describing the toolkit has been written and is included in the software distribution. We have experienced interference between the export and production versions of the toolkit. We will be requesting permission to reprogram funds in order to purchase a standalone PC onto which to offload the export version.

A qualitative study of clinic and community member perspectives on intervention toolkits: "Unless the toolkit is used it won't help solve the problem".

PubMed

Davis, Melinda M; Howk, Sonya; Spurlock, Margaret; McGinnis, Paul B; Cohen, Deborah J; Fagnan, Lyle J

2017-07-18

Intervention toolkits are common products of grant-funded research in public health and primary care settings. Toolkits are designed to address the knowledge translation gap by speeding implementation and dissemination of research into practice. However, few studies describe characteristics of effective intervention toolkits and their implementation. Therefore, we conducted this study to explore what clinic and community-based users want in intervention toolkits and to identify the factors that support application in practice. In this qualitative descriptive study we conducted focus groups and interviews with a purposive sample of community health coalition members, public health experts, and primary care professionals between November 2010 and January 2012. The transdisciplinary research team used thematic analysis to identify themes and a cross-case comparative analysis to explore variation by participant role and toolkit experience. Ninety six participants representing primary care (n = 54, 56%) and community settings (n = 42, 44%) participated in 18 sessions (13 focus groups, five key informant interviews). Participants ranged from those naïve through expert in toolkit development; many reported limited application of toolkits in actual practice. Participants wanted toolkits targeted at the right audience and demonstrated to be effective. Well organized toolkits, often with a quick start guide, with tools that were easy to tailor and apply were desired. Irrespective of perceived quality, participants experienced with practice change emphasized that leadership, staff buy-in, and facilitative support was essential for intervention toolkits to be translated into changes in clinic or public -health practice. Given the emphasis on toolkits in supporting implementation and dissemination of research and clinical guidelines, studies are warranted to determine when and how toolkits are used. Funders, policy makers, researchers, and leaders in primary care and public health are encouraged to allocate resources to foster both toolkit development and implementation. Support, through practice facilitation and organizational leadership, are critical for translating knowledge from intervention toolkits into practice.

Buying in to bioinformatics: an introduction to commercial sequence analysis software

PubMed Central

2015-01-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. PMID:25183247

Buying in to bioinformatics: an introduction to commercial sequence analysis software.

PubMed

Smith, David Roy

2015-07-01

Advancements in high-throughput nucleotide sequencing techniques have brought with them state-of-the-art bioinformatics programs and software packages. Given the importance of molecular sequence data in contemporary life science research, these software suites are becoming an essential component of many labs and classrooms, and as such are frequently designed for non-computer specialists and marketed as one-stop bioinformatics toolkits. Although beautifully designed and powerful, user-friendly bioinformatics packages can be expensive and, as more arrive on the market each year, it can be difficult for researchers, teachers and students to choose the right software for their needs, especially if they do not have a bioinformatics background. This review highlights some of the currently available and most popular commercial bioinformatics packages, discussing their prices, usability, features and suitability for teaching. Although several commercial bioinformatics programs are arguably overpriced and overhyped, many are well designed, sophisticated and, in my opinion, worth the investment. If you are just beginning your foray into molecular sequence analysis or an experienced genomicist, I encourage you to explore proprietary software bundles. They have the potential to streamline your research, increase your productivity, energize your classroom and, if anything, add a bit of zest to the often dry detached world of bioinformatics. © The Author 2014. Published by Oxford University Press.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy; Kim, Youngkwang; Conway, Claire; Conway, Darrel J.

2017-01-01

This paper describes the processes and results of Verification and Validation (VV) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The VV effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy (Compiler); Kim, Youngkwang; Conway, Claire (Compiler); Conway, Darrel

2017-01-01

This paper describes the processes and results of Verification and Validation (V&V) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The V&V effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Ada To X-Window Bindings

NASA Technical Reports Server (NTRS)

Souleles, Dean

1993-01-01

Ada to X-Window Bindings computer program developed to provide Ada programmers with complete interfaces to Xt Intrinsics and OSF Motif toolkits. Provides "Ada view" of some mostly C-language programming libraries. Package of software written in Ada and C languages.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

PubMed Central

Abbasi, Arash; Berry, Jeffrey C.; Callen, Steven T.; Chavez, Leonardo; Doust, Andrew N.; Feldman, Max J.; Gilbert, Kerrigan B.; Hodge, John G.; Hoyer, J. Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning. PMID:29209576

PlantCV v2: Image analysis software for high-throughput plant phenotyping.

PubMed

Gehan, Malia A; Fahlgren, Noah; Abbasi, Arash; Berry, Jeffrey C; Callen, Steven T; Chavez, Leonardo; Doust, Andrew N; Feldman, Max J; Gilbert, Kerrigan B; Hodge, John G; Hoyer, J Steen; Lin, Andy; Liu, Suxing; Lizárraga, César; Lorence, Argelia; Miller, Michael; Platon, Eric; Tessman, Monica; Sax, Tony

2017-01-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here we present the details and rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.

PlantCV v2: Image analysis software for high-throughput plant phenotyping

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

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

PlantCV v2: Image analysis software for high-throughput plant phenotyping

DOE PAGES

Gehan, Malia A.; Fahlgren, Noah; Abbasi, Arash; ...

2017-12-01

Systems for collecting image data in conjunction with computer vision techniques are a powerful tool for increasing the temporal resolution at which plant phenotypes can be measured non-destructively. Computational tools that are flexible and extendable are needed to address the diversity of plant phenotyping problems. We previously described the Plant Computer Vision (PlantCV) software package, which is an image processing toolkit for plant phenotyping analysis. The goal of the PlantCV project is to develop a set of modular, reusable, and repurposable tools for plant image analysis that are open-source and community-developed. Here in this paper we present the details andmore » rationale for major developments in the second major release of PlantCV. In addition to overall improvements in the organization of the PlantCV project, new functionality includes a set of new image processing and normalization tools, support for analyzing images that include multiple plants, leaf segmentation, landmark identification tools for morphometrics, and modules for machine learning.« less

PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

PubMed

Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

2016-10-01

The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour.

PubMed

Evans, Stephanie; Alden, Kieran; Cucurull-Sanchez, Lourdes; Larminie, Christopher; Coles, Mark C; Kullberg, Marika C; Timmis, Jon

2017-02-01

A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate and modify models using SBML solver output as an initial parameter set, allowing interventions to be applied once a steady state has been reached. Additionally, multiple SBML models can be generated where a subset of parameter values are perturbed using local and global sensitivity analysis techniques, revealing the model's sensitivity to the intervention. To illustrate the capabilities of ASPASIA, we demonstrate how this tool has generated novel hypotheses regarding the mechanisms by which Th17-cell plasticity may be controlled in vivo. By using ASPASIA in conjunction with an SBML model of Th17-cell polarisation, we predict that promotion of the Th1-associated transcription factor T-bet, rather than inhibition of the Th17-associated transcription factor RORγt, is sufficient to drive switching of Th17 cells towards an IFN-γ-producing phenotype. Our approach can be applied to all SBML-encoded models to predict the effect that intervention strategies have on system behaviour. ASPASIA, released under the Artistic License (2.0), can be downloaded from http://www.york.ac.uk/ycil/software.

YBYRÁ facilitates comparison of large phylogenetic trees.

PubMed

Machado, Denis Jacob

2015-07-01

The number and size of tree topologies that are being compared by phylogenetic systematists is increasing due to technological advancements in high-throughput DNA sequencing. However, we still lack tools to facilitate comparison among phylogenetic trees with a large number of terminals. The "YBYRÁ" project integrates software solutions for data analysis in phylogenetics. It comprises tools for (1) topological distance calculation based on the number of shared splits or clades, (2) sensitivity analysis and automatic generation of sensitivity plots and (3) clade diagnoses based on different categories of synapomorphies. YBYRÁ also provides (4) an original framework to facilitate the search for potential rogue taxa based on how much they affect average matching split distances (using MSdist). YBYRÁ facilitates comparison of large phylogenetic trees and outperforms competing software in terms of usability and time efficiency, specially for large data sets. The programs that comprises this toolkit are written in Python, hence they do not require installation and have minimum dependencies. The entire project is available under an open-source licence at http://www.ib.usp.br/grant/anfibios/researchSoftware.html .

LIVVkit: An extensible, python-based, land ice verification and validation toolkit for ice sheet models

NASA Astrophysics Data System (ADS)

Kennedy, Joseph H.; Bennett, Andrew R.; Evans, Katherine J.; Price, Stephen; Hoffman, Matthew; Lipscomb, William H.; Fyke, Jeremy; Vargo, Lauren; Boghozian, Adrianna; Norman, Matthew; Worley, Patrick H.

2017-06-01

To address the pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice sheet models is underway. Concurrent to the development of the Community Ice Sheet Model (CISM), the corresponding verification and validation (V&V) process is being coordinated through a new, robust, Python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVVkit). Incorporated into the typical ice sheet model development cycle, it provides robust and automated numerical verification, software verification, performance validation, and physical validation analyses on a variety of platforms, from personal laptops to the largest supercomputers. LIVVkit operates on sets of regression test and reference data sets, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-for-bit evaluation, and plots of model variables to indicate where differences occur. LIVVkit also provides an easily extensible framework to incorporate and analyze results of new intercomparison projects, new observation data, and new computing platforms. LIVVkit is designed for quick adaptation to additional ice sheet models via abstraction of model specific code, functions, and configurations into an ice sheet model description bundle outside the main LIVVkit structure. Ultimately, through shareable and accessible analysis output, LIVVkit is intended to help developers build confidence in their models and enhance the credibility of ice sheet models overall.

ECCE Toolkit: Prototyping Sensor-Based Interaction.

PubMed

Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

2017-02-23

Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit.

ECCE Toolkit: Prototyping Sensor-Based Interaction

PubMed Central

Bellucci, Andrea; Aedo, Ignacio; Díaz, Paloma

2017-01-01

Building and exploring physical user interfaces requires high technical skills and hours of specialized work. The behavior of multiple devices with heterogeneous input/output channels and connectivity has to be programmed in a context where not only the software interface matters, but also the hardware components are critical (e.g., sensors and actuators). Prototyping physical interaction is hindered by the challenges of: (1) programming interactions among physical sensors/actuators and digital interfaces; (2) implementing functionality for different platforms in different programming languages; and (3) building custom electronic-incorporated objects. We present ECCE (Entities, Components, Couplings and Ecosystems), a toolkit for non-programmers that copes with these issues by abstracting from low-level implementations, thus lowering the complexity of prototyping small-scale, sensor-based physical interfaces to support the design process. A user evaluation provides insights and use cases of the kind of applications that can be developed with the toolkit. PMID:28241502

The semantic measures library and toolkit: fast computation of semantic similarity and relatedness using biomedical ontologies.

PubMed

Harispe, Sébastien; Ranwez, Sylvie; Janaqi, Stefan; Montmain, Jacky

2014-03-01

The semantic measures library and toolkit are robust open-source and easy to use software solutions dedicated to semantic measures. They can be used for large-scale computations and analyses of semantic similarities between terms/concepts defined in terminologies and ontologies. The comparison of entities (e.g. genes) annotated by concepts is also supported. A large collection of measures is available. Not limited to a specific application context, the library and the toolkit can be used with various controlled vocabularies and ontology specifications (e.g. Open Biomedical Ontology, Resource Description Framework). The project targets both designers and practitioners of semantic measures providing a JAVA library, as well as a command-line tool that can be used on personal computers or computer clusters. Downloads, documentation, tutorials, evaluation and support are available at http://www.semantic-measures-library.org.

Scalable Performance Environments for Parallel Systems

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Olson, Robert D.; Aydt, Ruth A.; Madhyastha, Tara M.; Birkett, Thomas; Jensen, David W.; Nazief, Bobby A. A.; Totty, Brian K.

1991-01-01

As parallel systems expand in size and complexity, the absence of performance tools for these parallel systems exacerbates the already difficult problems of application program and system software performance tuning. Moreover, given the pace of technological change, we can no longer afford to develop ad hoc, one-of-a-kind performance instrumentation software; we need scalable, portable performance analysis tools. We describe an environment prototype based on the lessons learned from two previous generations of performance data analysis software. Our environment prototype contains a set of performance data transformation modules that can be interconnected in user-specified ways. It is the responsibility of the environment infrastructure to hide details of module interconnection and data sharing. The environment is written in C++ with the graphical displays based on X windows and the Motif toolkit. It allows users to interconnect and configure modules graphically to form an acyclic, directed data analysis graph. Performance trace data are represented in a self-documenting stream format that includes internal definitions of data types, sizes, and names. The environment prototype supports the use of head-mounted displays and sonic data presentation in addition to the traditional use of visual techniques.

iPhos: a toolkit to streamline the alkaline phosphatase-assisted comprehensive LC-MS phosphoproteome investigation

PubMed Central

2014-01-01

Background Comprehensive characterization of the phosphoproteome in living cells is critical in signal transduction research. But the low abundance of phosphopeptides among the total proteome in cells remains an obstacle in mass spectrometry-based proteomic analysis. To provide a solution, an alternative analytic strategy to confidently identify phosphorylated peptides by using the alkaline phosphatase (AP) treatment combined with high-resolution mass spectrometry was provided. While the process is applicable, the key integration along the pipeline was mostly done by tedious manual work. Results We developed a software toolkit, iPhos, to facilitate and streamline the work-flow of AP-assisted phosphoproteome characterization. The iPhos tookit includes one assister and three modules. The iPhos Peak Extraction Assister automates the batch mode peak extraction for multiple liquid chromatography mass spectrometry (LC-MS) runs. iPhos Module-1 can process the peak lists extracted from the LC-MS analyses derived from the original and dephosphorylated samples to mine out potential phosphorylated peptide signals based on mass shift caused by the loss of some multiples of phosphate groups. And iPhos Module-2 provides customized inclusion lists with peak retention time windows for subsequent targeted LC-MS/MS experiments. Finally, iPhos Module-3 facilitates to link the peptide identifications from protein search engines to the quantification results from pattern-based label-free quantification tools. We further demonstrated the utility of the iPhos toolkit on the data of human metastatic lung cancer cells (CL1-5). Conclusions In the comparison study of the control group of CL1-5 cell lysates and the treatment group of dasatinib-treated CL1-5 cell lysates, we demonstrated the applicability of the iPhos toolkit and reported the experimental results based on the iPhos-facilitated phosphoproteome investigation. And further, we also compared the strategy with pure DDA-based LC-MS/MS phosphoproteome investigation. The results of iPhos-facilitated targeted LC-MS/MS analysis convey more thorough and confident phosphopeptide identification than the results of pure DDA-based analysis. PMID:25521246

Pydpiper: a flexible toolkit for constructing novel registration pipelines.

PubMed

Friedel, Miriam; van Eede, Matthijs C; Pipitone, Jon; Chakravarty, M Mallar; Lerch, Jason P

2014-01-01

Using neuroimaging technologies to elucidate the relationship between genotype and phenotype and brain and behavior will be a key contribution to biomedical research in the twenty-first century. Among the many methods for analyzing neuroimaging data, image registration deserves particular attention due to its wide range of applications. Finding strategies to register together many images and analyze the differences between them can be a challenge, particularly given that different experimental designs require different registration strategies. Moreover, writing software that can handle different types of image registration pipelines in a flexible, reusable and extensible way can be challenging. In response to this challenge, we have created Pydpiper, a neuroimaging registration toolkit written in Python. Pydpiper is an open-source, freely available software package that provides multiple modules for various image registration applications. Pydpiper offers five key innovations. Specifically: (1) a robust file handling class that allows access to outputs from all stages of registration at any point in the pipeline; (2) the ability of the framework to eliminate duplicate stages; (3) reusable, easy to subclass modules; (4) a development toolkit written for non-developers; (5) four complete applications that run complex image registration pipelines "out-of-the-box." In this paper, we will discuss both the general Pydpiper framework and the various ways in which component modules can be pieced together to easily create new registration pipelines. This will include a discussion of the core principles motivating code development and a comparison of Pydpiper with other available toolkits. We also provide a comprehensive, line-by-line example to orient users with limited programming knowledge and highlight some of the most useful features of Pydpiper. In addition, we will present the four current applications of the code.

Pydpiper: a flexible toolkit for constructing novel registration pipelines

PubMed Central

Friedel, Miriam; van Eede, Matthijs C.; Pipitone, Jon; Chakravarty, M. Mallar; Lerch, Jason P.

2014-01-01

Using neuroimaging technologies to elucidate the relationship between genotype and phenotype and brain and behavior will be a key contribution to biomedical research in the twenty-first century. Among the many methods for analyzing neuroimaging data, image registration deserves particular attention due to its wide range of applications. Finding strategies to register together many images and analyze the differences between them can be a challenge, particularly given that different experimental designs require different registration strategies. Moreover, writing software that can handle different types of image registration pipelines in a flexible, reusable and extensible way can be challenging. In response to this challenge, we have created Pydpiper, a neuroimaging registration toolkit written in Python. Pydpiper is an open-source, freely available software package that provides multiple modules for various image registration applications. Pydpiper offers five key innovations. Specifically: (1) a robust file handling class that allows access to outputs from all stages of registration at any point in the pipeline; (2) the ability of the framework to eliminate duplicate stages; (3) reusable, easy to subclass modules; (4) a development toolkit written for non-developers; (5) four complete applications that run complex image registration pipelines “out-of-the-box.” In this paper, we will discuss both the general Pydpiper framework and the various ways in which component modules can be pieced together to easily create new registration pipelines. This will include a discussion of the core principles motivating code development and a comparison of Pydpiper with other available toolkits. We also provide a comprehensive, line-by-line example to orient users with limited programming knowledge and highlight some of the most useful features of Pydpiper. In addition, we will present the four current applications of the code. PMID:25126069

Update of GRASP/Ada reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1993-01-01

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

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST)

PubMed Central

Dowd, Scot E; Zaragoza, Joaquin; Rodriguez, Javier R; Oliver, Melvin J; Payton, Paxton R

2005-01-01

Background BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), which enhances the BLAST utility by improving usability, fault recovery, and scalability in a Windows desktop environment. Our goal was to develop an easy to use, fault tolerant, high-throughput BLAST solution that incorporates a comprehensive BLAST result viewer with curation and annotation functionality. Results W.ND-BLAST is a comprehensive Windows-based software toolkit that targets researchers, including those with minimal computer skills, and provides the ability increase the performance of BLAST by distributing BLAST queries to any number of Windows based machines across local area networks (LAN). W.ND-BLAST provides intuitive Graphic User Interfaces (GUI) for BLAST database creation, BLAST execution, BLAST output evaluation and BLAST result exportation. This software also provides several layers of fault tolerance and fault recovery to prevent loss of data if nodes or master machines fail. This paper lays out the functionality of W.ND-BLAST. W.ND-BLAST displays close to 100% performance efficiency when distributing tasks to 12 remote computers of the same performance class. A high throughput BLAST job which took 662.68 minutes (11 hours) on one average machine was completed in 44.97 minutes when distributed to 17 nodes, which included lower performance class machines. Finally, there is a comprehensive high-throughput BLAST Output Viewer (BOV) and Annotation Engine components, which provides comprehensive exportation of BLAST hits to text files, annotated fasta files, tables, or association files. Conclusion W.ND-BLAST provides an interactive tool that allows scientists to easily utilizing their available computing resources for high throughput and comprehensive sequence analyses. The install package for W.ND-BLAST is freely downloadable from . With registration the software is free, installation, networking, and usage instructions are provided as well as a support forum. PMID:15819992

PyEvolve: a toolkit for statistical modelling of molecular evolution.

PubMed

Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

2004-01-05

Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences - ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from approximately 10 days to approximately 6 hours. PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be used interactively or by writing and executing scripts. The toolkit uses efficient processes for specifying the parameterisation of statistical models, and implements numerous optimisations that make highly parameter rich likelihood functions solvable within hours on multi-cpu hardware. PyEvolve can be readily adapted in response to changing computational demands and hardware configurations to maximise performance. PyEvolve is released under the GPL and can be downloaded from http://cbis.anu.edu.au/software.

Loss of Coolant Accident (LOCA) / Emergency Core Coolant System (ECCS Evaluation of Risk-Informed Margins Management Strategies for a Representative Pressurized Water Reactor (PWR)

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

Szilard, Ronaldo Henriques

A Risk Informed Safety Margin Characterization (RISMC) toolkit and methodology are proposed for investigating nuclear power plant core, fuels design and safety analysis, including postulated Loss-of-Coolant Accident (LOCA) analysis. This toolkit, under an integrated evaluation model framework, is name LOCA toolkit for the US (LOTUS). This demonstration includes coupled analysis of core design, fuel design, thermal hydraulics and systems analysis, using advanced risk analysis tools and methods to investigate a wide range of results.

Analysis of live cell images: Methods, tools and opportunities.

PubMed

Nketia, Thomas A; Sailem, Heba; Rohde, Gustavo; Machiraju, Raghu; Rittscher, Jens

2017-02-15

Advances in optical microscopy, biosensors and cell culturing technologies have transformed live cell imaging. Thanks to these advances live cell imaging plays an increasingly important role in basic biology research as well as at all stages of drug development. Image analysis methods are needed to extract quantitative information from these vast and complex data sets. The aim of this review is to provide an overview of available image analysis methods for live cell imaging, in particular required preprocessing image segmentation, cell tracking and data visualisation methods. The potential opportunities recent advances in machine learning, especially deep learning, and computer vision provide are being discussed. This review includes overview of the different available software packages and toolkits. Copyright © 2017. Published by Elsevier Inc.

Practical computational toolkits for dendrimers and dendrons structure design.

PubMed

Martinho, Nuno; Silva, Liana C; Florindo, Helena F; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

Practical computational toolkits for dendrimers and dendrons structure design

NASA Astrophysics Data System (ADS)

Martinho, Nuno; Silva, Liana C.; Florindo, Helena F.; Brocchini, Steve; Barata, Teresa; Zloh, Mire

2017-09-01

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.

The ProteoRed MIAPE web toolkit: A User-friendly Framework to Connect and Share Proteomics Standards*

PubMed Central

Medina-Aunon, J. Alberto; Martínez-Bartolomé, Salvador; López-García, Miguel A.; Salazar, Emilio; Navajas, Rosana; Jones, Andrew R.; Paradela, Alberto; Albar, Juan P.

2011-01-01

The development of the HUPO-PSI's (Proteomics Standards Initiative) standard data formats and MIAPE (Minimum Information About a Proteomics Experiment) guidelines should improve proteomics data sharing within the scientific community. Proteomics journals have encouraged the use of these standards and guidelines to improve the quality of experimental reporting and ease the evaluation and publication of manuscripts. However, there is an evident lack of bioinformatics tools specifically designed to create and edit standard file formats and reports, or embed them within proteomics workflows. In this article, we describe a new web-based software suite (The ProteoRed MIAPE web toolkit) that performs several complementary roles related to proteomic data standards. First, it can verify that the reports fulfill the minimum information requirements of the corresponding MIAPE modules, highlighting inconsistencies or missing information. Second, the toolkit can convert several XML-based data standards directly into human readable MIAPE reports stored within the ProteoRed MIAPE repository. Finally, it can also perform the reverse operation, allowing users to export from MIAPE reports into XML files for computational processing, data sharing, or public database submission. The toolkit is thus the first application capable of automatically linking the PSI's MIAPE modules with the corresponding XML data exchange standards, enabling bidirectional conversions. This toolkit is freely available at http://www.proteored.org/MIAPE/. PMID:21983993

ITK: enabling reproducible research and open science

PubMed Central

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46. PMID:24600387

ITK: enabling reproducible research and open science.

PubMed

McCormick, Matthew; Liu, Xiaoxiao; Jomier, Julien; Marion, Charles; Ibanez, Luis

2014-01-01

Reproducibility verification is essential to the practice of the scientific method. Researchers report their findings, which are strengthened as other independent groups in the scientific community share similar outcomes. In the many scientific fields where software has become a fundamental tool for capturing and analyzing data, this requirement of reproducibility implies that reliable and comprehensive software platforms and tools should be made available to the scientific community. The tools will empower them and the public to verify, through practice, the reproducibility of observations that are reported in the scientific literature. Medical image analysis is one of the fields in which the use of computational resources, both software and hardware, are an essential platform for performing experimental work. In this arena, the introduction of the Insight Toolkit (ITK) in 1999 has transformed the field and facilitates its progress by accelerating the rate at which algorithmic implementations are developed, tested, disseminated and improved. By building on the efficiency and quality of open source methodologies, ITK has provided the medical image community with an effective platform on which to build a daily workflow that incorporates the true scientific practices of reproducibility verification. This article describes the multiple tools, methodologies, and practices that the ITK community has adopted, refined, and followed during the past decade, in order to become one of the research communities with the most modern reproducibility verification infrastructure. For example, 207 contributors have created over 2400 unit tests that provide over 84% code line test coverage. The Insight Journal, an open publication journal associated with the toolkit, has seen over 360,000 publication downloads. The median normalized closeness centrality, a measure of knowledge flow, resulting from the distributed peer code review system was high, 0.46.

The Model Analyst’s Toolkit: Scientific Model Development, Analysis, and Validation

DTIC Science & Technology

2014-11-20

Government Contract N00014-12-C-0653 Charles River Analytics p. 7 The new MAT system can be downloaded from our FTP site with a username and...password that we provide. We also updated our web site to tell visitors about the new release and to tell them how to request a copy of the new software...hemorrhaging are being applied  properly.  Laparoscopic  Surgery Training  System (LASTS)    (Phase II SBIR)  US Navy’s Office of Naval  Research (ONR)  Under

OSCAR4: a flexible architecture for chemical text-mining

PubMed Central

2011-01-01

The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed. PMID:21999457

SWMM5 Application Programming Interface and PySWMM: A ...

EPA Pesticide Factsheets

In support of the OpenWaterAnalytics open source initiative, the PySWMM project encompasses the development of a Python interfacing wrapper to SWMM5 with parallel ongoing development of the USEPA Stormwater Management Model (SWMM5) application programming interface (API). ... The purpose of this work is to increase the utility of the SWMM dll by creating a Toolkit API for accessing its functionality. The utility of the Toolkit is further enhanced with a wrapper to allow access from the Python scripting language. This work is being prosecuted as part of an Open Source development strategy and is being performed by volunteer software developers.

Rapid ISS Power Availability Simulator

NASA Technical Reports Server (NTRS)

Downing, Nicholas

2011-01-01

The ISS (International Space Station) Power Resource Officers (PROs) needed a tool to automate the calculation of thousands of ISS power availability simulations used to generate power constraint matrices. Each matrix contains 864 cells, and each cell represents a single power simulation that must be run. The tools available to the flight controllers were very operator intensive and not conducive to rapidly running the thousands of simulations necessary to generate the power constraint data. SOLAR is a Java-based tool that leverages commercial-off-the-shelf software (Satellite Toolkit) and an existing in-house ISS EPS model (SPEED) to rapidly perform thousands of power availability simulations. SOLAR has a very modular architecture and consists of a series of plug-ins that are loosely coupled. The modular architecture of the software allows for the easy replacement of the ISS power system model simulator, re-use of the Satellite Toolkit integration code, and separation of the user interface from the core logic. Satellite Toolkit (STK) is used to generate ISS eclipse and insulation times, solar beta angle, position of the solar arrays over time, and the amount of shadowing on the solar arrays, which is then provided to SPEED to calculate power generation forecasts. The power planning turn-around time is reduced from three months to two weeks (83-percent decrease) using SOLAR, and the amount of PRO power planning support effort is reduced by an estimated 30 percent.

Multiphysics Application Coupling Toolkit

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

Campbell, Michael T.

2013-12-02

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems;more » with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

LK Scripting Language

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

The LK scripting language is a simple and fast computer programming language designed for easy integration with existing software to enable automation of tasks. The LK language is used by NREL’s System Advisor Model (SAM), the SAM Software Development Kit (SDK), and SolTrace products. LK is easy extensible and adaptable to new software due to its small footprint and is designed to be statically linked into other software. It is written in standard C++, is cross-platform (Windows, Linux, and OSX), and includes optional portions that enable direct integration with graphical user interfaces written in the open source C++ wxWidgets Versionmore » 3.0+ toolkit.« less

Link Analysis in the Mission Planning Lab

NASA Technical Reports Server (NTRS)

McCarthy, Jessica A.; Cervantes, Benjamin W.; Daugherty, Sarah C.; Arroyo, Felipe; Mago, Divyang

2011-01-01

The legacy communications link analysis software currently used at Wallops Flight Facility involves processes that are different for command destruct, radar, and telemetry. There is a clear advantage to developing an easy-to-use tool that combines all the processes in one application. Link Analysis in the Mission Planning Lab (MPL) uses custom software and algorithms integrated with Analytical Graphics Inc. Satellite Toolkit (AGI STK). The MPL link analysis tool uses pre/post-mission data to conduct a dynamic link analysis between ground assets and the launch vehicle. Just as the legacy methods do, the MPL link analysis tool calculates signal strength and signal- to-noise according to the accepted processes for command destruct, radar, and telemetry assets. Graphs and other custom data are generated rapidly in formats for reports and presentations. STK is used for analysis as well as to depict plume angles and antenna gain patterns in 3D. The MPL has developed two interfaces with the STK software (see figure). The first interface is an HTML utility, which was developed in Visual Basic to enhance analysis for plume modeling and to offer a more user friendly, flexible tool. A graphical user interface (GUI) written in MATLAB (see figure upper right-hand corner) is also used to quickly depict link budget information for multiple ground assets. This new method yields a dramatic decrease in the time it takes to provide launch managers with the required link budgets to make critical pre-mission decisions. The software code used for these two custom utilities is a product of NASA's MPL.

A Browser-Based Multi-User Working Environment for Physicists

NASA Astrophysics Data System (ADS)

Erdmann, M.; Fischer, R.; Glaser, C.; Klingebiel, D.; Komm, M.; Müller, G.; Rieger, M.; Steggemann, J.; Urban, M.; Winchen, T.

2014-06-01

Many programs in experimental particle physics do not yet have a graphical interface, or demand strong platform and software requirements. With the most recent development of the VISPA project, we provide graphical interfaces to existing software programs and access to multiple computing clusters through standard web browsers. The scalable clientserver system allows analyses to be performed in sizable teams, and disburdens the individual physicist from installing and maintaining a software environment. The VISPA graphical interfaces are implemented in HTML, JavaScript and extensions to the Python webserver. The webserver uses SSH and RPC to access user data, code and processes on remote sites. As example applications we present graphical interfaces for steering the reconstruction framework OFFLINE of the Pierre-Auger experiment, and the analysis development toolkit PXL. The browser based VISPA system was field-tested in biweekly homework of a third year physics course by more than 100 students. We discuss the system deployment and the evaluation by the students.

Tailored Prevention of Inpatient Falls

PubMed Central

ZUYEV, LYUBOV; BENOIT, ANGELA N.; CHANG, FRANK Y.; DYKES, PATRICIA C.

2011-01-01

Patient falls and fall-related injuries are serious problems in hospitals. The Fall TIPS application aims to prevent patient falls by translating routine nursing fall risk assessment into a decision support intervention that communicates fall risk status and creates a tailored evidence-based plan of care that is accessible to the care team, patients, and family members. In our design and implementation of the Fall TIPS toolkit, we used the Spiral Software Development Life Cycle model. Three output tools available to be generated from the toolkit are bed poster, plan of care, and patient education handout. A preliminary design of the application was based on initial requirements defined by project leaders and informed by focus groups with end users. Preliminary design partially simulated the paper version of the Morse Fall Scale currently used in hospitals involved in the research study. Strengths and weaknesses of the first prototype were identified by heuristic evaluation. Usability testing was performed at sites where research study is implemented. Suggestions mentioned by end users participating in usability studies were either directly incorporated into the toolkit and output tools, were slightly modified, or will be addressed during training. The next step is implementation of the fall prevention toolkit on the pilot testing units. PMID:20975543

WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures

PubMed Central

2010-01-01

Background An important focus of genomic science is the discovery and characterization of all functional elements within genomes. In silico methods are used in genome studies to discover putative regulatory genomic elements (called words or motifs). Although a number of methods have been developed for motif discovery, most of them lack the scalability needed to analyze large genomic data sets. Methods This manuscript presents WordSeeker, an enumerative motif discovery toolkit that utilizes multi-core and distributed computational platforms to enable scalable analysis of genomic data. A controller task coordinates activities of worker nodes, each of which (1) enumerates a subset of the DNA word space and (2) scores words with a distributed Markov chain model. Results A comprehensive suite of performance tests was conducted to demonstrate the performance, speedup and efficiency of WordSeeker. The scalability of the toolkit enabled the analysis of the entire genome of Arabidopsis thaliana; the results of the analysis were integrated into The Arabidopsis Gene Regulatory Information Server (AGRIS). A public version of WordSeeker was deployed on the Glenn cluster at the Ohio Supercomputer Center. Conclusion WordSeeker effectively utilizes concurrent computing platforms to enable the identification of putative functional elements in genomic data sets. This capability facilitates the analysis of the large quantity of sequenced genomic data. PMID:21210985

Monte Carlo Simulation Tool Installation and Operation Guide

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

Aguayo Navarrete, Estanislao; Ankney, Austin S.; Berguson, Timothy J.

2013-09-02

This document provides information on software and procedures for Monte Carlo simulations based on the Geant4 toolkit, the ROOT data analysis software and the CRY cosmic ray library. These tools have been chosen for its application to shield design and activation studies as part of the simulation task for the Majorana Collaboration. This document includes instructions for installation, operation and modification of the simulation code in a high cyber-security computing environment, such as the Pacific Northwest National Laboratory network. It is intended as a living document, and will be periodically updated. It is a starting point for information collection bymore » an experimenter, and is not the definitive source. Users should consult with one of the authors for guidance on how to find the most current information for their needs.« less

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2013 CFR

2013-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2011 CFR

2011-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2014 CFR

2014-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

15 CFR Supplement No. 5 to Part 742 - Encryption Registration

Code of Federal Regulations, 2012 CFR

2012-01-01

... registration, i.e., the information as described in this Supplement, submitted as a support documentation... (h) Smartcards or other identity management (i) Computer or network forensics (j) Software (i) Operating systems (ii) Applications (k) Toolkits/ASICs/components (l) Information security including secure...

Windows Memory Forensic Data Visualization

DTIC Science & Technology

2014-06-12

clustering characteristics (Bastian, et al, 2009). The software is written in Java and utilizes the OpenGL library for rendering graphical content...Toolkit 2 nd ed. Burlington MA: Syngress. D3noob. (2013, February 8). Using a MYSQL database as a source of data. Message posted to http

Teaching Computer Literacy with Freeware and Shareware.

ERIC Educational Resources Information Center

Hobart, R. Dale; And Others

1988-01-01

Describes workshops given at Ferris State University for faculty and staff who want to acquire computer skills. Considered are a computer literacy and a software toolkit distributed to participants made from public domain/shareware resources. Stresses the benefits of shareware as an educational resource. (CW)

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

PubMed Central

Carter, Hannah; Diekhans, Mark; Ryan, Michael C.; Karchin, Rachel

2011-01-01

Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. Availability and Implementation: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM. Contact: karchin@jhu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21685053

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

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

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

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

Correlative and multivariate analysis of increased radon concentration in underground laboratory.

PubMed

Maletić, Dimitrije M; Udovičić, Vladimir I; Banjanac, Radomir M; Joković, Dejan R; Dragić, Aleksandar L; Veselinović, Nikola B; Filipović, Jelena

2014-11-01

The results of analysis using correlative and multivariate methods, as developed for data analysis in high-energy physics and implemented in the Toolkit for Multivariate Analysis software package, of the relations of the variation of increased radon concentration with climate variables in shallow underground laboratory is presented. Multivariate regression analysis identified a number of multivariate methods which can give a good evaluation of increased radon concentrations based on climate variables. The use of the multivariate regression methods will enable the investigation of the relations of specific climate variable with increased radon concentrations by analysis of regression methods resulting in 'mapped' underlying functional behaviour of radon concentrations depending on a wide spectrum of climate variables. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Roofline model toolkit: A practical tool for architectural and program analysis

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

Lo, Yu Jung; Williams, Samuel; Van Straalen, Brian

We present preliminary results of the Roofline Toolkit for multicore, many core, and accelerated architectures. This paper focuses on the processor architecture characterization engine, a collection of portable instrumented micro benchmarks implemented with Message Passing Interface (MPI), and OpenMP used to express thread-level parallelism. These benchmarks are specialized to quantify the behavior of different architectural features. Compared to previous work on performance characterization, these microbenchmarks focus on capturing the performance of each level of the memory hierarchy, along with thread-level parallelism, instruction-level parallelism and explicit SIMD parallelism, measured in the context of the compilers and run-time environments. We also measuremore » sustained PCIe throughput with four GPU memory managed mechanisms. By combining results from the architecture characterization with the Roofline model based solely on architectural specifications, this work offers insights for performance prediction of current and future architectures and their software systems. To that end, we instrument three applications and plot their resultant performance on the corresponding Roofline model when run on a Blue Gene/Q architecture.« less

Using Discrete Event Simulation for Programming Model Exploration at Extreme-Scale: Macroscale Components for the Structural Simulation Toolkit (SST).

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

Wilke, Jeremiah J; Kenny, Joseph P.

2015-02-01

Discrete event simulation provides a powerful mechanism for designing and testing new extreme- scale programming models for high-performance computing. Rather than debug, run, and wait for results on an actual system, design can first iterate through a simulator. This is particularly useful when test beds cannot be used, i.e. to explore hardware or scales that do not yet exist or are inaccessible. Here we detail the macroscale components of the structural simulation toolkit (SST). Instead of depending on trace replay or state machines, the simulator is architected to execute real code on real software stacks. Our particular user-space threading frameworkmore » allows massive scales to be simulated even on small clusters. The link between the discrete event core and the threading framework allows interesting performance metrics like call graphs to be collected from a simulated run. Performance analysis via simulation can thus become an important phase in extreme-scale programming model and runtime system design via the SST macroscale components.« less

Web-based Toolkit for Dynamic Generation of Data Processors

NASA Astrophysics Data System (ADS)

Patel, J.; Dascalu, S.; Harris, F. C.; Benedict, K. K.; Gollberg, G.; Sheneman, L.

2011-12-01

All computation-intensive scientific research uses structured datasets, including hydrology and all other types of climate-related research. When it comes to testing their hypotheses, researchers might use the same dataset differently, and modify, transform, or convert it to meet their research needs. Currently, many researchers spend a good amount of time performing data processing and building tools to speed up this process. They might routinely repeat the same process activities for new research projects, spending precious time that otherwise could be dedicated to analyzing and interpreting the data. Numerous tools are available to run tests on prepared datasets and many of them work with datasets in different formats. However, there is still a significant need for applications that can comprehensively handle data transformation and conversion activities and help prepare the various processed datasets required by the researchers. We propose a web-based application (a software toolkit) that dynamically generates data processors capable of performing data conversions, transformations, and customizations based on user-defined mappings and selections. As a first step, the proposed solution allows the users to define various data structures and, in the next step, can select various file formats and data conversions for their datasets of interest. In a simple scenario, the core of the proposed web-based toolkit allows the users to define direct mappings between input and output data structures. The toolkit will also support defining complex mappings involving the use of pre-defined sets of mathematical, statistical, date/time, and text manipulation functions. Furthermore, the users will be allowed to define logical cases for input data filtering and sampling. At the end of the process, the toolkit is designed to generate reusable source code and executable binary files for download and use by the scientists. The application is also designed to store all data structures and mappings defined by a user (an author), and allow the original author to modify them using standard authoring techniques. The users can change or define new mappings to create new data processors for download and use. In essence, when executed, the generated data processor binary file can take an input data file in a given format and output this data, possibly transformed, in a different file format. If they so desire, the users will be able modify directly the source code in order to define more complex mappings and transformations that are not currently supported by the toolkit. Initially aimed at supporting research in hydrology, the toolkit's functions and features can be either directly used or easily extended to other areas of climate-related research. The proposed web-based data processing toolkit will be able to generate various custom software processors for data conversion and transformation in a matter of seconds or minutes, saving a significant amount of researchers' time and allowing them to focus on core research issues.

TXM-Wizard: a program for advanced data collection and evaluation in full-field transmission X-ray microscopy

PubMed Central

Liu, Yijin; Meirer, Florian; Williams, Phillip A.; Wang, Junyue; Andrews, Joy C.; Pianetta, Piero

2012-01-01

Transmission X-ray microscopy (TXM) has been well recognized as a powerful tool for non-destructive investigation of the three-dimensional inner structure of a sample with spatial resolution down to a few tens of nanometers, especially when combined with synchrotron radiation sources. Recent developments of this technique have presented a need for new tools for both system control and data analysis. Here a software package developed in MATLAB for script command generation and analysis of TXM data is presented. The first toolkit, the script generator, allows automating complex experimental tasks which involve up to several thousand motor movements. The second package was designed to accomplish computationally intense tasks such as data processing of mosaic and mosaic tomography datasets; dual-energy contrast imaging, where data are recorded above and below a specific X-ray absorption edge; and TXM X-ray absorption near-edge structure imaging datasets. Furthermore, analytical and iterative tomography reconstruction algorithms were implemented. The compiled software package is freely available. PMID:22338691

JAva GUi for Applied Research (JAGUAR) v 3.0

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

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

LIVVkit: An extensible, python-based, land ice verification and validation toolkit for ice sheet models

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

Kennedy, Joseph H.; Bennett, Andrew R.; Evans, Katherine J.

To address the pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice sheet models is underway. Concurrent to the development of the Community Ice Sheet Model (CISM), the corresponding verification and validation (V&V) process is being coordinated through a new, robust, Python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVVkit). Incorporated into the typical ice sheet model development cycle, it provides robust and automated numerical verification, software verification, performance validation, and physical validation analyses on a variety of platforms, from personal laptopsmore » to the largest supercomputers. LIVVkit operates on sets of regression test and reference data sets, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-for-bit evaluation, and plots of model variables to indicate where differences occur. LIVVkit also provides an easily extensible framework to incorporate and analyze results of new intercomparison projects, new observation data, and new computing platforms. LIVVkit is designed for quick adaptation to additional ice sheet models via abstraction of model specific code, functions, and configurations into an ice sheet model description bundle outside the main LIVVkit structure. Furthermore, through shareable and accessible analysis output, LIVVkit is intended to help developers build confidence in their models and enhance the credibility of ice sheet models overall.« less

LIVVkit: An extensible, python-based, land ice verification and validation toolkit for ice sheet models

DOE PAGES

Kennedy, Joseph H.; Bennett, Andrew R.; Evans, Katherine J.; ...

2017-03-23

To address the pressing need to better understand the behavior and complex interaction of ice sheets within the global Earth system, significant development of continental-scale, dynamical ice sheet models is underway. Concurrent to the development of the Community Ice Sheet Model (CISM), the corresponding verification and validation (V&V) process is being coordinated through a new, robust, Python-based extensible software package, the Land Ice Verification and Validation toolkit (LIVVkit). Incorporated into the typical ice sheet model development cycle, it provides robust and automated numerical verification, software verification, performance validation, and physical validation analyses on a variety of platforms, from personal laptopsmore » to the largest supercomputers. LIVVkit operates on sets of regression test and reference data sets, and provides comparisons for a suite of community prioritized tests, including configuration and parameter variations, bit-for-bit evaluation, and plots of model variables to indicate where differences occur. LIVVkit also provides an easily extensible framework to incorporate and analyze results of new intercomparison projects, new observation data, and new computing platforms. LIVVkit is designed for quick adaptation to additional ice sheet models via abstraction of model specific code, functions, and configurations into an ice sheet model description bundle outside the main LIVVkit structure. Furthermore, through shareable and accessible analysis output, LIVVkit is intended to help developers build confidence in their models and enhance the credibility of ice sheet models overall.« less

WATERSHED HEALTH ASSESSMENT TOOLS-INVESTIGATING FISHERIES (WHAT-IF): A MODELING TOOLKIT FOR WATERSHED AND FISHERIES MANAGEMENT

EPA Science Inventory

The Watershed Health Assessment Tools-Investigating Fisheries (WHAT-IF) is a decision-analysis modeling toolkit for personal computers that supports watershed and fisheries management. The WHAT-IF toolkit includes a relational database, help-system functions and documentation, a...

Risk of Resource Failure and Toolkit Variation in Small-Scale Farmers and Herders

PubMed Central

Collard, Mark; Ruttle, April; Buchanan, Briggs; O’Brien, Michael J.

2012-01-01

Recent work suggests that global variation in toolkit structure among hunter-gatherers is driven by risk of resource failure such that as risk of resource failure increases, toolkits become more diverse and complex. Here we report a study in which we investigated whether the toolkits of small-scale farmers and herders are influenced by risk of resource failure in the same way. In the study, we applied simple linear and multiple regression analysis to data from 45 small-scale food-producing groups to test the risk hypothesis. Our results were not consistent with the hypothesis; none of the risk variables we examined had a significant impact on toolkit diversity or on toolkit complexity. It appears, therefore, that the drivers of toolkit structure differ between hunter-gatherers and small-scale food-producers. PMID:22844421

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

Open source software is commonly known for its web browsers, word processors and programming languages. However, there is a vast array of open source software focused on geographic information management and geospatial application building in general. As geo-professionals, having easy access to tools for our jobs is crucial. Open source software provides the opportunity to add a tool to your tool belt and carry it with you for your entire career - with no license fees, a supportive community and the opportunity to test, adopt and upgrade at your own pace. OSGeo is a US registered non-profit representing more than a dozen mature geospatial data management applications and programming resources. Tools cover areas such as desktop GIS, web-based mapping frameworks, metadata cataloging, spatial database analysis, image processing and more. Learn about some of these tools as they apply to AGU members, as well as how you can join OSGeo and its members in getting the job done with powerful open source tools. If you haven't heard of OSSIM, MapServer, OpenLayers, PostGIS, GRASS GIS or the many other projects under our umbrella - then you need to hear this talk. Invest in yourself - use open source!

Development and formative evaluation of the e-Health Implementation Toolkit (e-HIT).

PubMed

Murray, Elizabeth; May, Carl; Mair, Frances

2010-10-18

The use of Information and Communication Technology (ICT) or e-Health is seen as essential for a modern, cost-effective health service. However, there are well documented problems with implementation of e-Health initiatives, despite the existence of a great deal of research into how best to implement e-Health (an example of the gap between research and practice). This paper reports on the development and formative evaluation of an e-Health Implementation Toolkit (e-HIT) which aims to summarise and synthesise new and existing research on implementation of e-Health initiatives, and present it to senior managers in a user-friendly format. The content of the e-HIT was derived by combining data from a systematic review of reviews of barriers and facilitators to implementation of e-Health initiatives with qualitative data derived from interviews of "implementers", that is people who had been charged with implementing an e-Health initiative. These data were summarised, synthesised and combined with the constructs from the Normalisation Process Model. The software for the toolkit was developed by a commercial company (RocketScience). Formative evaluation was undertaken by obtaining user feedback. There are three components to the toolkit--a section on background and instructions for use aimed at novice users; the toolkit itself; and the report generated by completing the toolkit. It is available to download from http://www.ucl.ac.uk/pcph/research/ehealth/documents/e-HIT.xls. The e-HIT shows potential as a tool for enhancing future e-Health implementations. Further work is needed to make it fully web-enabled, and to determine its predictive potential for future implementations.

Development and formative evaluation of the e-Health Implementation Toolkit (e-HIT)

PubMed Central

2010-01-01

Background The use of Information and Communication Technology (ICT) or e-Health is seen as essential for a modern, cost-effective health service. However, there are well documented problems with implementation of e-Health initiatives, despite the existence of a great deal of research into how best to implement e-Health (an example of the gap between research and practice). This paper reports on the development and formative evaluation of an e-Health Implementation Toolkit (e-HIT) which aims to summarise and synthesise new and existing research on implementation of e-Health initiatives, and present it to senior managers in a user-friendly format. Results The content of the e-HIT was derived by combining data from a systematic review of reviews of barriers and facilitators to implementation of e-Health initiatives with qualitative data derived from interviews of "implementers", that is people who had been charged with implementing an e-Health initiative. These data were summarised, synthesised and combined with the constructs from the Normalisation Process Model. The software for the toolkit was developed by a commercial company (RocketScience). Formative evaluation was undertaken by obtaining user feedback. There are three components to the toolkit - a section on background and instructions for use aimed at novice users; the toolkit itself; and the report generated by completing the toolkit. It is available to download from http://www.ucl.ac.uk/pcph/research/ehealth/documents/e-HIT.xls Conclusions The e-HIT shows potential as a tool for enhancing future e-Health implementations. Further work is needed to make it fully web-enabled, and to determine its predictive potential for future implementations. PMID:20955594

A Qualitative Evaluation of Web-Based Cancer Care Quality Improvement Toolkit Use in the Veterans Health Administration.

PubMed

Bowman, Candice; Luck, Jeff; Gale, Randall C; Smith, Nina; York, Laura S; Asch, Steven

2015-01-01

Disease severity, complexity, and patient burden highlight cancer care as a target for quality improvement (QI) interventions. The Veterans Health Administration (VHA) implemented a series of disease-specific online cancer care QI toolkits. To describe characteristics of the toolkits, target users, and VHA cancer care facilities that influenced toolkit access and use and assess whether such resources were beneficial for users. Deductive content analysis of detailed notes from 94 telephone interviews with individuals from 48 VHA facilities. We evaluated toolkit access and use across cancer types, participation in learning collaboratives, and affiliation with VHA cancer care facilities. The presence of champions was identified as a strong facilitator of toolkit use, and learning collaboratives were important for spreading information about toolkit availability. Identified barriers included lack of personnel and financial resources and complicated approval processes to support tool use. Online cancer care toolkits are well received across cancer specialties and provider types. Clinicians, administrators, and QI staff may benefit from the availability of toolkits as they become more reliant on rapid access to strategies that support comprehensive delivery of evidence-based care. Toolkits should be considered as a complement to other QI approaches.

Technology User Groups and Early Childhood Education: A Preliminary Study

ERIC Educational Resources Information Center

Parette, Howard P.; Hourcade, Jack J.; Blum, Craig; Watts, Emily H.; Stoner, Julia B.; Wojcik, Brian W.; Chrismore, Shannon B.

2013-01-01

This article presents a preliminary examination of the potential of Technology User Groups as a professional development venue for early childhood education professionals in developing operational and functional competence in using hardware and software components of a Technology toolkit. Technology user groups are composed of varying numbers of…

Cancer imaging phenomics toolkit: quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.

PubMed

Davatzikos, Christos; Rathore, Saima; Bakas, Spyridon; Pati, Sarthak; Bergman, Mark; Kalarot, Ratheesh; Sridharan, Patmaa; Gastounioti, Aimilia; Jahani, Nariman; Cohen, Eric; Akbari, Hamed; Tunc, Birkan; Doshi, Jimit; Parker, Drew; Hsieh, Michael; Sotiras, Aristeidis; Li, Hongming; Ou, Yangming; Doot, Robert K; Bilello, Michel; Fan, Yong; Shinohara, Russell T; Yushkevich, Paul; Verma, Ragini; Kontos, Despina

2018-01-01

The growth of multiparametric imaging protocols has paved the way for quantitative imaging phenotypes that predict treatment response and clinical outcome, reflect underlying cancer molecular characteristics and spatiotemporal heterogeneity, and can guide personalized treatment planning. This growth has underlined the need for efficient quantitative analytics to derive high-dimensional imaging signatures of diagnostic and predictive value in this emerging era of integrated precision diagnostics. This paper presents cancer imaging phenomics toolkit (CaPTk), a new and dynamically growing software platform for analysis of radiographic images of cancer, currently focusing on brain, breast, and lung cancer. CaPTk leverages the value of quantitative imaging analytics along with machine learning to derive phenotypic imaging signatures, based on two-level functionality. First, image analysis algorithms are used to extract comprehensive panels of diverse and complementary features, such as multiparametric intensity histogram distributions, texture, shape, kinetics, connectomics, and spatial patterns. At the second level, these quantitative imaging signatures are fed into multivariate machine learning models to produce diagnostic, prognostic, and predictive biomarkers. Results from clinical studies in three areas are shown: (i) computational neuro-oncology of brain gliomas for precision diagnostics, prediction of outcome, and treatment planning; (ii) prediction of treatment response for breast and lung cancer, and (iii) risk assessment for breast cancer.

Full 3D visualization tool-kit for Monte Carlo and deterministic transport codes

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

Frambati, S.; Frignani, M.

2012-07-01

We propose a package of tools capable of translating the geometric inputs and outputs of many Monte Carlo and deterministic radiation transport codes into open source file formats. These tools are aimed at bridging the gap between trusted, widely-used radiation analysis codes and very powerful, more recent and commonly used visualization software, thus supporting the design process and helping with shielding optimization. Three main lines of development were followed: mesh-based analysis of Monte Carlo codes, mesh-based analysis of deterministic codes and Monte Carlo surface meshing. The developed kit is considered a powerful and cost-effective tool in the computer-aided design formore » radiation transport code users of the nuclear world, and in particular in the fields of core design and radiation analysis. (authors)« less

Medical image reconstruction algorithm based on the geometric information between sensor detector and ROI

NASA Astrophysics Data System (ADS)

Ham, Woonchul; Song, Chulgyu; Lee, Kangsan; Roh, Seungkuk

2016-05-01

In this paper, we propose a new image reconstruction algorithm considering the geometric information of acoustic sources and senor detector and review the two-step reconstruction algorithm which was previously proposed based on the geometrical information of ROI(region of interest) considering the finite size of acoustic sensor element. In a new image reconstruction algorithm, not only mathematical analysis is very simple but also its software implementation is very easy because we don't need to use the FFT. We verify the effectiveness of the proposed reconstruction algorithm by showing the simulation results by using Matlab k-wave toolkit.

VaST: A variability search toolkit

NASA Astrophysics Data System (ADS)

Sokolovsky, K. V.; Lebedev, A. A.

2018-01-01

Variability Search Toolkit (VaST) is a software package designed to find variable objects in a series of sky images. It can be run from a script or interactively using its graphical interface. VaST relies on source list matching as opposed to image subtraction. SExtractor is used to generate source lists and perform aperture or PSF-fitting photometry (with PSFEx). Variability indices that characterize scatter and smoothness of a lightcurve are computed for all objects. Candidate variables are identified as objects having high variability index values compared to other objects of similar brightness. The two distinguishing features of VaST are its ability to perform accurate aperture photometry of images obtained with non-linear detectors and handle complex image distortions. The software has been successfully applied to images obtained with telescopes ranging from 0.08 to 2.5 m in diameter equipped with a variety of detectors including CCD, CMOS, MIC and photographic plates. About 1800 variable stars have been discovered with VaST. It is used as a transient detection engine in the New Milky Way (NMW) nova patrol. The code is written in C and can be easily compiled on the majority of UNIX-like systems. VaST is free software available at http://scan.sai.msu.ru/vast/.

A Matlab toolkit for three-dimensional electrical impedance tomography: a contribution to the Electrical Impedance and Diffuse Optical Reconstruction Software project

NASA Astrophysics Data System (ADS)

Polydorides, Nick; Lionheart, William R. B.

2002-12-01

The objective of the Electrical Impedance and Diffuse Optical Reconstruction Software project is to develop freely available software that can be used to reconstruct electrical or optical material properties from boundary measurements. Nonlinear and ill posed problems such as electrical impedance and optical tomography are typically approached using a finite element model for the forward calculations and a regularized nonlinear solver for obtaining a unique and stable inverse solution. Most of the commercially available finite element programs are unsuitable for solving these problems because of their conventional inefficient way of calculating the Jacobian, and their lack of accurate electrode modelling. A complete package for the two-dimensional EIT problem was officially released by Vauhkonen et al at the second half of 2000. However most industrial and medical electrical imaging problems are fundamentally three-dimensional. To assist the development we have developed and released a free toolkit of Matlab routines which can be employed to solve the forward and inverse EIT problems in three dimensions based on the complete electrode model along with some basic visualization utilities, in the hope that it will stimulate further development. We also include a derivation of the formula for the Jacobian (or sensitivity) matrix based on the complete electrode model.

BAT - The Bayesian analysis toolkit

NASA Astrophysics Data System (ADS)

Caldwell, Allen; Kollár, Daniel; Kröninger, Kevin

2009-11-01

We describe the development of a new toolkit for data analysis. The analysis package is based on Bayes' Theorem, and is realized with the use of Markov Chain Monte Carlo. This gives access to the full posterior probability distribution. Parameter estimation, limit setting and uncertainty propagation are implemented in a straightforward manner.

Implementing a modeling software for animated protein-complex interactions using a physics simulation library.

PubMed

Ueno, Yutaka; Ito, Shuntaro; Konagaya, Akihiko

2014-12-01

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Agent-based models of cellular systems.

PubMed

Cannata, Nicola; Corradini, Flavio; Merelli, Emanuela; Tesei, Luca

2013-01-01

Software agents are particularly suitable for engineering models and simulations of cellular systems. In a very natural and intuitive manner, individual software components are therein delegated to reproduce "in silico" the behavior of individual components of alive systems at a given level of resolution. Individuals' actions and interactions among individuals allow complex collective behavior to emerge. In this chapter we first introduce the readers to software agents and multi-agent systems, reviewing the evolution of agent-based modeling of biomolecular systems in the last decade. We then describe the main tools, platforms, and methodologies available for programming societies of agents, possibly profiting also of toolkits that do not require advanced programming skills.

Web-Altairis: An Internet-Enabled Ground System

NASA Technical Reports Server (NTRS)

Miller, Phil; Coleman, Jason; Gemoets, Darren; Hughes, Kevin

2000-01-01

This paper describes Web-Altairis, an Internet-enabled ground system software package funded by the Advanced Automation and Architectures Branch (Code 588) of NASA's Goddard Space Flight Center. Web-Altairis supports the trend towards "lights out" ground systems, where the control center is unattended and problems are resolved by remote operators. This client/server software runs on most popular platforms and provides for remote data visualization using the rich functionality of the VisAGE toolkit. Web-Altairis also supports satellite commanding over the Internet. This paper describes the structure of Web-Altairis and VisAGE, the underlying technologies, the provisions for security, and our experiences in developing and testing the software.

A Data Audit and Analysis Toolkit To Support Assessment of the First College Year.

ERIC Educational Resources Information Center

Paulson, Karen

This "toolkit" provides a process by which institutions can identify and use information resources to enhance the experiences and outcomes of first-year students. The toolkit contains a "Technical Manual" designed for use by the technical personnel who will be conducting the data audit and associated analyses. Administrators who want more…

Teaching Undergraduate Software Engineering Using Open Source Development Tools

DTIC Science & Technology

2012-01-01

ware. Some example appliances are: a LAMP stack, Redmine, MySQL database, Moodle, Tom- cat on Apache, and Bugzilla. Some of the important features...Ada, C, C++, PHP , Py- thon, etc., and also supports a wide range of SDKs such as Google’s Android SDK and the Google Web Toolkit SDK. Additionally

The Mathlet Toolkit: Creating Dynamic Applets for Differential Equations and Dynamical Systems

ERIC Educational Resources Information Center

Decker, Robert

2011-01-01

Dynamic/interactive graphing applets can be used to supplement standard computer algebra systems such as Maple, Mathematica, Derive, or TI calculators, in courses such as Calculus, Differential Equations, and Dynamical Systems. The addition of this type of software can lead to discovery learning, with students developing their own conjectures, and…

Security Assessment Simulation Toolkit (SAST) Final Report

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

Meitzler, Wayne D.; Ouderkirk, Steven J.; Hughes, Chad O.

2009-11-15

The Department of Defense Technical Support Working Group (DoD TSWG) investment in the Pacific Northwest National Laboratory (PNNL) Security Assessment Simulation Toolkit (SAST) research planted a technology seed that germinated into a suite of follow-on Research and Development (R&D) projects culminating in software that is used by multiple DoD organizations. The DoD TSWG technology transfer goal for SAST is already in progress. The Defense Information Systems Agency (DISA), the Defense-wide Information Assurance Program (DIAP), the Marine Corps, Office Of Naval Research (ONR) National Center For Advanced Secure Systems Research (NCASSR) and Office Of Secretary Of Defense International Exercise Program (OSDmore » NII) are currently investing to take SAST to the next level. PNNL currently distributes the software to over 6 government organizations and 30 DoD users. For the past five DoD wide Bulwark Defender exercises, the adoption of this new technology created an expanding role for SAST. In 2009, SAST was also used in the OSD NII International Exercise and is currently scheduled for use in 2010.« less

BIT: Biosignal Igniter Toolkit.

PubMed

da Silva, Hugo Plácido; Lourenço, André; Fred, Ana; Martins, Raúl

2014-06-01

The study of biosignals has had a transforming role in multiple aspects of our society, which go well beyond the health sciences domains to which they were traditionally associated with. While biomedical engineering is a classical discipline where the topic is amply covered, today biosignals are a matter of interest for students, researchers and hobbyists in areas including computer science, informatics, electrical engineering, among others. Regardless of the context, the use of biosignals in experimental activities and practical projects is heavily bounded by the cost, and limited access to adequate support materials. In this paper we present an accessible, albeit versatile toolkit, composed of low-cost hardware and software, which was created to reinforce the engagement of different people in the field of biosignals. The hardware consists of a modular wireless biosignal acquisition system that can be used to support classroom activities, interface with other devices, or perform rapid prototyping of end-user applications. The software comprehends a set of programming APIs, a biosignal processing toolbox, and a framework for real time data acquisition and postprocessing. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Capturing Petascale Application Characteristics with the Sequoia Toolkit

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

Vetter, Jeffrey S; Bhatia, Nikhil; Grobelny, Eric M

2005-01-01

Characterization of the computation, communication, memory, and I/O demands of current scientific applications is crucial for identifying which technologies will enable petascale scientific computing. In this paper, we present the Sequoia Toolkit for characterizing HPC applications. The Sequoia Toolkit consists of the Sequoia trace capture library and the Sequoia Event Analysis Library, or SEAL, that facilitates the development of tools for analyzing Sequoia event traces. Using the Sequoia Toolkit, we have characterized the behavior of application runs with up to 2048 application processes. To illustrate the use of the Sequoia Toolkit, we present a preliminary characterization of LAMMPS, a molecularmore » dynamics application of great interest to the computational biology community.« less

Implementation of an oblique-sectioning visualization tool for line-of-sight stereotactic neurosurgical navigation using the AVW toolkit

NASA Astrophysics Data System (ADS)

Bates, Lisa M.; Hanson, Dennis P.; Kall, Bruce A.; Meyer, Frederic B.; Robb, Richard A.

1998-06-01

An important clinical application of biomedical imaging and visualization techniques is provision of image guided neurosurgical planning and navigation techniques using interactive computer display systems in the operating room. Current systems provide interactive display of orthogonal images and 3D surface or volume renderings integrated with and guided by the location of a surgical probe. However, structures in the 'line-of-sight' path which lead to the surgical target cannot be directly visualized, presenting difficulty in obtaining full understanding of the 3D volumetric anatomic relationships necessary for effective neurosurgical navigation below the cortical surface. Complex vascular relationships and histologic boundaries like those found in artereovenous malformations (AVM's) also contribute to the difficulty in determining optimal approaches prior to actual surgical intervention. These difficulties demonstrate the need for interactive oblique imaging methods to provide 'line-of-sight' visualization. Capabilities for 'line-of- sight' interactive oblique sectioning are present in several current neurosurgical navigation systems. However, our implementation is novel, in that it utilizes a completely independent software toolkit, AVW (A Visualization Workshop) developed at the Mayo Biomedical Imaging Resource, integrated with a current neurosurgical navigation system, the COMPASS stereotactic system at Mayo Foundation. The toolkit is a comprehensive, C-callable imaging toolkit containing over 500 optimized imaging functions and structures. The powerful functionality and versatility of the AVW imaging toolkit provided facile integration and implementation of desired interactive oblique sectioning using a finite set of functions. The implementation of the AVW-based code resulted in higher-level functions for complete 'line-of-sight' visualization.

Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data

PubMed Central

Kim, Taemook; Seo, Hogyu David; Hennighausen, Lothar; Lee, Daeyoup

2018-01-01

Abstract Octopus-toolkit is a stand-alone application for retrieving and processing large sets of next-generation sequencing (NGS) data with a single step. Octopus-toolkit is an automated set-up-and-analysis pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2, STAR, Samtools, and HOMER applications. All the applications are installed on the user's computer when the program starts. Upon the installation, it can automatically retrieve original files of various epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq, DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression omnibus data repository. The downloaded files can then be sequentially processed to generate BAM and BigWig files, which are used for advanced analyses and visualization. Currently, it can process NGS data from popular model genomes such as, human (Homo sapiens), mouse (Mus musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana), zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae) genomes. With the processed files from Octopus-toolkit, the meta-analysis of various data sets, motif searches for DNA-binding proteins, and the identification of differentially expressed genes and/or protein-binding sites can be easily conducted with few commands by users. Overall, Octopus-toolkit facilitates the systematic and integrative analysis of available epigenomic and transcriptomic NGS big data. PMID:29420797

Third Party TMDL Development Toolkit

EPA Pesticide Factsheets

Water Environment Federation's toolkit provides basic steps in which an organization or group other than the lead water quality agency takes responsibility for developing the TMDL document and supporting analysis.

N values estimation based on photon flux simulation with Geant4 toolkit.

PubMed

Sun, Z J; Danjaji, M; Kim, Y

2018-06-01

N values are routinely introduced in photon activation analysis (PAA) as the ratio of special activities of product nuclides to compare the relative intensities of different reaction channels. They determine the individual activities of each radioisotope and the total activity of the sample, which are the primary concerns of radiation safety. Traditionally, N values are calculated from the gamma spectroscopy in real measurements by normalizing the activities of individual nuclides to the reference reaction [ 58 Ni(γ, n) 57 Ni] of the nickel monitor simultaneously irradiated in photon activation. Is it possible to use photon flux simulated by Monte Carlo software to calculate N values even before the actual irradiation starts? This study has applied Geant4 toolkit, a popular platform of simulating the passage of particles through matter, to generate photon flux in the samples. Assisted with photonuclear cross section from IAEA database, it is feasible to predict N values in different experimental setups for simulated target material. We have validated of this method and its consistency with Geant4. Results also show that N values are highly correlated with the beam parameters of incoming electrons and the setup of the electron-photon converter. Copyright © 2018 Elsevier Ltd. All rights reserved.

Scientific Data Analysis Toolkit: A Versatile Add-in to Microsoft Excel for Windows

ERIC Educational Resources Information Center

Halpern, Arthur M.; Frye, Stephen L.; Marzzacco, Charles J.

2018-01-01

Scientific Data Analysis Toolkit (SDAT) is a rigorous, versatile, and user-friendly data analysis add-in application for Microsoft Excel for Windows (PC). SDAT uses the familiar Excel environment to carry out most of the analytical tasks used in data analysis. It has been designed for student use in manipulating and analyzing data encountered in…

The SpeX Prism Library Analysis Toolkit: Design Considerations and First Results

NASA Astrophysics Data System (ADS)

Burgasser, Adam J.; Aganze, Christian; Escala, Ivana; Lopez, Mike; Choban, Caleb; Jin, Yuhui; Iyer, Aishwarya; Tallis, Melisa; Suarez, Adrian; Sahi, Maitrayee

2016-01-01

Various observational and theoretical spectral libraries now exist for galaxies, stars, planets and other objects, which have proven useful for classification, interpretation, simulation and model development. Effective use of these libraries relies on analysis tools, which are often left to users to develop. In this poster, we describe a program to develop a combined spectral data repository and Python-based analysis toolkit for low-resolution spectra of very low mass dwarfs (late M, L and T dwarfs), which enables visualization, spectral index analysis, classification, atmosphere model comparison, and binary modeling for nearly 2000 library spectra and user-submitted data. The SpeX Prism Library Analysis Toolkit (SPLAT) is being constructed as a collaborative, student-centered, learning-through-research model with high school, undergraduate and graduate students and regional science teachers, who populate the database and build the analysis tools through quarterly challenge exercises and summer research projects. In this poster, I describe the design considerations of the toolkit, its current status and development plan, and report the first published results led by undergraduate students. The combined data and analysis tools are ideal for characterizing cool stellar and exoplanetary atmospheres (including direct exoplanetary spectra observations by Gemini/GPI, VLT/SPHERE, and JWST), and the toolkit design can be readily adapted for other spectral datasets as well.This material is based upon work supported by the National Aeronautics and Space Administration under Grant No. NNX15AI75G. SPLAT code can be found at https://github.com/aburgasser/splat.

Formal Verification Toolkit for Requirements and Early Design Stages

NASA Technical Reports Server (NTRS)

Badger, Julia M.; Miller, Sheena Judson

2011-01-01

Efficient flight software development from natural language requirements needs an effective way to test designs earlier in the software design cycle. A method to automatically derive logical safety constraints and the design state space from natural language requirements is described. The constraints can then be checked using a logical consistency checker and also be used in a symbolic model checker to verify the early design of the system. This method was used to verify a hybrid control design for the suit ports on NASA Johnson Space Center's Space Exploration Vehicle against safety requirements.

NAIF Toolkit - Extended

NASA Technical Reports Server (NTRS)

Acton, Charles H., Jr.; Bachman, Nathaniel J.; Semenov, Boris V.; Wright, Edward D.

2010-01-01

The Navigation Ancillary Infor ma tion Facility (NAIF) at JPL, acting under the direction of NASA s Office of Space Science, has built a data system named SPICE (Spacecraft Planet Instrument Cmatrix Events) to assist scientists in planning and interpreting scientific observations (see figure). SPICE provides geometric and some other ancillary information needed to recover the full value of science instrument data, including correlation of individual instrument data sets with data from other instruments on the same or other spacecraft. This data system is used to produce space mission observation geometry data sets known as SPICE kernels. It is also used to read SPICE kernels and to compute derived quantities such as positions, orientations, lighting angles, etc. The SPICE toolkit consists of a subroutine/ function library, executable programs (both large applications and simple utilities that focus on kernel management), and simple examples of using SPICE toolkit subroutines. This software is very accurate, thoroughly tested, and portable to all computers. It is extremely stable and reusable on all missions. Since the previous version, three significant capabilities have been added: Interactive Data Language (IDL) interface, MATLAB interface, and a geometric event finder subsystem.

A Java-Enabled Interactive Graphical Gas Turbine Propulsion System Simulator

NASA Technical Reports Server (NTRS)

Reed, John A.; Afjeh, Abdollah A.

1997-01-01

This paper describes a gas turbine simulation system which utilizes the newly developed Java language environment software system. The system provides an interactive graphical environment which allows the quick and efficient construction and analysis of arbitrary gas turbine propulsion systems. The simulation system couples a graphical user interface, developed using the Java Abstract Window Toolkit, and a transient, space- averaged, aero-thermodynamic gas turbine analysis method, both entirely coded in the Java language. The combined package provides analytical, graphical and data management tools which allow the user to construct and control engine simulations by manipulating graphical objects on the computer display screen. Distributed simulations, including parallel processing and distributed database access across the Internet and World-Wide Web (WWW), are made possible through services provided by the Java environment.

NURBS-Based Geometry for Integrated Structural Analysis

NASA Technical Reports Server (NTRS)

Oliver, James H.

1997-01-01

This grant was initiated in April 1993 and completed in September 1996. The primary goal of the project was to exploit the emerging defacto CAD standard of Non- Uniform Rational B-spline (NURBS) based curve and surface geometry to integrate and streamline the process of turbomachinery structural analysis. We focused our efforts on critical geometric modeling challenges typically posed by the requirements of structural analysts. We developed a suite of software tools that facilitate pre- and post-processing of NURBS-based turbomachinery blade models for finite element structural analyses. We also developed tools to facilitate the modeling of blades in their manufactured (or cold) state based on nominal operating shape and conditions. All of the software developed in the course of this research is written in the C++ language using the Iris Inventor 3D graphical interface tool-kit from Silicon Graphics. In addition to enhanced modularity, improved maintainability, and efficient prototype development, this design facilitates the re-use of code developed for other NASA projects and provides a uniform and professional 'look and feel' for all applications developed by the Iowa State Team.

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit

PubMed Central

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-01-01

Background Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Results Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Conclusion Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers. PMID:18328109

Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit.

PubMed

O'Boyle, Noel M; Morley, Chris; Hutchison, Geoffrey R

2008-03-09

Scripting languages such as Python are ideally suited to common programming tasks in cheminformatics such as data analysis and parsing information from files. However, for reasons of efficiency, cheminformatics toolkits such as the OpenBabel toolkit are often implemented in compiled languages such as C++. We describe Pybel, a Python module that provides access to the OpenBabel toolkit. Pybel wraps the direct toolkit bindings to simplify common tasks such as reading and writing molecular files and calculating fingerprints. Extensive use is made of Python iterators to simplify loops such as that over all the molecules in a file. A Pybel Molecule can be easily interconverted to an OpenBabel OBMol to access those methods or attributes not wrapped by Pybel. Pybel allows cheminformaticians to rapidly develop Python scripts that manipulate chemical information. It is open source, available cross-platform, and offers the power of the OpenBabel toolkit to Python programmers.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

The connectome viewer toolkit: an open source framework to manage, analyze, and visualize connectomes.

PubMed

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit - a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/

The Connectome Viewer Toolkit: An Open Source Framework to Manage, Analyze, and Visualize Connectomes

PubMed Central

Gerhard, Stephan; Daducci, Alessandro; Lemkaddem, Alia; Meuli, Reto; Thiran, Jean-Philippe; Hagmann, Patric

2011-01-01

Advanced neuroinformatics tools are required for methods of connectome mapping, analysis, and visualization. The inherent multi-modality of connectome datasets poses new challenges for data organization, integration, and sharing. We have designed and implemented the Connectome Viewer Toolkit – a set of free and extensible open source neuroimaging tools written in Python. The key components of the toolkit are as follows: (1) The Connectome File Format is an XML-based container format to standardize multi-modal data integration and structured metadata annotation. (2) The Connectome File Format Library enables management and sharing of connectome files. (3) The Connectome Viewer is an integrated research and development environment for visualization and analysis of multi-modal connectome data. The Connectome Viewer's plugin architecture supports extensions with network analysis packages and an interactive scripting shell, to enable easy development and community contributions. Integration with tools from the scientific Python community allows the leveraging of numerous existing libraries for powerful connectome data mining, exploration, and comparison. We demonstrate the applicability of the Connectome Viewer Toolkit using Diffusion MRI datasets processed by the Connectome Mapper. The Connectome Viewer Toolkit is available from http://www.cmtk.org/ PMID:21713110

A Software Tool for Estimation of Burden of Infectious Diseases in Europe Using Incidence-Based Disability Adjusted Life Years

PubMed Central

Lewandowski, Daniel; Mangen, Marie-Josee J.; Plass, Dietrich; McDonald, Scott A.; van Lier, Alies; Haagsma, Juanita A.; Maringhini, Guido; Pini, Alessandro; Kramarz, Piotr; Kretzschmar, Mirjam E.

2017-01-01

The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS). To meet this goal, a user-friendly software tool (BCoDE toolkit), was developed. This stand-alone application, written in C++, is open-access and freely available for download from the website of the European Centre for Disease Prevention and Control (ECDC). With the BCoDE toolkit, one can calculate DALYs by simply entering the age group- and sex-specific number of cases for one or more of selected sets of 32 communicable diseases (CDs) and 6 healthcare associated infections (HAIs). Disease progression models (i.e., outcome trees) for these communicable diseases were created following a thorough literature review of their disease progression pathway. The BCoDE toolkit runs Monte Carlo simulations of the input parameters and provides disease-specific results, including 95% uncertainty intervals, and permits comparisons between the different disease models entered. Results can be displayed as mean and median overall DALYs, DALYs per 100,000 population, and DALYs related to mortality vs. disability. Visualization options summarize complex epidemiological data, with the goal of improving communication and knowledge transfer for decision-making. PMID:28107447

A Software Tool for Estimation of Burden of Infectious Diseases in Europe Using Incidence-Based Disability Adjusted Life Years.

PubMed

Colzani, Edoardo; Cassini, Alessandro; Lewandowski, Daniel; Mangen, Marie-Josee J; Plass, Dietrich; McDonald, Scott A; van Lier, Alies; Haagsma, Juanita A; Maringhini, Guido; Pini, Alessandro; Kramarz, Piotr; Kretzschmar, Mirjam E

2017-01-01

The burden of disease framework facilitates the assessment of the health impact of diseases through the use of summary measures of population health such as Disability-Adjusted Life Years (DALYs). However, calculating, interpreting and communicating the results of studies using this methodology poses a challenge. The aim of the Burden of Communicable Disease in Europe (BCoDE) project is to summarize the impact of communicable disease in the European Union and European Economic Area Member States (EU/EEA MS). To meet this goal, a user-friendly software tool (BCoDE toolkit), was developed. This stand-alone application, written in C++, is open-access and freely available for download from the website of the European Centre for Disease Prevention and Control (ECDC). With the BCoDE toolkit, one can calculate DALYs by simply entering the age group- and sex-specific number of cases for one or more of selected sets of 32 communicable diseases (CDs) and 6 healthcare associated infections (HAIs). Disease progression models (i.e., outcome trees) for these communicable diseases were created following a thorough literature review of their disease progression pathway. The BCoDE toolkit runs Monte Carlo simulations of the input parameters and provides disease-specific results, including 95% uncertainty intervals, and permits comparisons between the different disease models entered. Results can be displayed as mean and median overall DALYs, DALYs per 100,000 population, and DALYs related to mortality vs. disability. Visualization options summarize complex epidemiological data, with the goal of improving communication and knowledge transfer for decision-making.

Digital beacon receiver for ionospheric TEC measurement developed with GNU Radio

NASA Astrophysics Data System (ADS)

Yamamoto, M.

2008-11-01

A simple digital receiver named GNU Radio Beacon Receiver (GRBR) was developed for the satellite-ground beacon experiment to measure the ionospheric total electron content (TEC). The open-source software toolkit for the software defined radio, GNU Radio, is utilized to realize the basic function of the receiver and perform fast signal processing. The software is written in Python for a LINUX PC. The open-source hardware called Universal Software Radio Peripheral (USRP), which best matches the GNU Radio, is used as a front-end to acquire the satellite beacon signals of 150 and 400 MHz. The first experiment was successful as results from GRBR showed very good agreement to those from the co-located analog beacon receiver. Detailed design information and software codes are open at the URL http://www.rish.kyoto-u.ac.jp/digitalbeacon/.

PeakML/mzMatch: a file format, Java library, R library, and tool-chain for mass spectrometry data analysis.

PubMed

Scheltema, Richard A; Jankevics, Andris; Jansen, Ritsert C; Swertz, Morris A; Breitling, Rainer

2011-04-01

The recent proliferation of high-resolution mass spectrometers has generated a wealth of new data analysis methods. However, flexible integration of these methods into configurations best suited to the research question is hampered by heterogeneous file formats and monolithic software development. The mzXML, mzData, and mzML file formats have enabled uniform access to unprocessed raw data. In this paper we present our efforts to produce an equally simple and powerful format, PeakML, to uniformly exchange processed intermediary and result data. To demonstrate the versatility of PeakML, we have developed an open source Java toolkit for processing, filtering, and annotating mass spectra in a customizable pipeline (mzMatch), as well as a user-friendly data visualization environment (PeakML Viewer). The PeakML format in particular enables the flexible exchange of processed data between software created by different groups or companies, as we illustrate by providing a PeakML-based integration of the widely used XCMS package with mzMatch data processing tools. As an added advantage, downstream analysis can benefit from direct access to the full mass trace information underlying summarized mass spectrometry results, providing the user with the means to rapidly verify results. The PeakML/mzMatch software is freely available at http://mzmatch.sourceforge.net, with documentation, tutorials, and a community forum.

PiSCES: Pi(scine) stream community estimation software: A tool for nationwide fish assemblage predictions

EPA Science Inventory

Background/Question/Methods What species of fish might someone find in a local stream? How might that community change as a result of changes to characteristics of the stream and its watershed? PiSCES is a browser-based toolkit developed to predict a fish community for any NHD-Pl...

DICOM image quantification secondary capture (DICOM IQSC) integrated with numeric results, regions, and curves: implementation and applications in nuclear medicine

NASA Astrophysics Data System (ADS)

Cao, Xinhua; Xu, Xiaoyin; Voss, Stephan

2017-03-01

In this paper, we describe an enhanced DICOM Secondary Capture (SC) that integrates Image Quantification (IQ) results, Regions of Interest (ROIs), and Time Activity Curves (TACs) with screen shots by embedding extra medical imaging information into a standard DICOM header. A software toolkit of DICOM IQSC has been developed to implement the SC-centered information integration of quantitative analysis for routine practice of nuclear medicine. Primary experiments show that the DICOM IQSC method is simple and easy to implement seamlessly integrating post-processing workstations with PACS for archiving and retrieving IQ information. Additional DICOM IQSC applications in routine nuclear medicine and clinic research are also discussed.

Cazymes Analysis Toolkit (CAT): Webservice for searching and analyzing carbohydrateactive enzymes in a newly sequenced organism using CAZy database

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

Karpinets, Tatiana V; Park, Byung; Syed, Mustafa H

2010-01-01

The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire non-redundant sequences of the CAZy database. Themore » second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains (DUF) and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit (CAT), and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.« less

CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

PubMed

Park, Byung H; Karpinets, Tatiana V; Syed, Mustafa H; Leuze, Michael R; Uberbacher, Edward C

2010-12-01

The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire nonredundant sequences of the CAZy database. The second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit, and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.

Field Ground Truthing Data Collector - a Mobile Toolkit for Image Analysis and Processing

NASA Astrophysics Data System (ADS)

Meng, X.

2012-07-01

Field Ground Truthing Data Collector is one of the four key components of the NASA funded ICCaRS project, being developed in Southeast Michigan. The ICCaRS ground truthing toolkit entertains comprehensive functions: 1) Field functions, including determining locations through GPS, gathering and geo-referencing visual data, laying out ground control points for AEROKAT flights, measuring the flight distance and height, and entering observations of land cover (and use) and health conditions of ecosystems and environments in the vicinity of the flight field; 2) Server synchronization functions, such as, downloading study-area maps, aerial photos and satellite images, uploading and synchronizing field-collected data with the distributed databases, calling the geospatial web services on the server side to conduct spatial querying, image analysis and processing, and receiving the processed results in field for near-real-time validation; and 3) Social network communication functions for direct technical assistance and pedagogical support, e.g., having video-conference calls in field with the supporting educators, scientists, and technologists, participating in Webinars, or engaging discussions with other-learning portals. This customized software package is being built on Apple iPhone/iPad and Google Maps/Earth. The technical infrastructures, data models, coupling methods between distributed geospatial data processing and field data collector tools, remote communication interfaces, coding schema, and functional flow charts will be illustrated and explained at the presentation. A pilot case study will be also demonstrated.

WESTPA: An interoperable, highly scalable software package for weighted ensemble simulation and analysis

PubMed Central

Zwier, Matthew C.; Adelman, Joshua L.; Kaus, Joseph W.; Pratt, Adam J.; Wong, Kim F.; Rego, Nicholas B.; Suárez, Ernesto; Lettieri, Steven; Wang, David W.; Grabe, Michael; Zuckerman, Daniel M.; Chong, Lillian T.

2015-01-01

The weighted ensemble (WE) path sampling approach orchestrates an ensemble of parallel calculations with intermittent communication to enhance the sampling of rare events, such as molecular associations or conformational changes in proteins or peptides. Trajectories are replicated and pruned in a way that focuses computational effort on under-explored regions of configuration space while maintaining rigorous kinetics. To enable the simulation of rare events at any scale (e.g. atomistic, cellular), we have developed an open-source, interoperable, and highly scalable software package for the execution and analysis of WE simulations: WESTPA (The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis). WESTPA scales to thousands of CPU cores and includes a suite of analysis tools that have been implemented in a massively parallel fashion. The software has been designed to interface conveniently with any dynamics engine and has already been used with a variety of molecular dynamics (e.g. GROMACS, NAMD, OpenMM, AMBER) and cell-modeling packages (e.g. BioNetGen, MCell). WESTPA has been in production use for over a year, and its utility has been demonstrated for a broad set of problems, ranging from atomically detailed host-guest associations to non-spatial chemical kinetics of cellular signaling networks. The following describes the design and features of WESTPA, including the facilities it provides for running WE simulations, storing and analyzing WE simulation data, as well as examples of input and output. PMID:26392815

A personal health information toolkit for health intervention research.

PubMed

Kizakevich, Paul N; Eckhoff, Randall; Weger, Stacey; Weeks, Adam; Brown, Janice; Bryant, Stephanie; Bakalov, Vesselina; Zhang, Yuying; Lyden, Jennifer; Spira, James

2014-01-01

With the emergence of mobile health (mHealth) apps, there is a growing demand for better tools for developing and evaluating mobile health interventions. Recently we developed the Personal Health Intervention Toolkit (PHIT), a software framework which eases app implementation and facilitates scientific evaluation. PHIT integrates self-report and physiological sensor instruments, evidence-based advisor logic, and self-help interventions such as meditation, health education, and cognitive behavior change. PHIT can be used to facilitate research, interventions for chronic diseases, risky behaviors, sleep, medication adherence, environmental monitoring, momentary data collection health screening, and clinical decision support. In a series of usability evaluations, participants reported an overall usability score of 4.5 on a 1-5 Likert scale and an 85 score on the System Usability Scale, indicating a high percentile rank of 95%.

ChemDoodle Web Components: HTML5 toolkit for chemical graphics, interfaces, and informatics.

PubMed

Burger, Melanie C

2015-01-01

ChemDoodle Web Components (abbreviated CWC, iChemLabs, LLC) is a light-weight (~340 KB) JavaScript/HTML5 toolkit for chemical graphics, structure editing, interfaces, and informatics based on the proprietary ChemDoodle desktop software. The library uses and WebGL technologies and other HTML5 features to provide solutions for creating chemistry-related applications for the web on desktop and mobile platforms. CWC can serve a broad range of scientific disciplines including crystallography, materials science, organic and inorganic chemistry, biochemistry and chemical biology. CWC is freely available for in-house use and is open source (GPL v3) for all other uses.Graphical abstractAdd interactive 2D and 3D chemical sketchers, graphics, and spectra to websites and apps with ChemDoodle Web Components.

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

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

2008-01-01

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

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

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

2008-01-01

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

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

Nandigam, V.; Crosby, C.; Baru, C.

2012-12-01

The NSF-funded OpenTopography facility provides online access to Earth science-oriented high-resolution LIDAR topography data, online processing tools, and derivative products. The underlying cyberinfrastructure employs a multi-tier service oriented architecture that is comprised of an infrastructure tier, a processing services tier, and an application tier. The infrastructure tier consists of storage, compute resources as well as supporting databases. The services tier consists of the set of processing routines each deployed as a Web service. The applications tier provides client interfaces to the system. (e.g. Portal). We propose a "pluggable" infrastructure design that will allow new scientific algorithms and processing routines developed and maintained by the community to be integrated into the OpenTopography system so that the wider earth science community can benefit from its availability. All core components in OpenTopography are available as Web services using a customized open-source Opal toolkit. The Opal toolkit provides mechanisms to manage and track job submissions, with the help of a back-end database. It allows monitoring of job and system status by providing charting tools. All core components in OpenTopography have been developed, maintained and wrapped as Web services using Opal by OpenTopography developers. However, as the scientific community develops new processing and analysis approaches this integration approach is not scalable efficiently. Most of the new scientific applications will have their own active development teams performing regular updates, maintenance and other improvements. It would be optimal to have the application co-located where its developers can continue to actively work on it while still making it accessible within the OpenTopography workflow for processing capabilities. We will utilize a software framework for remote integration of these scientific applications into the OpenTopography system. This will be accomplished by virtually extending the OpenTopography service over the various infrastructures running these scientific applications and processing routines. This involves packaging and distributing a customized instance of the Opal toolkit that will wrap the software application as an OPAL-based web service and integrate it into the OpenTopography framework. We plan to make this as automated as possible. A structured specification of service inputs and outputs along with metadata annotations encoded in XML can be utilized to automate the generation of user interfaces, with appropriate tools tips and user help features, and generation of other internal software. The OpenTopography Opal toolkit will also include the customizations that will enable security authentication, authorization and the ability to write application usage and job statistics back to the OpenTopography databases. This usage information could then be reported to the original service providers and used for auditing and performance improvements. This pluggable framework will enable the application developers to continue to work on enhancing their application while making the latest iteration available in a timely manner to the earth sciences community. This will also help us establish an overall framework that other scientific application providers will also be able to use going forward.

Biomechanical Analysis of Locust Jumping in a Physically Realistic Virtual Environment

NASA Astrophysics Data System (ADS)

Cofer, David; Cymbalyuk, Gennady; Heitler, William; Edwards, Donald

2008-03-01

The biomechanical and neural components that underlie locust jumping have been extensively studied. Previous research suggested that jump energy is stored primarily in the extensor apodeme, and in a band of cuticle called the semi-lunar process (SLP). As it has thus far proven impossible to experimentally alter the SLP without rendering a locust unable to jump, it has not been possible to test whether the energy stored in the SLP has a significant impact on the jump. To address problems such as this we have developed a software toolkit, AnimatLab, which allows researchers to build and test virtual organisms. We used this software to build a virtual locust, and then asked how the SLP is utilized during jumping. The results show that without the SLP the jump distance was reduced by almost half. Further, the simulations were also able to show that loss of the SLP had a significant impact on the final phase of the jump. We are currently working on postural control mechanisms for targeted jumping in locust.

Developing Signal-Pattern-Recognition Programs

NASA Technical Reports Server (NTRS)

Shelton, Robert O.; Hammen, David

2006-01-01

Pattern Interpretation and Recognition Application Toolkit Environment (PIRATE) is a block-oriented software system that aids the development of application programs that analyze signals in real time in order to recognize signal patterns that are indicative of conditions or events of interest. PIRATE was originally intended for use in writing application programs to recognize patterns in space-shuttle telemetry signals received at Johnson Space Center's Mission Control Center: application programs were sought to (1) monitor electric currents on shuttle ac power busses to recognize activations of specific power-consuming devices, (2) monitor various pressures and infer the states of affected systems by applying a Kalman filter to the pressure signals, (3) determine fuel-leak rates from sensor data, (4) detect faults in gyroscopes through analysis of system measurements in the frequency domain, and (5) determine drift rates in inertial measurement units by regressing measurements against time. PIRATE can also be used to develop signal-pattern-recognition software for different purposes -- for example, to monitor and control manufacturing processes.

Cross-Layer Modeling Framework for Energy-Efficient Resilience

DTIC Science & Technology

2014-04-01

functional block diagram of the software architecture of PEARL, which stands for: Power Efficient and Resilient Embedded Processing with Real - Time ... DVFS ). The goal of the run- time manager is to minimize power consumption, while maintaining system resilience targets (on average) and meeting... real - time performance targets. The integrated performance, power and resilience models are nothing but the analytical modeling toolkit described in

Software Testbed for Developing and Evaluating Integrated Autonomous Systems

DTIC Science & Technology

2015-03-01

EUROPA planning system for plan generation. The adaptive controller executes the new plan, using augmented, hierarchical finite state machines to...using the Internet Communications Engine ( ICE ), an object-oriented toolkit for building distributed applications. TABLE OF CONTENTS 1...ANML model is translated into the New Domain Definition Language (NDDL) and sent to NASA???s EUROPA planning system for plan generation. The adaptive

A user-friendly software package to ease the use of VIC hydrologic model for practitioners

NASA Astrophysics Data System (ADS)

Wi, S.; Ray, P.; Brown, C.

2016-12-01

The VIC (Variable Infiltration Capacity) hydrologic and river routing model simulates the water and energy fluxes that occur near the land surface and provides users with useful information regarding the quantity and timing of available water at points of interest within the basin. However, despite its popularity (proved by numerous applications in the literature), its wider adoption is hampered by the considerable effort required to prepare model inputs; e.g., input files storing spatial information related to watershed topography, soil properties, and land cover. This study presents a user-friendly software package (named VIC Setup Toolkit) developed within the MATLAB (matrix laboratory) framework and accessible through an intuitive graphical user interface. The VIC Setup Toolkit enables users to navigate the model building process confidently through prompts and automation, with an intention to promote the use of the model for both practical and academic purposes. The automated processes include watershed delineation, climate and geographical input set-up, model parameter calibration, graph generation and output evaluation. We demonstrate the package's usefulness in various case studies with the American River, Oklahoma River, Feather River and Zambezi River basins.

FATES: a flexible analysis toolkit for the exploration of single-particle mass spectrometer data

NASA Astrophysics Data System (ADS)

Sultana, Camille M.; Cornwell, Gavin C.; Rodriguez, Paul; Prather, Kimberly A.

2017-04-01

Single-particle mass spectrometer (SPMS) analysis of aerosols has become increasingly popular since its invention in the 1990s. Today many iterations of commercial and lab-built SPMSs are in use worldwide. However, supporting analysis toolkits for these powerful instruments are outdated, have limited functionality, or are versions that are not available to the scientific community at large. In an effort to advance this field and allow better communication and collaboration between scientists, we have developed FATES (Flexible Analysis Toolkit for the Exploration of SPMS data), a MATLAB toolkit easily extensible to an array of SPMS designs and data formats. FATES was developed to minimize the computational demands of working with large data sets while still allowing easy maintenance, modification, and utilization by novice programmers. FATES permits scientists to explore, without constraint, complex SPMS data with simple scripts in a language popular for scientific numerical analysis. In addition FATES contains an array of data visualization graphic user interfaces (GUIs) which can aid both novice and expert users in calibration of raw data; exploration of the dependence of mass spectral characteristics on size, time, and peak intensity; and investigations of clustered data sets.

Ridesharing options analysis and practitioners' toolkit

DOT National Transportation Integrated Search

2010-12-01

The purpose of this toolkit is to elaborate upon the recent changes in ridesharing, introduce the wide variety that exists in ridesharing programs today, and the developments in technology and funding availability that create greater incentives for p...

An automatic speech recognition system with speaker-independent identification support

NASA Astrophysics Data System (ADS)

Caranica, Alexandru; Burileanu, Corneliu

2015-02-01

The novelty of this work relies on the application of an open source research software toolkit (CMU Sphinx) to train, build and evaluate a speech recognition system, with speaker-independent support, for voice-controlled hardware applications. Moreover, we propose to use the trained acoustic model to successfully decode offline voice commands on embedded hardware, such as an ARMv6 low-cost SoC, Raspberry PI. This type of single-board computer, mainly used for educational and research activities, can serve as a proof-of-concept software and hardware stack for low cost voice automation systems.

An open-source LabVIEW application toolkit for phasic heart rate analysis in psychophysiological research.

PubMed

Duley, Aaron R; Janelle, Christopher M; Coombes, Stephen A

2004-11-01

The cardiovascular system has been extensively measured in a variety of research and clinical domains. Despite technological and methodological advances in cardiovascular science, the analysis and evaluation of phasic changes in heart rate persists as a way to assess numerous psychological concomitants. Some researchers, however, have pointed to constraints on data analysis when evaluating cardiac activity indexed by heart rate or heart period. Thus, an off-line application toolkit for heart rate analysis is presented. The program, written with National Instruments' LabVIEW, incorporates a variety of tools for off-line extraction and analysis of heart rate data. Current methods and issues concerning heart rate analysis are highlighted, and how the toolkit provides a flexible environment to ameliorate common problems that typically lead to trial rejection is discussed. Source code for this program may be downloaded from the Psychonomic Society Web archive at www.psychonomic.org/archive/.

Provider perceptions of an integrated primary care quality improvement strategy: The PPAQ toolkit.

PubMed

Beehler, Gregory P; Lilienthal, Kaitlin R

2017-02-01

The Primary Care Behavioral Health (PCBH) model of integrated primary care is challenging to implement with high fidelity. The Primary Care Behavioral Health Provider Adherence Questionnaire (PPAQ) was designed to assess provider adherence to essential model components and has recently been adapted into a quality improvement toolkit. The aim of this pilot project was to gather preliminary feedback on providers' perceptions of the acceptability and utility of the PPAQ toolkit for making beneficial practice changes. Twelve mental health providers working in Department of Veterans Affairs integrated primary care clinics participated in semistructured interviews to gather quantitative and qualitative data. Descriptive statistics and qualitative content analysis were used to analyze data. Providers identified several positive features of the PPAQ toolkit organization and structure that resulted in high ratings of acceptability, while also identifying several toolkit components in need of modification to improve usability. Toolkit content was considered highly representative of the (PCBH) model and therefore could be used as a diagnostic self-assessment of model adherence. The toolkit was considered to be high in applicability to providers regardless of their degree of prior professional preparation or current clinical setting. Additionally, providers identified several system-level contextual factors that could impact the usefulness of the toolkit. These findings suggest that frontline mental health providers working in (PCBH) settings may be receptive to using an adherence-focused toolkit for ongoing quality improvement. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

An introduction to Space Weather Integrated Modeling

NASA Astrophysics Data System (ADS)

Zhong, D.; Feng, X.

2012-12-01

The need for a software toolkit that integrates space weather models and data is one of many challenges we are facing with when applying the models to space weather forecasting. To meet this challenge, we have developed Space Weather Integrated Modeling (SWIM) that is capable of analysis and visualizations of the results from a diverse set of space weather models. SWIM has a modular design and is written in Python, by using NumPy, matplotlib, and the Visualization ToolKit (VTK). SWIM provides data management module to read a variety of spacecraft data products and a specific data format of Solar-Interplanetary Conservation Element/Solution Element MHD model (SIP-CESE MHD model) for the study of solar-terrestrial phenomena. Data analysis, visualization and graphic user interface modules are also presented in a user-friendly way to run the integrated models and visualize the 2-D and 3-D data sets interactively. With these tools we can locally or remotely analysis the model result rapidly, such as extraction of data on specific location in time-sequence data sets, plotting interplanetary magnetic field lines, multi-slicing of solar wind speed, volume rendering of solar wind density, animation of time-sequence data sets, comparing between model result and observational data. To speed-up the analysis, an in-situ visualization interface is used to support visualizing the data 'on-the-fly'. We also modified some critical time-consuming analysis and visualization methods with the aid of GPU and multi-core CPU. We have used this tool to visualize the data of SIP-CESE MHD model in real time, and integrated the Database Model of shock arrival, Shock Propagation Model, Dst forecasting model and SIP-CESE MHD model developed by SIGMA Weather Group at State Key Laboratory of Space Weather/CAS.

RISMC Toolkit and Methodology Research and Development Plan for External Hazards Analysis

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

Coleman, Justin Leigh

This report includes the description and development plan for a Risk Informed Safety Margins Characterization (RISMC) toolkit and methodology that will evaluate multihazard risk in an integrated manner to support the operating nuclear fleet.

Unipro UGENE: a unified bioinformatics toolkit.

PubMed

Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail

2012-04-15

Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality. UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http://ugene.unipro.ru/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.

FHIR Healthcare Directories: Adopting Shared Interfaces to Achieve Interoperable Medical Device Data Integration.

PubMed

Tyndall, Timothy; Tyndall, Ayami

2018-01-01

Healthcare directories are vital for interoperability among healthcare providers, researchers and patients. Past efforts at directory services have not provided the tools to allow integration of the diverse data sources. Many are overly strict, incompatible with legacy databases, and do not provide Data Provenance. A more architecture-independent system is needed to enable secure, GDPR-compatible (8) service discovery across organizational boundaries. We review our development of a portable Data Provenance Toolkit supporting provenance within Health Information Exchange (HIE) systems. The Toolkit has been integrated with client software and successfully leveraged in clinical data integration. The Toolkit validates provenance stored in a Blockchain or Directory record and creates provenance signatures, providing standardized provenance that moves with the data. This healthcare directory suite implements discovery of healthcare data by HIE and EHR systems via FHIR. Shortcomings of past directory efforts include the ability to map complex datasets and enabling interoperability via exchange endpoint discovery. By delivering data without dictating how it is stored we improve exchange and facilitate discovery on a multi-national level through open source, fully interoperable tools. With the development of Data Provenance resources we enhance exchange and improve security and usability throughout the health data continuum.

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

von Laszewski, G.; Gawor, J.; Lane, P.

In this paper we report on the features of the Java Commodity Grid Kit (Java CoG Kit). The Java CoG Kit provides middleware for accessing Grid functionality from the Java framework. Java CoG Kit middleware is general enough to design a variety of advanced Grid applications with quite different user requirements. Access to the Grid is established via Globus Toolkit protocols, allowing the Java CoG Kit to also communicate with the services distributed as part of the C Globus Toolkit reference implementation. Thus, the Java CoG Kit provides Grid developers with the ability to utilize the Grid, as well asmore » numerous additional libraries and frameworks developed by the Java community to enable network, Internet, enterprise and peer-to-peer computing. A variety of projects have successfully used the client libraries of the Java CoG Kit to access Grids driven by the C Globus Toolkit software. In this paper we also report on the efforts to develop serverside Java CoG Kit components. As part of this research we have implemented a prototype pure Java resource management system that enables one to run Grid jobs on platforms on which a Java virtual machine is supported, including Windows NT machines.« less

XVIS: Visualization for the Extreme-Scale Scientific-Computation Ecosystem Final Scientific/Technical Report

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

Geveci, Berk; Maynard, Robert

The XVis project brings together the key elements of research to enable scientific discovery at extreme scale. Scientific computing will no longer be purely about how fast computations can be performed. Energy constraints, processor changes, and I/O limitations necessitate significant changes in both the software applications used in scientific computation and the ways in which scientists use them. Components for modeling, simulation, analysis, and visualization must work together in a computational ecosystem, rather than working independently as they have in the past. The XVis project brought together collaborators from predominant DOE projects for visualization on accelerators and combining their respectivemore » features into a new visualization toolkit called VTK-m.« less

Development of an Integrated Human Factors Toolkit

NASA Technical Reports Server (NTRS)

Resnick, Marc L.

2003-01-01

An effective integration of human abilities and limitations is crucial to the success of all NASA missions. The Integrated Human Factors Toolkit facilitates this integration by assisting system designers and analysts to select the human factors tools that are most appropriate for the needs of each project. The HF Toolkit contains information about a broad variety of human factors tools addressing human requirements in the physical, information processing and human reliability domains. Analysis of each tool includes consideration of the most appropriate design stage, the amount of expertise in human factors that is required, the amount of experience with the tool and the target job tasks that are needed, and other factors that are critical for successful use of the tool. The benefits of the Toolkit include improved safety, reliability and effectiveness of NASA systems throughout the agency. This report outlines the initial stages of development for the Integrated Human Factors Toolkit.

Mars Science Laboratory Boot Robustness Testing

NASA Technical Reports Server (NTRS)

Banazadeh, Payam; Lam, Danny

2011-01-01

Mars Science Laboratory (MSL) is one of the most complex spacecrafts in the history of mankind. Due to the nature of its complexity, a large number of flight software (FSW) requirements have been written for implementation. In practice, these requirements necessitate very complex and very precise flight software with no room for error. One of flight software's responsibilities is to be able to boot up and check the state of all devices on the spacecraft after the wake up process. This boot up and initialization is crucial to the mission success since any misbehavior of different devices needs to be handled through the flight software. I have created a test toolkit that allows the FSW team to exhaustively test the flight software under variety of different unexpected scenarios and validate that flight software can handle any situation after booting up. The test includes initializing different devices on spacecraft to different configurations and validate at the end of the flight software boot up that the flight software has initialized those devices to what they are suppose to be in that particular scenario.

ETE: a python Environment for Tree Exploration.

PubMed

Huerta-Cepas, Jaime; Dopazo, Joaquín; Gabaldón, Toni

2010-01-13

Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org.

ETE: a python Environment for Tree Exploration

PubMed Central

2010-01-01

Background Many bioinformatics analyses, ranging from gene clustering to phylogenetics, produce hierarchical trees as their main result. These are used to represent the relationships among different biological entities, thus facilitating their analysis and interpretation. A number of standalone programs are available that focus on tree visualization or that perform specific analyses on them. However, such applications are rarely suitable for large-scale surveys, in which a higher level of automation is required. Currently, many genome-wide analyses rely on tree-like data representation and hence there is a growing need for scalable tools to handle tree structures at large scale. Results Here we present the Environment for Tree Exploration (ETE), a python programming toolkit that assists in the automated manipulation, analysis and visualization of hierarchical trees. ETE libraries provide a broad set of tree handling options as well as specific methods to analyze phylogenetic and clustering trees. Among other features, ETE allows for the independent analysis of tree partitions, has support for the extended newick format, provides an integrated node annotation system and permits to link trees to external data such as multiple sequence alignments or numerical arrays. In addition, ETE implements a number of built-in analytical tools, including phylogeny-based orthology prediction and cluster validation techniques. Finally, ETE's programmable tree drawing engine can be used to automate the graphical rendering of trees with customized node-specific visualizations. Conclusions ETE provides a complete set of methods to manipulate tree data structures that extends current functionality in other bioinformatic toolkits of a more general purpose. ETE is free software and can be downloaded from http://ete.cgenomics.org. PMID:20070885

Guide to NavyFOAM V1.0

DTIC Science & Technology

2011-04-01

NavyFOAM has been developed using an open-source CFD software tool-kit ( OpenFOAM ) that draws heavily upon object-oriented programming. The...numerical methods and the physical models in the original version of OpenFOAM have been upgraded in an effort to improve accuracy and robustness of...computational fluid dynamics OpenFOAM , Object Oriented Programming (OOP) (CFD), NavyFOAM, 16. SECURITY CLASSIFICATION OF: a. REPORT UNCLASSIFIED b

Modeling of microporous silicon betaelectric converter with 63Ni plating in GEANT4 toolkit*

NASA Astrophysics Data System (ADS)

Zelenkov, P. V.; Sidorov, V. G.; Lelekov, E. T.; Khoroshko, A. Y.; Bogdanov, S. V.; Lelekov, A. T.

2016-04-01

The model of electron-hole pairs generation rate distribution in semiconductor is needed to optimize the parameters of microporous silicon betaelectric converter, which uses 63Ni isotope radiation. By using Monte-Carlo methods of GEANT4 software with ultra-low energy electron physics models this distribution in silicon was calculated and approximated with exponential function. Optimal pore configuration was estimated.

A Scalable, Open Source Platform for Data Processing, Archiving and Dissemination

DTIC Science & Technology

2016-01-01

Object Oriented Data Technology (OODT) big data toolkit developed by NASA and the Work-flow INstance Generation and Selection (WINGS) scientific work...to several challenge big data problems and demonstrated the utility of OODT-WINGS in addressing them. Specific demonstrated analyses address i...source software, Apache, Object Oriented Data Technology, OODT, semantic work-flows, WINGS, big data , work- flow management 16. SECURITY CLASSIFICATION OF

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.

A clinical research analytics toolkit for cohort study.

PubMed

Yu, Yiqin; Zhu, Yu; Sun, Xingzhi; Tao, Ying; Zhang, Shuo; Xu, Linhao; Pan, Yue

2012-01-01

This paper presents a clinical informatics toolkit that can assist physicians to conduct cohort studies effectively and efficiently. The toolkit has three key features: 1) support of procedures defined in epidemiology, 2) recommendation of statistical methods in data analysis, and 3) automatic generation of research reports. On one hand, our system can help physicians control research quality by leveraging the integrated knowledge of epidemiology and medical statistics; on the other hand, it can improve productivity by reducing the complexities for physicians during their cohort studies.

UQTk Version 3.0.3 User Manual

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

Sargsyan, Khachik; Safta, Cosmin; Chowdhary, Kamaljit Singh

2017-05-01

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions. Version 3.0.3 offers intrusive and non-intrusive methods for propagating input uncertainties through computational models, tools for sen- sitivity analysis, methods for sparse surrogate construction, and Bayesian inference tools for inferring parameters from experimental data. This manual discusses the download and installation process for UQTk, provides pointers to the UQ methods used in the toolkit, and describes some of the examples provided with the toolkit.

THE EPANET PROGRAMMER'S TOOLKIT FOR ANALYSIS OF WATER DISTRIBUTION SYSTEMS

EPA Science Inventory

The EPANET Programmer's Toolkit is a collection of functions that helps simplify computer programming of water distribution network analyses. the functions can be used to read in a pipe network description file, modify selected component properties, run multiple hydraulic and wa...

New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data

PubMed Central

Gogoshin, Grigoriy; Boerwinkle, Eric

2017-01-01

Abstract Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology—type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types—single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite levels, epidemiological variables, endpoints, and phenotypes, etc. PMID:27681505

New Algorithm and Software (BNOmics) for Inferring and Visualizing Bayesian Networks from Heterogeneous Big Biological and Genetic Data.

PubMed

Gogoshin, Grigoriy; Boerwinkle, Eric; Rodin, Andrei S

2017-04-01

Bayesian network (BN) reconstruction is a prototypical systems biology data analysis approach that has been successfully used to reverse engineer and model networks reflecting different layers of biological organization (ranging from genetic to epigenetic to cellular pathway to metabolomic). It is especially relevant in the context of modern (ongoing and prospective) studies that generate heterogeneous high-throughput omics datasets. However, there are both theoretical and practical obstacles to the seamless application of BN modeling to such big data, including computational inefficiency of optimal BN structure search algorithms, ambiguity in data discretization, mixing data types, imputation and validation, and, in general, limited scalability in both reconstruction and visualization of BNs. To overcome these and other obstacles, we present BNOmics, an improved algorithm and software toolkit for inferring and analyzing BNs from omics datasets. BNOmics aims at comprehensive systems biology-type data exploration, including both generating new biological hypothesis and testing and validating the existing ones. Novel aspects of the algorithm center around increasing scalability and applicability to varying data types (with different explicit and implicit distributional assumptions) within the same analysis framework. An output and visualization interface to widely available graph-rendering software is also included. Three diverse applications are detailed. BNOmics was originally developed in the context of genetic epidemiology data and is being continuously optimized to keep pace with the ever-increasing inflow of available large-scale omics datasets. As such, the software scalability and usability on the less than exotic computer hardware are a priority, as well as the applicability of the algorithm and software to the heterogeneous datasets containing many data types-single-nucleotide polymorphisms and other genetic/epigenetic/transcriptome variables, metabolite levels, epidemiological variables, endpoints, and phenotypes, etc.

artdaq: DAQ software development made simple

NASA Astrophysics Data System (ADS)

Biery, Kurt; Flumerfelt, Eric; Freeman, John; Ketchum, Wesley; Lukhanin, Gennadiy; Rechenmacher, Ron

2017-10-01

For a few years now, the artdaq data acquisition software toolkit has provided numerous experiments with ready-to-use components which allow for rapid development and deployment of DAQ systems. Developed within the Fermilab Scientific Computing Division, artdaq provides data transfer, event building, run control, and event analysis functionality. This latter feature includes built-in support for the art event analysis framework, allowing experiments to run art modules for real-time filtering, compression, disk writing and online monitoring. As art, also developed at Fermilab, is also used for offline analysis, a major advantage of artdaq is that it allows developers to easily switch between developing online and offline software. artdaq continues to be improved. Support for an alternate mode of running whereby data from some subdetector components are only streamed if requested has been added; this option will reduce unnecessary DAQ throughput. Real-time reporting of DAQ metrics has been implemented, along with the flexibility to choose the format through which experiments receive the reports; these formats include the Ganglia, Graphite and syslog software packages, along with flat ASCII files. Additionally, work has been performed investigating more flexible modes of online monitoring, including the capability to run multiple online monitoring processes on different hosts, each running its own set of art modules. Finally, a web-based GUI interface through which users can configure details of their DAQ system has been implemented, increasing the ease of use of the system. Already successfully deployed on the LArlAT, DarkSide-50, DUNE 35ton and Mu2e experiments, artdaq will be employed for SBND and is a strong candidate for use on ICARUS and protoDUNE. With each experiment comes new ideas for how artdaq can be made more flexible and powerful. The above improvements will be described, along with potential ideas for the future.

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

Graf, Norman A.; /SLAC

Maximizing the physics performance of detectors being designed for the International Linear Collider, while remaining sensitive to cost constraints, requires a powerful, efficient, and flexible simulation, reconstruction and analysis environment to study the capabilities of a large number of different detector designs. The preparation of Letters Of Intent for the International Linear Collider involved the detailed study of dozens of detector options, layouts and readout technologies; the final physics benchmarking studies required the reconstruction and analysis of hundreds of millions of events. We describe the Java-based software toolkit (org.lcsim) which was used for full event reconstruction and analysis. The componentsmore » are fully modular and are available for tasks from digitization of tracking detector signals through to cluster finding, pattern recognition, track-fitting, calorimeter clustering, individual particle reconstruction, jet-finding, and analysis. The detector is defined by the same xml input files used for the detector response simulation, ensuring the simulation and reconstruction geometries are always commensurate by construction. We discuss the architecture as well as the performance.« less

The Visualization Toolkit (VTK): Rewriting the rendering code for modern graphics cards

NASA Astrophysics Data System (ADS)

Hanwell, Marcus D.; Martin, Kenneth M.; Chaudhary, Aashish; Avila, Lisa S.

2015-09-01

The Visualization Toolkit (VTK) is an open source, permissively licensed, cross-platform toolkit for scientific data processing, visualization, and data analysis. It is over two decades old, originally developed for a very different graphics card architecture. Modern graphics cards feature fully programmable, highly parallelized architectures with large core counts. VTK's rendering code was rewritten to take advantage of modern graphics cards, maintaining most of the toolkit's programming interfaces. This offers the opportunity to compare the performance of old and new rendering code on the same systems/cards. Significant improvements in rendering speeds and memory footprints mean that scientific data can be visualized in greater detail than ever before. The widespread use of VTK means that these improvements will reap significant benefits.

AutoMicromanager: A microscopy scripting toolkit for LABVIEW and other programming environments

NASA Astrophysics Data System (ADS)

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

AutoMicromanager: a microscopy scripting toolkit for LABVIEW and other programming environments.

PubMed

Ashcroft, Brian Alan; Oosterkamp, Tjerk

2010-11-01

We present a scripting toolkit for the acquisition and analysis of a wide variety of imaging data by integrating the ease of use of various programming environments such as LABVIEW, IGOR PRO, MATLAB, SCILAB, and others. This toolkit is designed to allow the user to quickly program a variety of standard microscopy components for custom microscopy applications allowing much more flexibility than other packages. Included are both programming tools as well as graphical user interface classes allowing a standard, consistent, and easy to maintain scripting environment. This programming toolkit allows easy access to most commonly used cameras, stages, and shutters through the Micromanager project so the scripter can focus on their custom application instead of boilerplate code generation.

ATK-ForceField: a new generation molecular dynamics software package

NASA Astrophysics Data System (ADS)

Schneider, Julian; Hamaekers, Jan; Chill, Samuel T.; Smidstrup, Søren; Bulin, Johannes; Thesen, Ralph; Blom, Anders; Stokbro, Kurt

2017-12-01

ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

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

Sierra Thermal/Fluid Team

SIERRA/Aero is a compressible fluid dynamics program intended to solve a wide variety compressible fluid flows including transonic and hypersonic problems. This document describes the commands for assembling a fluid model for analysis with this module, henceforth referred to simply as Aero for brevity. Aero is an application developed using the SIERRA Toolkit (STK). The intent of STK is to provide a set of tools for handling common tasks that programmers encounter when developing a code for numerical simulation. For example, components of STK provide field allocation and management, and parallel input/output of field and mesh data. These services alsomore » allow the development of coupled mechanics analysis software for a massively parallel computing environment. In the definitions of the commands that follow, the term Real_Max denotes the largest floating point value that can be represented on a given computer. Int_Max is the largest such integer value.« less

Interactive Visualization of Computational Fluid Dynamics using Mosaic

NASA Technical Reports Server (NTRS)

Clucas, Jean; Watson, Velvin; Chancellor, Marisa K. (Technical Monitor)

1994-01-01

The Web provides new Methods for accessing Information world-wide, but the current text-and-pictures approach neither utilizes all the Web's possibilities not provides for its limitations. While the inclusion of pictures and animations in a paper communicates more effectively than text alone, It Is essentially an extension of the concept of "publication." Also, as use of the Web increases putting images and animations online will quickly load even the "Information Superhighway." We need to find forms of communication that take advantage of the special nature of the Web. This paper presents one approach: the use of the Internet and the Mosaic interface for data sharing and collaborative analysis. We will describe (and In the presentation, demonstrate) our approach: using FAST (Flow Analysis Software Toolkit), a scientific visualization package, as a data viewer and interactive tool called from MOSAIC. Our intent is to stimulate the development of other tools that utilize the unique nature of electronic communication.

Creating Centralized Reporting for Microsoft Host Protection Technologies:The Enhanced Mitigation Experience Toolkit (EMET)

DTIC Science & Technology

2016-08-11

INSTITUTE | CARNEGIE MELLON UNIVERSITY [Distribution Statement A] This material has been approved for public release and unlimited distribution...Copyright 2016 Carnegie Mellon University This material is based upon work funded and supported by the Department of Defense under Contract No. FA8721...05-C-0003 with Carnegie Mellon University for the operation of the Software Engineer- ing Institute, a federally funded research and development

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

Jonathan Helmus, Scott Collis

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

Microscopic Simulations of Charge Transport in Disordered Organic Semiconductors

PubMed Central

2011-01-01

Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor. PMID:22076120

Development of an educational 'toolkit' for health professionals and their patients with prediabetes: the WAKEUP study (Ways of Addressing Knowledge Education and Understanding in Pre-diabetes).

PubMed

Evans, P H; Greaves, C; Winder, R; Fearn-Smith, J; Campbell, J L

2007-07-01

To identify key messages about pre-diabetes and to design, develop and pilot an educational toolkit to address the information needs of patients and health professionals. Mixed qualitative methodology within an action research framework. Focus group interviews with patients and health professionals and discussion with an expert reference group aimed to identify the important messages and produce a draft toolkit. Two action research cycles were then conducted in two general practices, during which the draft toolkit was used and video-taped consultations and follow-up patient interviews provided further data. Framework analysis techniques were used to examine the data and to elicit action points for improving the toolkit. The key messages about pre-diabetes concerned the seriousness of the condition, the preventability of progression to diabetes, and the need for lifestyle change. As well as feedback on the acceptability and use of the toolkit, four main themes were identified in the data: knowledge and education needs (of both patients and health professionals); communicating knowledge and motivating change; redesign of practice systems to support pre-diabetes management and the role of the health professional. The toolkit we developed was found to be an acceptable and useful resource for both patients and health practitioners. Three key messages about pre-diabetes were identified. A toolkit of information materials for patients with pre-diabetes and the health professionals and ideas for improving practice systems for managing pre-diabetes were developed and successfully piloted. Further work is needed to establish the best mode of delivery of the WAKEUP toolkit.

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

NASA Astrophysics Data System (ADS)

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

2010-12-01

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

Robust Requirements Tracing via Internet Search Technology: Improving an IV and V Technique. Phase 2

NASA Technical Reports Server (NTRS)

Hayes, Jane; Dekhtyar, Alex

2004-01-01

There are three major objectives to this phase of the work. (1) Improvement of Information Retrieval (IR) methods for Independent Verification and Validation (IV&V) requirements tracing. Information Retrieval methods are typically developed for very large (order of millions - tens of millions and more documents) document collections and therefore, most successfully used methods somewhat sacrifice precision and recall in order to achieve efficiency. At the same time typical IR systems treat all user queries as independent of each other and assume that relevance of documents to queries is subjective for each user. The IV&V requirements tracing problem has a much smaller data set to operate on, even for large software development projects; the set of queries is predetermined by the high-level specification document and individual requirements considered as query input to IR methods are not necessarily independent from each other. Namely, knowledge about the links for one requirement may be helpful in determining the links of another requirement. Finally, while the final decision on the exact form of the traceability matrix still belongs to the IV&V analyst, his/her decisions are much less arbitrary than those of an Internet search engine user. All this suggests that the information available to us in the framework of the IV&V tracing problem can be successfully leveraged to enhance standard IR techniques, which in turn would lead to increased recall and precision. We developed several new methods during Phase II; (2) IV&V requirements tracing IR toolkit. Based on the methods developed in Phase I and their improvements developed in Phase II, we built a toolkit of IR methods for IV&V requirements tracing. The toolkit has been integrated, at the data level, with SAIC's SuperTracePlus (STP) tool; (3) Toolkit testing. We tested the methods included in the IV&V requirements tracing IR toolkit on a number of projects.

chemf: A purely functional chemistry toolkit.

PubMed

Höck, Stefan; Riedl, Rainer

2012-12-20

Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project.

chemf: A purely functional chemistry toolkit

PubMed Central

2012-01-01

Background Although programming in a type-safe and referentially transparent style offers several advantages over working with mutable data structures and side effects, this style of programming has not seen much use in chemistry-related software. Since functional programming languages were designed with referential transparency in mind, these languages offer a lot of support when writing immutable data structures and side-effects free code. We therefore started implementing our own toolkit based on the above programming paradigms in a modern, versatile programming language. Results We present our initial results with functional programming in chemistry by first describing an immutable data structure for molecular graphs together with a couple of simple algorithms to calculate basic molecular properties before writing a complete SMILES parser in accordance with the OpenSMILES specification. Along the way we show how to deal with input validation, error handling, bulk operations, and parallelization in a purely functional way. At the end we also analyze and improve our algorithms and data structures in terms of performance and compare it to existing toolkits both object-oriented and purely functional. All code was written in Scala, a modern multi-paradigm programming language with a strong support for functional programming and a highly sophisticated type system. Conclusions We have successfully made the first important steps towards a purely functional chemistry toolkit. The data structures and algorithms presented in this article perform well while at the same time they can be safely used in parallelized applications, such as computer aided drug design experiments, without further adjustments. This stands in contrast to existing object-oriented toolkits where thread safety of data structures and algorithms is a deliberate design decision that can be hard to implement. Finally, the level of type-safety achieved by Scala highly increased the reliability of our code as well as the productivity of the programmers involved in this project. PMID:23253942

Big Data in HEP: A comprehensive use case study

NASA Astrophysics Data System (ADS)

Gutsche, Oliver; Cremonesi, Matteo; Elmer, Peter; Jayatilaka, Bo; Kowalkowski, Jim; Pivarski, Jim; Sehrish, Saba; Mantilla Surez, Cristina; Svyatkovskiy, Alexey; Tran, Nhan

2017-10-01

Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems collectively called Big Data technologies have emerged to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and promise a fresh look at analysis of very large datasets and could potentially reduce the time-to-physics with increased interactivity. In this talk, we present an active LHC Run 2 analysis, searching for dark matter with the CMS detector, as a testbed for Big Data technologies. We directly compare the traditional NTuple-based analysis with an equivalent analysis using Apache Spark on the Hadoop ecosystem and beyond. In both cases, we start the analysis with the official experiment data formats and produce publication physics plots. We will discuss advantages and disadvantages of each approach and give an outlook on further studies needed.

Searching social networks for subgraph patterns

NASA Astrophysics Data System (ADS)

Ogaard, Kirk; Kase, Sue; Roy, Heather; Nagi, Rakesh; Sambhoos, Kedar; Sudit, Moises

2013-06-01

Software tools for Social Network Analysis (SNA) are being developed which support various types of analysis of social networks extracted from social media websites (e.g., Twitter). Once extracted and stored in a database such social networks are amenable to analysis by SNA software. This data analysis often involves searching for occurrences of various subgraph patterns (i.e., graphical representations of entities and relationships). The authors have developed the Graph Matching Toolkit (GMT) which provides an intuitive Graphical User Interface (GUI) for a heuristic graph matching algorithm called the Truncated Search Tree (TruST) algorithm. GMT is a visual interface for graph matching algorithms processing large social networks. GMT enables an analyst to draw a subgraph pattern by using a mouse to select categories and labels for nodes and links from drop-down menus. GMT then executes the TruST algorithm to find the top five occurrences of the subgraph pattern within the social network stored in the database. GMT was tested using a simulated counter-insurgency dataset consisting of cellular phone communications within a populated area of operations in Iraq. The results indicated GMT (when executing the TruST graph matching algorithm) is a time-efficient approach to searching large social networks. GMT's visual interface to a graph matching algorithm enables intelligence analysts to quickly analyze and summarize the large amounts of data necessary to produce actionable intelligence.

FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET

PubMed Central

Lerner, Eitan; Chung, SangYoon; Weiss, Shimon; Michalet, Xavier

2016-01-01

Single-molecule Förster Resonance Energy Transfer (smFRET) allows probing intermolecular interactions and conformational changes in biomacromolecules, and represents an invaluable tool for studying cellular processes at the molecular scale. smFRET experiments can detect the distance between two fluorescent labels (donor and acceptor) in the 3-10 nm range. In the commonly employed confocal geometry, molecules are free to diffuse in solution. When a molecule traverses the excitation volume, it emits a burst of photons, which can be detected by single-photon avalanche diode (SPAD) detectors. The intensities of donor and acceptor fluorescence can then be related to the distance between the two fluorophores. While recent years have seen a growing number of contributions proposing improvements or new techniques in smFRET data analysis, rarely have those publications been accompanied by software implementation. In particular, despite the widespread application of smFRET, no complete software package for smFRET burst analysis is freely available to date. In this paper, we introduce FRETBursts, an open source software for analysis of freely-diffusing smFRET data. FRETBursts allows executing all the fundamental steps of smFRET bursts analysis using state-of-the-art as well as novel techniques, while providing an open, robust and well-documented implementation. Therefore, FRETBursts represents an ideal platform for comparison and development of new methods in burst analysis. We employ modern software engineering principles in order to minimize bugs and facilitate long-term maintainability. Furthermore, we place a strong focus on reproducibility by relying on Jupyter notebooks for FRETBursts execution. Notebooks are executable documents capturing all the steps of the analysis (including data files, input parameters, and results) and can be easily shared to replicate complete smFRET analyzes. Notebooks allow beginners to execute complex workflows and advanced users to customize the analysis for their own needs. By bundling analysis description, code and results in a single document, FRETBursts allows to seamless share analysis workflows and results, encourages reproducibility and facilitates collaboration among researchers in the single-molecule community. PMID:27532626

Tank Information System (tis): a Case Study in Migrating Web Mapping Application from Flex to Dojo for Arcgis Server and then to Open Source

NASA Astrophysics Data System (ADS)

Pulsani, B. R.

2017-11-01

Tank Information System is a web application which provides comprehensive information about minor irrigation tanks of Telangana State. As part of the program, a web mapping application using Flex and ArcGIS server was developed to make the data available to the public. In course of time as Flex be-came outdated, a migration of the client interface to the latest JavaScript based technologies was carried out. Initially, the Flex based application was migrated to ArcGIS JavaScript API using Dojo Toolkit. Both the client applications used published services from ArcGIS server. To check the migration pattern from proprietary to open source, the JavaScript based ArcGIS application was later migrated to OpenLayers and Dojo Toolkit which used published service from GeoServer. The migration pattern noticed in the study especially emphasizes upon the use of Dojo Toolkit and PostgreSQL database for ArcGIS server so that migration to open source could be performed effortlessly. The current ap-plication provides a case in study which could assist organizations in migrating their proprietary based ArcGIS web applications to open source. Furthermore, the study reveals cost benefits of adopting open source against commercial software's.

New Additions to the Toolkit for Forward/Inverse Problems in Electrocardiography within the SCIRun Problem Solving Environment.

PubMed

Coll-Font, Jaume; Burton, Brett M; Tate, Jess D; Erem, Burak; Swenson, Darrel J; Wang, Dafang; Brooks, Dana H; van Dam, Peter; Macleod, Rob S

2014-09-01

Cardiac electrical imaging often requires the examination of different forward and inverse problem formulations based on mathematical and numerical approximations of the underlying source and the intervening volume conductor that can generate the associated voltages on the surface of the body. If the goal is to recover the source on the heart from body surface potentials, the solution strategy must include numerical techniques that can incorporate appropriate constraints and recover useful solutions, even though the problem is badly posed. Creating complete software solutions to such problems is a daunting undertaking. In order to make such tools more accessible to a broad array of researchers, the Center for Integrative Biomedical Computing (CIBC) has made an ECG forward/inverse toolkit available within the open source SCIRun system. Here we report on three new methods added to the inverse suite of the toolkit. These new algorithms, namely a Total Variation method, a non-decreasing TMP inverse and a spline-based inverse, consist of two inverse methods that take advantage of the temporal structure of the heart potentials and one that leverages the spatial characteristics of the transmembrane potentials. These three methods further expand the possibilities of researchers in cardiology to explore and compare solutions to their particular imaging problem.

A Dose of Reality: Radiation Analysis for Realistic Human Spacecraft

NASA Technical Reports Server (NTRS)

Barzilla, J. E.; Lee, K. T.

2017-01-01

INTRODUCTION As with most computational analyses, a tradeoff exists between problem complexity, resource availability and response accuracy when modeling radiation transport from the source to a detector. The largest amount of analyst time for setting up an analysis is often spent ensuring that any simplifications made have minimal impact on the results. The vehicle shield geometry of interest is typically simplified from the original CAD design in order to reduce computation time, but this simplification requires the analyst to "re-draw" the geometry with a limited set of volumes in order to accommodate a specific radiation transport software package. The resulting low-fidelity geometry model cannot be shared with or compared to other radiation transport software packages, and the process can be error prone with increased model complexity. The work presented here demonstrates the use of the DAGMC (Direct Accelerated Geometry for Monte Carlo) Toolkit from the University of Wisconsin, to model the impacts of several space radiation sources on a CAD drawing of the US Lab module. METHODS The DAGMC toolkit workflow begins with the export of an existing CAD geometry from the native CAD to the ACIS format. The ACIS format file is then cleaned using SpaceClaim to remove small holes and component overlaps. Metadata is then assigned to the cleaned geometry file using CUBIT/Trelis from csimsoft (Registered Trademark). The DAGMC plugin script removes duplicate shared surfaces, facets the geometry to a specified tolerance, and ensures that the faceted geometry is water tight. This step also writes the material and scoring information to a standard input file format that the analyst can alter as desired prior to running the radiation transport program. The scoring results can be transformed, via python script, into a 3D format that is viewable in a standard graphics program. RESULTS The CAD model of the US Lab module of the International Space Station, inclusive of all the racks and components, was simplified to remove holes and volume overlaps. Problematic features within the drawing were also removed or repaired to prevent runtime issues. The cleaned drawing was then run through the DAGMC workflow to prepare for analysis. Pilot tests modeling transport of 1GeV proton and 800MeV/A oxygen sources show that reasonable results are converged upon in an acceptable amount of overall computation time from drawing preparation to data analysis. The FLUKA radiation transport code will next be used to model both a GCR and a trapped radiation source. These results will then be compared with measurements that have been made by the radiation instrumentation deployed inside the US Lab module. DISCUSSION Early analyses have indicated that the DAGMC workflow is a promising toolkit for running vehicle geometries of interest to NASA through multiple radiation transport codes. In addition, recent work has shown that a realistic human phantom, provided via a subcontract with the University of Florida, can be placed inside any vehicle geometry for a combinatorial analysis. This added functionality gives the user the ability to score various parameters at the organ level, and the results can then be used as input for cancer risk models.

[Central online quality assurance in radiology: an IT solution exemplified by the German Breast Cancer Screening Program].

PubMed

Czwoydzinski, J; Girnus, R; Sommer, A; Heindel, W; Lenzen, H

2011-09-01

Physical-technical quality assurance is one of the essential tasks of the National Reference Centers in the German Breast Cancer Screening Program. For this purpose the mammography units are required to transfer the measured values of the constancy tests on a daily basis and all phantom images created for this purpose on a weekly basis to the reference centers. This is a serious logistical challenge. To meet these requirements, we developed an innovative software tool. By the end of 2005, we had already developed web-based software (MammoControl) allowing the transmission of constancy test results via entry forms. For automatic analysis and transmission of the phantom images, we then introduced an extension (MammoControl DIANA). This was based on Java, Java Web Start, the NetBeans Rich Client Platform, the Pixelmed Java DICOM Toolkit and the ImageJ library. MammoControl DIANA was designed to run locally in the mammography units. This allows automated on-site image analysis. Both results and compressed images can then be transmitted to the reference center. We developed analysis modules for the daily and monthly consistency tests and additionally for a homogeneity test. The software we developed facilitates the immediate availability of measurement results, phantom images, and DICOM header data in all reference centers. This allows both targeted guidance and short response time in the case of errors. We achieved a consistent IT-based evaluation with standardized tools for the entire screening program in Germany. © Georg Thieme Verlag KG Stuttgart · New York.

Visualization Software for VisIT Java Client

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

Billings, Jay Jay; Smith, Robert W

The VisIT Java Client (JVC) library is a lightweight thin client that is designed and written purely in the native language of Java (the Python & JavaScript versions of the library use the same concept) and communicates with any new unmodified standalone version of VisIT, a high performance computing parallel visualization toolkit, over traditional or web sockets and dynamically determines capabilities of the running VisIT instance whether local or remote.

A Python Interface for the Dakota Iterative Systems Analysis Toolkit

NASA Astrophysics Data System (ADS)

Piper, M.; Hutton, E.; Syvitski, J. P.

2016-12-01

Uncertainty quantification is required to improve the accuracy, reliability, and accountability of Earth science models. Dakota is a software toolkit, developed at Sandia National Laboratories, that provides an interface between models and a library of analysis methods, including support for sensitivity analysis, uncertainty quantification, optimization, and calibration techniques. Dakota is a powerful tool, but its learning curve is steep: the user not only must understand the structure and syntax of the Dakota input file, but also must develop intermediate code, called an analysis driver, that allows Dakota to run a model. The CSDMS Dakota interface (CDI) is a Python package that wraps and extends Dakota's user interface. It simplifies the process of configuring and running a Dakota experiment. A user can program to the CDI, allowing a Dakota experiment to be scripted. The CDI creates Dakota input files and provides a generic analysis driver. Any model written in Python that exposes a Basic Model Interface (BMI), as well as any model componentized in the CSDMS modeling framework, automatically works with the CDI. The CDI has a plugin architecture, so models written in other languages, or those that don't expose a BMI, can be accessed by the CDI by programmatically extending a template; an example is provided in the CDI distribution. Currently, six Dakota analysis methods have been implemented for examples from the much larger Dakota library. To demonstrate the CDI, we performed an uncertainty quantification experiment with the HydroTrend hydrological water balance and transport model. In the experiment, we evaluated the response of long-term suspended sediment load at the river mouth (Qs) to uncertainty in two input parameters, annual mean temperature (T) and precipitation (P), over a series of 100-year runs, using the polynomial chaos method. Through Dakota, we calculated moments, local and global (Sobol') sensitivity indices, and probability density and cumulative distribution functions for the response.

Lessons about Virtual-Environment Software Systems from 20 years of VE building

PubMed Central

Taylor, Russell M.; Jerald, Jason; VanderKnyff, Chris; Wendt, Jeremy; Borland, David; Marshburn, David; Sherman, William R.; Whitton, Mary C.

2010-01-01

What are desirable and undesirable features of virtual-environment (VE) software architectures? What should be present (and absent) from such systems if they are to be optimally useful? How should they be structured? To help answer these questions we present experience from application designers, toolkit designers, and VE system architects along with examples of useful features from existing systems. Topics are organized under the major headings of: 3D space management, supporting display hardware, interaction, event management, time management, computation, portability, and the observation that less can be better. Lessons learned are presented as discussion of the issues, field experiences, nuggets of knowledge, and case studies. PMID:20567602

ASERA: A Spectrum Eye Recognition Assistant

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2018-04-01

ASERA, ASpectrum Eye Recognition Assistant, aids in quasar spectral recognition and redshift measurement and can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). This interactive software allows users to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. ASERA is an efficient and user-friendly semi-automated toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope) and is available as a standalone Java application and as a Java applet. The software offers several functions, including wavelength and flux scale settings, zoom in and out, redshift estimation, and spectral line identification.

A comparative study of gamma-ray interaction and absorption in some building materials using Zeff-toolkit

NASA Astrophysics Data System (ADS)

Mann, Kulwinder Singh; Heer, Manmohan Singh; Rani, Asha

2016-07-01

The gamma-ray shielding behaviour of a material can be investigated by determining its various interaction and energy-absorption parameters (such as mass attenuation coefficients, mass energy absorption coefficients, and corresponding effective atomic numbers and electron densities). Literature review indicates that the effective atomic number (Zeff) has been used as extensive parameters for evaluating the effects and defect in the chosen materials caused by ionising radiations (X-rays and gamma-rays). A computer program (Zeff-toolkit) has been designed for obtaining the mean value of effective atomic number calculated by three different methods. A good agreement between the results obtained with Zeff-toolkit, Auto_Zeff software and experimentally measured values of Zeff has been observed. Although the Zeff-toolkit is capable of computing effective atomic numbers for both photon interaction (Zeff,PI) and energy absorption (Zeff,En) using three methods in each. No similar computer program is available in the literature which simultaneously computes these parameters simultaneously. The computed parameters have been compared and correlated in the wide energy range (0.001-20 MeV) for 10 commonly used building materials. The prominent variations in these parameters with gamma-ray photon energy have been observed due to the dominance of various absorption and scattering phenomena. The mean values of two effective atomic numbers (Zeff,PI and Zeff,En) are equivalent at energies below 0.002 MeV and above 0.3 MeV, indicating the dominance of gamma-ray absorption (photoelectric and pair production) over scattering (Compton) at these energies. Conversely in the energy range 0.002-0.3 MeV, the Compton scattering of gamma-rays dominates the absorption. From the 10 chosen samples of building materials, 2 soils showed better shielding behaviour than did other 8 materials.

PAGANI Toolkit: Parallel graph-theoretical analysis package for brain network big data.

PubMed

Du, Haixiao; Xia, Mingrui; Zhao, Kang; Liao, Xuhong; Yang, Huazhong; Wang, Yu; He, Yong

2018-05-01

The recent collection of unprecedented quantities of neuroimaging data with high spatial resolution has led to brain network big data. However, a toolkit for fast and scalable computational solutions is still lacking. Here, we developed the PArallel Graph-theoretical ANalysIs (PAGANI) Toolkit based on a hybrid central processing unit-graphics processing unit (CPU-GPU) framework with a graphical user interface to facilitate the mapping and characterization of high-resolution brain networks. Specifically, the toolkit provides flexible parameters for users to customize computations of graph metrics in brain network analyses. As an empirical example, the PAGANI Toolkit was applied to individual voxel-based brain networks with ∼200,000 nodes that were derived from a resting-state fMRI dataset of 624 healthy young adults from the Human Connectome Project. Using a personal computer, this toolbox completed all computations in ∼27 h for one subject, which is markedly less than the 118 h required with a single-thread implementation. The voxel-based functional brain networks exhibited prominent small-world characteristics and densely connected hubs, which were mainly located in the medial and lateral fronto-parietal cortices. Moreover, the female group had significantly higher modularity and nodal betweenness centrality mainly in the medial/lateral fronto-parietal and occipital cortices than the male group. Significant correlations between the intelligence quotient and nodal metrics were also observed in several frontal regions. Collectively, the PAGANI Toolkit shows high computational performance and good scalability for analyzing connectome big data and provides a friendly interface without the complicated configuration of computing environments, thereby facilitating high-resolution connectomics research in health and disease. © 2018 Wiley Periodicals, Inc.

Visualization techniques to aid in the analysis of multi-spectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, Edward W.; Domik, Gitta O.; Ayres, Thomas R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions, and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists.

GRO/EGRET data analysis software: An integrated system of custom and commercial software using standard interfaces

NASA Technical Reports Server (NTRS)

Laubenthal, N. A.; Bertsch, D.; Lal, N.; Etienne, A.; Mcdonald, L.; Mattox, J.; Sreekumar, P.; Nolan, P.; Fierro, J.

1992-01-01

The Energetic Gamma Ray Telescope Experiment (EGRET) on the Compton Gamma Ray Observatory has been in orbit for more than a year and is being used to map the full sky for gamma rays in a wide energy range from 30 to 20,000 MeV. Already these measurements have resulted in a wide range of exciting new information on quasars, pulsars, galactic sources, and diffuse gamma ray emission. The central part of the analysis is done with sky maps that typically cover an 80 x 80 degree section of the sky for an exposure time of several days. Specific software developed for this program generates the counts, exposure, and intensity maps. The analysis is done on a network of UNIX based workstations and takes full advantage of a custom-built user interface called X-dialog. The maps that are generated are stored in the FITS format for a collection of energies. These, along with similar diffuse emission background maps generated from a model calculation, serve as input to a maximum likelihood program that produces maps of likelihood with optional contours that are used to evaluate regions for sources. Likelihood also evaluates the background corrected intensity at each location for each energy interval from which spectra can be generated. Being in a standard FITS format permits all of the maps to be easily accessed by the full complement of tools available in several commercial astronomical analysis systems. In the EGRET case, IDL is used to produce graphics plots in two and three dimensions and to quickly implement any special evaluation that might be desired. Other custom-built software, such as the spectral and pulsar analyses, take advantage of the XView toolkit for display and Postscript output for the color hard copy. This poster paper outlines the data flow and provides examples of the user interfaces and output products. It stresses the advantages that are derived from the integration of the specific instrument-unique software and powerful commercial tools for graphics and statistical evaluation. This approach has several proven advantages including flexibility, a minimum of development effort, ease of use, and portability.

Literature Review on Systems of Systems (SoS): A Methodology With Preliminary Results

DTIC Science & Technology

2013-11-01

Appendix H. The Enhanced ISAAC Neural Simulation Toolkit (EINSTein) 73  Appendix I. The Map Aware Nonuniform Automata (MANA) Agent-Based Model 81...83  Figure I-3. Quadrant chart addressing SoS and associated SoSA designs for the Map Aware Nonuniform Automata (MANA) agent...Map Aware Nonuniform Automata (MANA) agent-based model. 85  Table I-2. SoS and SoSA software component maturation scores associated with the Map

Fluorescence Behavioral Imaging (FBI) Tracks Identity in Heterogeneous Groups of Drosophila

PubMed Central

Ramdya, Pavan; Schaffter, Thomas; Floreano, Dario; Benton, Richard

2012-01-01

Distinguishing subpopulations in group behavioral experiments can reveal the impact of differences in genetic, pharmacological and life-histories on social interactions and decision-making. Here we describe Fluorescence Behavioral Imaging (FBI), a toolkit that uses transgenic fluorescence to discriminate subpopulations, imaging hardware that simultaneously records behavior and fluorescence expression, and open-source software for automated, high-accuracy determination of genetic identity. Using FBI, we measure courtship partner choice in genetically mixed groups of Drosophila. PMID:23144871

Fluorescence behavioral imaging (FBI) tracks identity in heterogeneous groups of Drosophila.

PubMed

Ramdya, Pavan; Schaffter, Thomas; Floreano, Dario; Benton, Richard

2012-01-01

Distinguishing subpopulations in group behavioral experiments can reveal the impact of differences in genetic, pharmacological and life-histories on social interactions and decision-making. Here we describe Fluorescence Behavioral Imaging (FBI), a toolkit that uses transgenic fluorescence to discriminate subpopulations, imaging hardware that simultaneously records behavior and fluorescence expression, and open-source software for automated, high-accuracy determination of genetic identity. Using FBI, we measure courtship partner choice in genetically mixed groups of Drosophila.

Continuous Energy Photon Transport Implementation in MCATK

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

Adams, Terry R.; Trahan, Travis John; Sweezy, Jeremy Ed

2016-10-31

The Monte Carlo Application ToolKit (MCATK) code development team has implemented Monte Carlo photon transport into the MCATK software suite. The current particle transport capabilities in MCATK, which process the tracking and collision physics, have been extended to enable tracking of photons using the same continuous energy approximation. We describe the four photoatomic processes implemented, which are coherent scattering, incoherent scattering, pair-production, and photoelectric absorption. The accompanying background, implementation, and verification of these processes will be presented.

Solar Sail Spaceflight Simulation

NASA Technical Reports Server (NTRS)

Lisano, Michael; Evans, James; Ellis, Jordan; Schimmels, John; Roberts, Timothy; Rios-Reyes, Leonel; Scheeres, Daniel; Bladt, Jeff; Lawrence, Dale; Piggott, Scott

2007-01-01

The Solar Sail Spaceflight Simulation Software (S5) toolkit provides solar-sail designers with an integrated environment for designing optimal solar-sail trajectories, and then studying the attitude dynamics/control, navigation, and trajectory control/correction of sails during realistic mission simulations. Unique features include a high-fidelity solar radiation pressure model suitable for arbitrarily-shaped solar sails, a solar-sail trajectory optimizer, capability to develop solar-sail navigation filter simulations, solar-sail attitude control models, and solar-sail high-fidelity force models.

Python Open source Waveform ExtractoR (POWER): an open source, Python package to monitor and post-process numerical relativity simulations

NASA Astrophysics Data System (ADS)

Johnson, Daniel; Huerta, E. A.; Haas, Roland

2018-01-01

Numerical simulations of Einstein’s field equations provide unique insights into the physics of compact objects moving at relativistic speeds, and which are driven by strong gravitational interactions. Numerical relativity has played a key role to firmly establish gravitational wave astrophysics as a new field of research, and it is now paving the way to establish whether gravitational wave radiation emitted from compact binary mergers is accompanied by electromagnetic and astro-particle counterparts. As numerical relativity continues to blend in with routine gravitational wave data analyses to validate the discovery of gravitational wave events, it is essential to develop open source tools to streamline these studies. Motivated by our own experience as users and developers of the open source, community software, the Einstein Toolkit, we present an open source, Python package that is ideally suited to monitor and post-process the data products of numerical relativity simulations, and compute the gravitational wave strain at future null infinity in high performance environments. We showcase the application of this new package to post-process a large numerical relativity catalog and extract higher-order waveform modes from numerical relativity simulations of eccentric binary black hole mergers and neutron star mergers. This new software fills a critical void in the arsenal of tools provided by the Einstein Toolkit consortium to the numerical relativity community.

RGG: A general GUI Framework for R scripts

PubMed Central

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

2009-01-01

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

Update of GRASP/Ada reverse engineering tools for Ada

NASA Technical Reports Server (NTRS)

Cross, James H., II

1992-01-01

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

The Nuclear Energy Advanced Modeling and Simulation Safeguards and Separations Reprocessing Plant Toolkit

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

McCaskey, Alex; Billings, Jay Jay; de Almeida, Valmor F

2011-08-01

This report details the progress made in the development of the Reprocessing Plant Toolkit (RPTk) for the DOE Nuclear Energy Advanced Modeling and Simulation (NEAMS) program. RPTk is an ongoing development effort intended to provide users with an extensible, integrated, and scalable software framework for the modeling and simulation of spent nuclear fuel reprocessing plants by enabling the insertion and coupling of user-developed physicochemical modules of variable fidelity. The NEAMS Safeguards and Separations IPSC (SafeSeps) and the Enabling Computational Technologies (ECT) supporting program element have partnered to release an initial version of the RPTk with a focus on software usabilitymore » and utility. RPTk implements a data flow architecture that is the source of the system's extensibility and scalability. Data flows through physicochemical modules sequentially, with each module importing data, evolving it, and exporting the updated data to the next downstream module. This is accomplished through various architectural abstractions designed to give RPTk true plug-and-play capabilities. A simple application of this architecture, as well as RPTk data flow and evolution, is demonstrated in Section 6 with an application consisting of two coupled physicochemical modules. The remaining sections describe this ongoing work in full, from system vision and design inception to full implementation. Section 3 describes the relevant software development processes used by the RPTk development team. These processes allow the team to manage system complexity and ensure stakeholder satisfaction. This section also details the work done on the RPTk ``black box'' and ``white box'' models, with a special focus on the separation of concerns between the RPTk user interface and application runtime. Section 4 and 5 discuss that application runtime component in more detail, and describe the dependencies, behavior, and rigorous testing of its constituent components.« less

Modular preoperative planning software for computer-aided oral implantology and the application of a novel stereolithographic template: a pilot study.

PubMed

Chen, Xiaojun; Yuan, Jianbing; Wang, Chengtao; Huang, Yuanliang; Kang, Lu

2010-09-01

In the field of oral implantology, there is a trend toward computer-aided implant surgery, especially the application of computerized tomography (CT)-derived surgical templates. However, because of relatively unsatisfactory match between the templates and receptor sites, conventional surgical templates may not be accurate enough for the severely resorbed edentulous cases during the procedure of transferring the preoperative plan to the actual surgery. The purpose of this study is to introduce a novel bone-tooth-combined-supported surgical guide, which is designed by utilizing a special modular software and fabricated via stereolithography technique using both laser scanning and CT imaging, thus improving the fit accuracy and reliability. A modular preoperative planning software was developed for computer-aided oral implantology. With the introduction of dynamic link libraries and some well-known free, open-source software libraries such as Visualization Toolkit (Kitware, Inc., New York, USA) and Insight Toolkit (Kitware, Inc.) a plug-in evolutive software architecture was established, allowing for expandability, accessibility, and maintainability in our system. To provide a link between the preoperative plan and the actual surgery, a novel bone-tooth-combined-supported surgical template was fabricated, utilizing laser scanning, image registration, and rapid prototyping. Clinical studies were conducted on four partially edentulous cases to make a comparison with the conventional bone-supported templates. The fixation was more stable than tooth-supported templates because laser scanning technology obtained detailed dentition information, which brought about the unique topography between the match surface of the templates and the adjacent teeth. The average distance deviations at the coronal and apical point of the implant were 0.66 mm (range: 0.3-1.2) and 0.86 mm (range: 0.4-1.2), and the average angle deviation was 1.84 degrees (range: 0.6-2.8 degrees ). This pilot study proves that the novel combined-supported templates are superior to the conventional ones. However, more clinical cases will be conducted to demonstrate their feasibility and reliability.

MOlecular MAterials Property Prediction Package (MOMAP) 1.0: a software package for predicting the luminescent properties and mobility of organic functional materials

NASA Astrophysics Data System (ADS)

Niu, Yingli; Li, Wenqiang; Peng, Qian; Geng, Hua; Yi, Yuanping; Wang, Linjun; Nan, Guangjun; Wang, Dong; Shuai, Zhigang

2018-04-01

MOlecular MAterials Property Prediction Package (MOMAP) is a software toolkit for molecular materials property prediction. It focuses on luminescent properties and charge mobility properties. This article contains a brief descriptive introduction of key features, theoretical models and algorithms of the software, together with examples that illustrate the performance. First, we present the theoretical models and algorithms for molecular luminescent properties calculation, which includes the excited-state radiative/non-radiative decay rate constant and the optical spectra. Then, a multi-scale simulation approach and its algorithm for the molecular charge mobility are described. This approach is based on hopping model and combines with Kinetic Monte Carlo and molecular dynamics simulations, and it is especially applicable for describing a large category of organic semiconductors, whose inter-molecular electronic coupling is much smaller than intra-molecular charge reorganisation energy.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

GCView: the genomic context viewer for protein homology searches

PubMed Central

Grin, Iwan; Linke, Dirk

2011-01-01

Genomic neighborhood can provide important insights into evolution and function of a protein or gene. When looking at operons, changes in operon structure and composition can only be revealed by looking at the operon as a whole. To facilitate the analysis of the genomic context of a query in multiple organisms we have developed Genomic Context Viewer (GCView). GCView accepts results from one or multiple protein homology searches such as BLASTp as input. For each hit, the neighboring protein-coding genes are extracted, the regions of homology are labeled for each input and the results are presented as a clear, interactive graphical output. It is also possible to add more searches to iteratively refine the output. GCView groups outputs by the hits for different proteins. This allows for easy comparison of different operon compositions and structures. The tool is embedded in the framework of the Bioinformatics Toolkit of the Max-Planck Institute for Developmental Biology (MPI Toolkit). Job results from the homology search tools inside the MPI Toolkit can be forwarded to GCView and results can be subsequently analyzed by sequence analysis tools. Results are stored online, allowing for later reinspection. GCView is freely available at http://toolkit.tuebingen.mpg.de/gcview. PMID:21609955

PEA: an integrated R toolkit for plant epitranscriptome analysis.

PubMed

Zhai, Jingjing; Song, Jie; Cheng, Qian; Tang, Yunjia; Ma, Chuang

2018-05-29

The epitranscriptome, also known as chemical modifications of RNA (CMRs), is a newly discovered layer of gene regulation, the biological importance of which emerged through analysis of only a small fraction of CMRs detected by high-throughput sequencing technologies. Understanding of the epitranscriptome is hampered by the absence of computational tools for the systematic analysis of epitranscriptome sequencing data. In addition, no tools have yet been designed for accurate prediction of CMRs in plants, or to extend epitranscriptome analysis from a fraction of the transcriptome to its entirety. Here, we introduce PEA, an integrated R toolkit to facilitate the analysis of plant epitranscriptome data. The PEA toolkit contains a comprehensive collection of functions required for read mapping, CMR calling, motif scanning and discovery, and gene functional enrichment analysis. PEA also takes advantage of machine learning technologies for transcriptome-scale CMR prediction, with high prediction accuracy, using the Positive Samples Only Learning algorithm, which addresses the two-class classification problem by using only positive samples (CMRs), in the absence of negative samples (non-CMRs). Hence PEA is a versatile epitranscriptome analysis pipeline covering CMR calling, prediction, and annotation, and we describe its application to predict N6-methyladenosine (m6A) modifications in Arabidopsis thaliana. Experimental results demonstrate that the toolkit achieved 71.6% sensitivity and 73.7% specificity, which is superior to existing m6A predictors. PEA is potentially broadly applicable to the in-depth study of epitranscriptomics. PEA Docker image is available at https://hub.docker.com/r/malab/pea, source codes and user manual are available at https://github.com/cma2015/PEA. chuangma2006@gmail.com. Supplementary data are available at Bioinformatics online.

Automated metadata--final project report

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

Schissel, David

This report summarizes the work of the Automated Metadata, Provenance Cataloging, and Navigable Interfaces: Ensuring the Usefulness of Extreme-Scale Data Project (MPO Project) funded by the United States Department of Energy (DOE), Offices of Advanced Scientific Computing Research and Fusion Energy Sciences. Initially funded for three years starting in 2012, it was extended for 6 months with additional funding. The project was a collaboration between scientists at General Atomics, Lawrence Berkley National Laboratory (LBNL), and Massachusetts Institute of Technology (MIT). The group leveraged existing computer science technology where possible, and extended or created new capabilities where required. The MPO projectmore » was able to successfully create a suite of software tools that can be used by a scientific community to automatically document their scientific workflows. These tools were integrated into workflows for fusion energy and climate research illustrating the general applicability of the project’s toolkit. Feedback was very positive on the project’s toolkit and the value of such automatic workflow documentation to the scientific endeavor.« less

Microgrid Design Toolkit (MDT) Technical Documentation and Component Summaries

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

Arguello, Bryan; Gearhart, Jared Lee; Jones, Katherine A.

2015-09-01

The Microgrid Design Toolkit (MDT) is a decision support software tool for microgrid designers to use during the microgrid design process. The models that support the two main capabilities in MDT are described. The first capability, the Microgrid Sizing Capability (MSC), is used to determine the size and composition of a new microgrid in the early stages of the design process. MSC is a mixed-integer linear program that is focused on developing a microgrid that is economically viable when connected to the grid. The second capability is focused on refining a microgrid design for operation in islanded mode. This secondmore » capability relies on two models: the Technology Management Optimization (TMO) model and Performance Reliability Model (PRM). TMO uses a genetic algorithm to create and refine a collection of candidate microgrid designs. It uses PRM, a simulation based reliability model, to assess the performance of these designs. TMO produces a collection of microgrid designs that perform well with respect to one or more performance metrics.« less

Nuclear spectroscopy with Geant4. The superheavy challenge

NASA Astrophysics Data System (ADS)

Sarmiento, Luis G.

2016-12-01

The simulation toolkit Geant4 was originally developed at CERN for high-energy physics. Over the years it has been established as a swiss army knife not only in particle physics but it has seen an accelerated expansion towards nuclear physics and more recently to medical imaging and γ- and ion- therapy to mention but a handful of new applications. The validity of Geant4 is vast and large across many particles, ions, materials, and physical processes with typically various different models to choose from. Unfortunately, atomic nuclei with atomic number Z > 100 are not properly supported. This is likely due to the rather novelty of the field, its comparably small user base, and scarce evaluated experimental data. To circumvent this situation different workarounds have been used over the years. In this work the simulation toolkit Geant4 will be introduced with its different components and the effort to bring the software to the heavy and superheavy region will be described.

A simple tool for preliminary hazard identification and quick assessment in craftwork and small/medium enterprises (SME).

PubMed

Colombini, Daniela; Occhipinti, E; Di Leone, G

2012-01-01

During the last Congress of the International Ergonomics Association (IEA), Beijing, August 2009, an international group was founded aimed at developing a "toolkit for MSD prevention" within IEA and in collaboration with World Health Organization (WHO). Possible users of toolkits are: members of health and safety committees, health and safety representatives, line supervisors; labor inspectors; health workers implementing basic occupational health services; occupational health and safety specialists.According to ISO standard 11228 series and the new Draft CD ISO 12259-2009: Application document guides for the potential user, a computer software ( in Excel®) was create dealing with hazard "mapping" in handicraft The proposed methodology, using specific key enters and quick assessment criteria, allows a simple ergonomics hazard identification and risk estimation. Thus it makes possible to decide for which professional hazards a more exhaustive risk assessment will be necessary and which professional consultant should be involved (occupational physician, safety engineer, industrial hygienist, etc.).

New Careers in Nursing Scholar Alumni Toolkit: Development of an Innovative Resource for Transition to Practice.

PubMed

Mauro, Ann Marie P; Escallier, Lori A; Rosario-Sim, Maria G

2016-01-01

The transition from student to professional nurse is challenging and may be more difficult for underrepresented minority nurses. The Robert Wood Johnson Foundation New Careers in Nursing (NCIN) program supported development of a toolkit that would serve as a transition-to-practice resource to promote retention of NCIN alumni and other new nurses. Thirteen recent NCIN alumni (54% male, 23% Hispanic/Latino, 23% African Americans) from 3 schools gave preliminary content feedback. An e-mail survey was sent to a convenience sample of 29 recent NCIN alumni who evaluated the draft toolkit using a Likert scale (poor = 1; excellent = 5). Twenty NCIN alumni draft toolkit reviewers (response rate 69%) were primarily female (80%) and Hispanic/Latino (40%). Individual chapters' mean overall rating of 4.67 demonstrated strong validation. Mean scores for overall toolkit content (4.57), usability (4.5), relevance (4.79), and quality (4.71) were also excellent. Qualitative comments were analyzed using thematic content analysis and supported the toolkit's relevance and utility. A multilevel peer review process was also conducted. Peer reviewer feedback resulted in a 6-chapter document that offers resources for successful transition to practice and lays the groundwork for continued professional growth. Future research is needed to determine the ideal time to introduce this resource. Copyright © 2016 Elsevier Inc. All rights reserved.

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

We have developed BioSmalltalk, a new environment system for pure object-oriented bioinformatics programming. Adaptive end-user programming systems tend to become more important for discovering biological knowledge, as is demonstrated by the emergence of open-source programming toolkits for bioinformatics in the past years. Our software is intended to bridge the gap between bioscientists and rapid software prototyping while preserving the possibility of scaling to whole-system biology applications. BioSmalltalk performs better in terms of execution time and memory usage than Biopython and BioPerl for some classical situations. BioSmalltalk is cross-platform and freely available (MIT license) through the Google Project Hosting at http://code.google.com/p/biosmalltalk hernan.morales@gmail.com Supplementary data are available at Bioinformatics online.

EPANET Multi-Species Extension Software and User's Manual ...

EPA Pesticide Factsheets

Software and User's Manual EPANET is used in homeland security research to model contamination threats to water systems. Historically, EPANET has been limited to tracking the dynamics of a single chemical transported through a network of pipes and storage tanks, such as a fluoride used in a tracer study or free chlorine used in a disinfection decay study. Recently, the NHSRC released a new extension to EPANET called EPANET-MSX (Multi-Species eXtension) that allows for the consideration of multiple interacting species in the bulk flow and on the pipe walls. This capability has been incorporated into both a stand-alone executable program as well as a toolkit library of functions that programmers can use to build customized applications.

Big Data in HEP: A comprehensive use case study

DOE PAGES

Gutsche, Oliver; Cremonesi, Matteo; Elmer, Peter; ...

2017-11-23

Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems collectively called Big Data technologies have emerged to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and promise a fresh look at analysis of very large datasets and could potentially reduce the time-to-physics with increased interactivity.more » In this talk, we present an active LHC Run 2 analysis, searching for dark matter with the CMS detector, as a testbed for Big Data technologies. We directly compare the traditional NTuple-based analysis with an equivalent analysis using Apache Spark on the Hadoop ecosystem and beyond. In both cases, we start the analysis with the official experiment data formats and produce publication physics plots. Lastly, we will discuss advantages and disadvantages of each approach and give an outlook on further studies needed.« less

Big Data in HEP: A comprehensive use case study

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

Gutsche, Oliver; Cremonesi, Matteo; Elmer, Peter

Experimental Particle Physics has been at the forefront of analyzing the worlds largest datasets for decades. The HEP community was the first to develop suitable software and computing tools for this task. In recent times, new toolkits and systems collectively called Big Data technologies have emerged to support the analysis of Petabyte and Exabyte datasets in industry. While the principles of data analysis in HEP have not changed (filtering and transforming experiment-specific data formats), these new technologies use different approaches and promise a fresh look at analysis of very large datasets and could potentially reduce the time-to-physics with increased interactivity.more » In this talk, we present an active LHC Run 2 analysis, searching for dark matter with the CMS detector, as a testbed for Big Data technologies. We directly compare the traditional NTuple-based analysis with an equivalent analysis using Apache Spark on the Hadoop ecosystem and beyond. In both cases, we start the analysis with the official experiment data formats and produce publication physics plots. Lastly, we will discuss advantages and disadvantages of each approach and give an outlook on further studies needed.« less

Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models

PubMed Central

Stephens, Zachary D.; Hudson, Matthew E.; Mainzer, Liudmila S.; Taschuk, Morgan; Weber, Matthew R.; Iyer, Ravishankar K.

2016-01-01

An obstacle to validating and benchmarking methods for genome analysis is that there are few reference datasets available for which the “ground truth” about the mutational landscape of the sample genome is known and fully validated. Additionally, the free and public availability of real human genome datasets is incompatible with the preservation of donor privacy. In order to better analyze and understand genomic data, we need test datasets that model all variants, reflecting known biology as well as sequencing artifacts. Read simulators can fulfill this requirement, but are often criticized for limited resemblance to true data and overall inflexibility. We present NEAT (NExt-generation sequencing Analysis Toolkit), a set of tools that not only includes an easy-to-use read simulator, but also scripts to facilitate variant comparison and tool evaluation. NEAT has a wide variety of tunable parameters which can be set manually on the default model or parameterized using real datasets. The software is freely available at github.com/zstephens/neat-genreads. PMID:27893777

Analyzing large-scale spiking neural data with HRLAnalysis™

PubMed Central

Thibeault, Corey M.; O'Brien, Michael J.; Srinivasa, Narayan

2014-01-01

The additional capabilities provided by high-performance neural simulation environments and modern computing hardware has allowed for the modeling of increasingly larger spiking neural networks. This is important for exploring more anatomically detailed networks but the corresponding accumulation in data can make analyzing the results of these simulations difficult. This is further compounded by the fact that many existing analysis packages were not developed with large spiking data sets in mind. Presented here is a software suite developed to not only process the increased amount of spike-train data in a reasonable amount of time, but also provide a user friendly Python interface. We describe the design considerations, implementation and features of the HRLAnalysis™ suite. In addition, performance benchmarks demonstrating the speedup of this design compared to a published Python implementation are also presented. The result is a high-performance analysis toolkit that is not only usable and readily extensible, but also straightforward to interface with existing Python modules. PMID:24634655

Integration of Enhanced Propagation, Environmental Variability, and Network Performance Models into the InfraMAP Software Toolkit

DTIC Science & Technology

2007-11-01

distribution is unlimited. Z November 2007 Li DTRA01-00-C-0063 David Norris and Robert Gibson Prepared by: BBN Technologies 1300 North 17th Street Suite...TA - CD C.AUT040WS WU - 02091 David E. Norris Robert G. Gibson 7. PERVORMS ONSAIZATIMN RAW(S) AM AURS118" L PIRU OANIZATMO ASPORT...be useful in determining the relative importance with which to treat the predictions. Support of synergy-based localization - Confidence bounds

SmaggIce User Guide. 1.0

NASA Technical Reports Server (NTRS)

Baez, Marivell; Vickerman, Mary; Choo, Yung

2000-01-01

SmaggIce (Surface Modeling And Grid Generation for Iced Airfoils) is one of NASNs aircraft icing research codes developed at the Glenn Research Center. It is a software toolkit used in the process of aerodynamic performance prediction of iced airfoils. It includes tools which complement the 2D grid-based Computational Fluid Dynamics (CFD) process: geometry probing; surface preparation for gridding: smoothing and re-discretization of geometry. Future releases will also include support for all aspects of gridding: domain decomposition; perimeter discretization; grid generation and modification.

THYME: Toolkit for Hybrid Modeling of Electric Power Systems

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

Nutaro Kalyan Perumalla, James Joseph

2011-01-01

THYME is an object oriented library for building models of wide area control and communications in electric power systems. This software is designed as a module to be used with existing open source simulators for discrete event systems in general and communication systems in particular. THYME consists of a typical model for simulating electro-mechanical transients (e.g., as are used in dynamic stability studies), data handling objects to work with CDF and PTI formatted power flow data, and sample models of discrete sensors and controllers.

A Software Agent Toolkit for Effective Information Processing in the Battle Command Domain

DTIC Science & Technology

2006-11-01

the ADE will be based on a popular Integrated Development Environment (IDE) such as NetBeans or Eclipse. We further specified that the IDE is to be...JBuilder, NetBeans , and Eclipse. We quickly eliminated Visual Studio and JBuilder because they did not meet our basic requirements of being Java...based and freely obtainable. This left us with NetBeans and Eclipse. Each is a solid IDE with features that permit extensions well suited to our

A Facility and Architecture for Autonomy Research

NASA Technical Reports Server (NTRS)

Pisanich, Greg; Clancy, Daniel (Technical Monitor)

2002-01-01

Autonomy is a key enabling factor in the advancement of the remote robotic exploration. There is currently a large gap between autonomy software at the research level and software that is ready for insertion into near-term space missions. The Mission Simulation Facility (MST) will bridge this gap by providing a simulation framework and suite of simulation tools to support research in autonomy for remote exploration. This system will allow developers of autonomy software to test their models in a high-fidelity simulation and evaluate their system's performance against a set of integrated, standardized simulations. The Mission Simulation ToolKit (MST) uses a distributed architecture with a communication layer that is built on top of the standardized High Level Architecture (HLA). This architecture enables the use of existing high fidelity models, allows mixing simulation components from various computing platforms and enforces the use of a standardized high-level interface among components. The components needed to achieve a realistic simulation can be grouped into four categories: environment generation (terrain, environmental features), robotic platform behavior (robot dynamics), instrument models (camera/spectrometer/etc.), and data analysis. The MST will provide basic components in these areas but allows users to plug-in easily any refined model by means of a communication protocol. Finally, a description file defines the robot and environment parameters for easy configuration and ensures that all the simulation models share the same information.

Designing and evaluating an interprofessional shared decision-making and goal-setting decision aid for patients with diabetes in clinical care--systematic decision aid development and study protocol.

PubMed

Yu, Catherine H; Stacey, Dawn; Sale, Joanna; Hall, Susan; Kaplan, David M; Ivers, Noah; Rezmovitz, Jeremy; Leung, Fok-Han; Shah, Baiju R; Straus, Sharon E

2014-01-22

Care of patients with diabetes often occurs in the context of other chronic illness. Competing disease priorities and competing patient-physician priorities present challenges in the provision of care for the complex patient. Guideline implementation interventions to date do not acknowledge these intricacies of clinical practice. As a result, patients and providers are left overwhelmed and paralyzed by the sheer volume of recommendations and tasks. An individualized approach to the patient with diabetes and multiple comorbid conditions using shared decision-making (SDM) and goal setting has been advocated as a patient-centred approach that may facilitate prioritization of treatment options. Furthermore, incorporating interprofessional integration into practice may overcome barriers to implementation. However, these strategies have not been taken up extensively in clinical practice. To systematically develop and test an interprofessional SDM and goal-setting toolkit for patients with diabetes and other chronic diseases, following the Knowledge to Action framework. 1. Feasibility study: Individual interviews with primary care physicians, nurses, dietitians, pharmacists, and patients with diabetes will be conducted, exploring their experiences with shared decision-making and priority-setting, including facilitators and barriers, the relevance of a decision aid and toolkit for priority-setting, and how best to integrate it into practice.2. Toolkit development: Based on this data, an evidence-based multi-component SDM toolkit will be developed. The toolkit will be reviewed by content experts (primary care, endocrinology, geriatricians, nurses, dietitians, pharmacists, patients) for accuracy and comprehensiveness.3. Heuristic evaluation: A human factors engineer will review the toolkit and identify, list and categorize usability issues by severity.4. Usability testing: This will be done using cognitive task analysis.5. Iterative refinement: Throughout the development process, the toolkit will be refined through several iterative cycles of feedback and redesign. Interprofessional shared decision-making regarding priority-setting with the use of a decision aid toolkit may help prioritize care of individuals with multiple comorbid conditions. Adhering to principles of user-centered design, we will develop and refine a toolkit to assess the feasibility of this approach.

Designing and evaluating an interprofessional shared decision-making and goal-setting decision aid for patients with diabetes in clinical care - systematic decision aid development and study protocol

PubMed Central

2014-01-01

Background Care of patients with diabetes often occurs in the context of other chronic illness. Competing disease priorities and competing patient-physician priorities present challenges in the provision of care for the complex patient. Guideline implementation interventions to date do not acknowledge these intricacies of clinical practice. As a result, patients and providers are left overwhelmed and paralyzed by the sheer volume of recommendations and tasks. An individualized approach to the patient with diabetes and multiple comorbid conditions using shared decision-making (SDM) and goal setting has been advocated as a patient-centred approach that may facilitate prioritization of treatment options. Furthermore, incorporating interprofessional integration into practice may overcome barriers to implementation. However, these strategies have not been taken up extensively in clinical practice. Objectives To systematically develop and test an interprofessional SDM and goal-setting toolkit for patients with diabetes and other chronic diseases, following the Knowledge to Action framework. Methods 1. Feasibility study: Individual interviews with primary care physicians, nurses, dietitians, pharmacists, and patients with diabetes will be conducted, exploring their experiences with shared decision-making and priority-setting, including facilitators and barriers, the relevance of a decision aid and toolkit for priority-setting, and how best to integrate it into practice. 2. Toolkit development: Based on this data, an evidence-based multi-component SDM toolkit will be developed. The toolkit will be reviewed by content experts (primary care, endocrinology, geriatricians, nurses, dietitians, pharmacists, patients) for accuracy and comprehensiveness. 3. Heuristic evaluation: A human factors engineer will review the toolkit and identify, list and categorize usability issues by severity. 4. Usability testing: This will be done using cognitive task analysis. 5. Iterative refinement: Throughout the development process, the toolkit will be refined through several iterative cycles of feedback and redesign. Discussion Interprofessional shared decision-making regarding priority-setting with the use of a decision aid toolkit may help prioritize care of individuals with multiple comorbid conditions. Adhering to principles of user-centered design, we will develop and refine a toolkit to assess the feasibility of this approach. PMID:24450385

Opal web services for biomedical applications.

PubMed

Ren, Jingyuan; Williams, Nadya; Clementi, Luca; Krishnan, Sriram; Li, Wilfred W

2010-07-01

Biomedical applications have become increasingly complex, and they often require large-scale high-performance computing resources with a large number of processors and memory. The complexity of application deployment and the advances in cluster, grid and cloud computing require new modes of support for biomedical research. Scientific Software as a Service (sSaaS) enables scalable and transparent access to biomedical applications through simple standards-based Web interfaces. Towards this end, we built a production web server (http://ws.nbcr.net) in August 2007 to support the bioinformatics application called MEME. The server has grown since to include docking analysis with AutoDock and AutoDock Vina, electrostatic calculations using PDB2PQR and APBS, and off-target analysis using SMAP. All the applications on the servers are powered by Opal, a toolkit that allows users to wrap scientific applications easily as web services without any modification to the scientific codes, by writing simple XML configuration files. Opal allows both web forms-based access and programmatic access of all our applications. The Opal toolkit currently supports SOAP-based Web service access to a number of popular applications from the National Biomedical Computation Resource (NBCR) and affiliated collaborative and service projects. In addition, Opal's programmatic access capability allows our applications to be accessed through many workflow tools, including Vision, Kepler, Nimrod/K and VisTrails. From mid-August 2007 to the end of 2009, we have successfully executed 239,814 jobs. The number of successfully executed jobs more than doubled from 205 to 411 per day between 2008 and 2009. The Opal-enabled service model is useful for a wide range of applications. It provides for interoperation with other applications with Web Service interfaces, and allows application developers to focus on the scientific tool and workflow development. Web server availability: http://ws.nbcr.net.

DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

PubMed Central

Gouws, André; Woods, Will; Millman, Rebecca; Morland, Antony; Green, Gary

2008-01-01

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data. PMID:19352444

Virtual Solar Energy Center: A Case Study of the Use of Advanced Visualization Techniques for the Comprehension of Complex Engineering Products and Processes

NASA Astrophysics Data System (ADS)

Ritter, Kenneth August, III

Industry has a continuing need to train its workforce on recent engineering developments, but many engineering products and processes are hard to explain because of limitations of size, visibility, time scale, cost, and safety. The product or process might be difficult to see because it is either very large or very small, because it is enclosed within an opaque container, or because it happens very fast or very slowly. Some engineering products and processes are also costly or unsafe to use for training purposes, and sometimes the domain expert is not physically available at the training location. All these limitations can potentially be addressed using advanced visualization techniques such as virtual reality. This dissertation describes the development of an immersive virtual reality application using the Six Sigma DMADV process to explain the main equipment and processes used in a concentrating solar power plant. The virtual solar energy center (VEC) application was initially developed and tested in a Cave Automatic Virtual Environment (CAVE) during 2013 and 2014. The software programs used for development were SolidWorks, 3ds Max Design, and Unity 3D. Current hardware and software technologies that could complement this research were analyzed. The NVIDA GRID Visual Computing Appliance (VCA) was chosen as the rendering solution for animating complex CAD models in this application. The MiddleVR software toolkit was selected as the toolkit for VR interactions and CAVE display. A non-immersive 3D version of the VEC application was tested and shown to be an effective training tool in late 2015. An immersive networked version of the VEC allows the user to receive live instruction from a trainer being projected via depth camera imagery from a remote location. Four comparative analysis studies were performed. These studies used the average normalized gain from pre-test scores to determine the effectiveness of the various training methods. With the DMADV approach, solutions were identified and verified during each iteration of the development, which saved valuable time and resulted in better results being achieved in each revision of the application, with the final version having 88% positive responses and same effectiveness as other methods assessed.

WebViz: A web browser based application for collaborative analysis of 3D data

NASA Astrophysics Data System (ADS)

Ruegg, C. S.

2011-12-01

In the age of high speed Internet where people can interact instantly, scientific tools have lacked technology which can incorporate this concept of communication using the web. To solve this issue a web application for geological studies has been created, tentatively titled WebViz. This web application utilizes tools provided by Google Web Toolkit to create an AJAX web application capable of features found in non web based software. Using these tools, a web application can be created to act as piece of software from anywhere in the globe with a reasonably speedy Internet connection. An application of this technology can be seen with data regarding the recent tsunami from the major japan earthquakes. After constructing the appropriate data to fit a computer render software called HVR, WebViz can request images of the tsunami data and display it to anyone who has access to the application. This convenience alone makes WebViz a viable solution, but the option to interact with this data with others around the world causes WebViz to be taken as a serious computational tool. WebViz also can be used on any javascript enabled browser such as those found on modern tablets and smart phones over a fast wireless connection. Due to the fact that WebViz's current state is built using Google Web Toolkit the portability of the application is in it's most efficient form. Though many developers have been involved with the project, each person has contributed to increase the usability and speed of the application. In the project's most recent form a dramatic speed increase has been designed as well as a more efficient user interface. The speed increase has been informally noticed in recent uses of the application in China and Australia with the hosting server being located at the University of Minnesota. The user interface has been improved to not only look better but the functionality has been improved. Major functions of the application are rotating the 3D object using buttons. These buttons have been replaced with a new layout that is easier to understand the function and is also easy to use with mobile devices. With these new changes, WebViz is easier to control and use for general use.

Spice Tools Supporting Planetary Remote Sensing

NASA Astrophysics Data System (ADS)

Acton, C.; Bachman, N.; Semenov, B.; Wright, E.

2016-06-01

NASA's "SPICE"* ancillary information system has gradually become the de facto international standard for providing scientists the fundamental observation geometry needed to perform photogrammetry, map making and other kinds of planetary science data analysis. SPICE provides position and orientation ephemerides of both the robotic spacecraft and the target body; target body size and shape data; instrument mounting alignment and field-of-view geometry; reference frame specifications; and underlying time system conversions. SPICE comprises not only data, but also a large suite of software, known as the SPICE Toolkit, used to access those data and subsequently compute derived quantities-items such as instrument viewing latitude/longitude, lighting angles, altitude, etc. In existence since the days of the Magellan mission to Venus, the SPICE system has continuously grown to better meet the needs of scientists and engineers. For example, originally the SPICE Toolkit was offered only in Fortran 77, but is now available in C, IDL, MATLAB, and Java Native Interface. SPICE calculations were originally available only using APIs (subroutines), but can now be executed using a client-server interface to a geometry engine. Originally SPICE "products" were only available in numeric form, but now SPICE data visualization is also available. The SPICE components are free of cost, license and export restrictions. Substantial tutorials and programming lessons help new users learn to employ SPICE calculations in their own programs. The SPICE system is implemented and maintained by the Navigation and Ancillary Information Facility (NAIF)-a component of NASA's Planetary Data System (PDS). * Spacecraft, Planet, Instrument, Camera-matrix, Events

NASA Tech Briefs, February 2014

NASA Technical Reports Server (NTRS)

2014-01-01

Topics include: JWST Integrated Simulation and Test (JIST) Core; Software for Non-Contact Measurement of an Individual's Heart Rate Using a Common Camera; Rapid Infrared Pixel Grating Response Testbed; Temperature Measurement and Stabilization in a Birefringent Whispering Gallery Resonator; JWST IV and V Simulation and Test (JIST) Solid State Recorder (SSR) Simulator; Development of a Precision Thermal Doubler for Deep Space; Improving Friction Stir Welds Using Laser Peening; Methodology of Evaluating Margins of Safety in Critical Brazed Joints; Interactive Inventory Monitoring; Sensor for Spatial Detection of Single-Event Effects in Semiconductor-Based Electronics; Reworked CCGA-624 Interconnect Package Reliability for Extreme Thermal Environments; Current-Controlled Output Driver for Directly Coupled Loads; Bulk Metallic Glasses and Matrix Composites as Spacecraft Shielding; Touch Temperature Coating for Electrical Equipment on Spacecraft; Li-Ion Electrolytes Containing Flame-Retardant Additives; Autonomous Robotic Manipulation (ARM); CARVE Log; Platform Perspective Toolkit; Convex Hull-Based Plume and Anomaly Detection; Pre-Filtration of GOSAT Data Using Only Level 1 Data and an Intelligent Filter to Remove Low Clouds; Affordability Comparison Tool - ACT; "Ascent - Commemorating Shuttle" for iPad; Cassini Mission App; Light-Weight Workflow Engine: A Server for Executing Generic Workflows; Model for System Engineering of the CheMin Instrument; Timeline Central Concepts; Parallel Particle Filter Toolkit; Particle Filter Simulation and Analysis Enabling Non-Traditional Navigation; Quasi-Terminator Orbits for Mapping Small Primitive Bodies; The Subgrid-Scale Scalar Variance Under Supercritical Pressure Conditions; Sliding Gait for ATHLETE Mobility; and Automated Generation of Adaptive Filter Using a Genetic Algorithm and Cyclic Rule Reduction.

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

DOE PAGES

Essinger, Steven D.; Reichenberger, Erin; Morrison, Calvin; ...

2015-01-21

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with themore » data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. Furthermore, a tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial.« less

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

PubMed Central

Essinger, Steven D.; Reichenberger, Erin; Morrison, Calvin; Blackwood, Christopher B.; Rosen, Gail L.

2015-01-01

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with the data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. A tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial. Availability: http://www.ece.drexel.edu/gailr/EESI/tutorial.php. PMID:25607539

Designing informed game-based rehabilitation tasks leveraging advances in virtual reality.

PubMed

Lange, Belinda; Koenig, Sebastian; Chang, Chien-Yen; McConnell, Eric; Suma, Evan; Bolas, Mark; Rizzo, Albert

2012-01-01

This paper details a brief history and rationale for the use of virtual reality (VR) technology for clinical research and intervention, and then focuses on game-based VR applications in the area of rehabilitation. An analysis of the match between rehabilitation task requirements and the assets available with VR technology is presented. Low-cost camera-based systems capable of tracking user behavior at sufficient levels for game-based virtual rehabilitation activities are currently available for in-home use. Authoring software is now being developed that aims to provide clinicians with a usable toolkit for leveraging this technology. This will facilitate informed professional input on software design, development and application to ensure safe and effective use in the rehabilitation context. The field of rehabilitation generally stands to benefit from the continual advances in VR technology, concomitant system cost reductions and an expanding clinical research literature and knowledge base. Home-based activity within VR systems that are low-cost, easy to deploy and maintain, and meet the requirements for "good" interactive rehabilitation tasks could radically improve users' access to care, adherence to prescribed training and subsequently enhance functional activity in everyday life in clinical populations.

Modeling and Grid Generation of Iced Airfoils

NASA Technical Reports Server (NTRS)

Vickerman, Mary B.; Baez, Marivell; Braun, Donald C.; Hackenberg, Anthony W.; Pennline, James A.; Schilling, Herbert W.

2007-01-01

SmaggIce Version 2.0 is a software toolkit for geometric modeling and grid generation for two-dimensional, singleand multi-element, clean and iced airfoils. A previous version of SmaggIce was described in Preparing and Analyzing Iced Airfoils, NASA Tech Briefs, Vol. 28, No. 8 (August 2004), page 32. To recapitulate: Ice shapes make it difficult to generate quality grids around airfoils, yet these grids are essential for predicting ice-induced complex flow. This software efficiently creates high-quality structured grids with tools that are uniquely tailored for various ice shapes. SmaggIce Version 2.0 significantly enhances the previous version primarily by adding the capability to generate grids for multi-element airfoils. This version of the software is an important step in streamlining the aeronautical analysis of ice airfoils using computational fluid dynamics (CFD) tools. The user may prepare the ice shape, define the flow domain, decompose it into blocks, generate grids, modify/divide/merge blocks, and control grid density and smoothness. All these steps may be performed efficiently even for the difficult glaze and rime ice shapes. Providing the means to generate highly controlled grids near rough ice, the software includes the creation of a wrap-around block (called the "viscous sublayer block"), which is a thin, C-type block around the wake line and iced airfoil. For multi-element airfoils, the software makes use of grids that wrap around and fill in the areas between the viscous sub-layer blocks for all elements that make up the airfoil. A scripting feature records the history of interactive steps, which can be edited and replayed later to produce other grids. Using this version of SmaggIce, ice shape handling and grid generation can become a practical engineering process, rather than a laborious research effort.

Effect of the good school toolkit on school staff mental health, sense of job satisfaction and perceptions of school climate: Secondary analysis of a cluster randomised trial.

PubMed

Kayiwa, Joshua; Clarke, Kelly; Knight, Louise; Allen, Elizabeth; Walakira, Eddy; Namy, Sophie; Merrill, Katherine G; Naker, Dipak; Devries, Karen

2017-08-01

The Good School Toolkit, a complex behavioural intervention delivered in Ugandan primary schools, has been shown to reduce school staff-perpetrated physical violence against students. We aimed to assess the effect of this intervention on staff members' mental health, sense of job satisfaction and perception of school climate. We analysed data from a cluster-randomised trial administered in 42 primary schools in Luwero district, Uganda. The trial was comprised of cross-sectional baseline (June/July 2012) and endline (June/July 2014) surveys among staff and students. Twenty-one schools were randomly selected to receive the Toolkit, whilst 21 schools constituted a wait-listed control group. We generated composite measures to assess staff members' perceptions of the school climate and job satisfaction. The trial is registered at clinicaltrials.gov (NCT01678846). No schools dropped out of the study and all 591 staff members who completed the endline survey were included in the analysis. Staff in schools receiving the Toolkit had more positive perspectives of their school climate compared to staff in control schools (difference in mean scores 2.19, 95% Confidence Interval 0.92, 3.39). We did not find any significant differences for job satisfaction and mental health. In conclusion, interventions like the Good School Toolkit that reduce physical violence by school staff against students can improve staff perceptions of the school climate, and could help to build more positive working and learning environments in Ugandan schools. Copyright © 2017 Elsevier Inc. All rights reserved.

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

Coupled field-structural analysis of HGTR fuel brick using ABAQUS

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

Mohanty, S.; Jain, R.; Majumdar, S.

2012-07-01

High-temperature, gas-cooled reactors (HTGRs) are usually helium-gas cooled, with a graphite core that can operate at reactor outlet temperatures much higher than can conventional light water reactors. In HTGRs, graphite components moderate and reflect neutrons. During reactor operation, high temperature and high irradiation cause damage to the graphite crystal and grains and create other defects. This cumulative structural damage during the reactor lifetime leads to changes in graphite properties, which can alter the ability to support the designed loads. The aim of the present research is to develop a finite-element code using commercially available ABAQUS software for the structural integritymore » analysis of graphite core components under extreme temperature and irradiation conditions. In addition, the Reactor Geometry Generator tool-kit, developed at Argonne National Laboratory, is used to generate finite-element mesh for complex geometries such as fuel bricks with multiple pin holes and coolant flow channels. This paper presents the proposed concept and discusses results of stress analysis simulations of a fuel block with H-451 grade material properties. (authors)« less

Towards a Web-Enabled Geovisualization and Analytics Platform for the Energy and Water Nexus

NASA Astrophysics Data System (ADS)

Sanyal, J.; Chandola, V.; Sorokine, A.; Allen, M.; Berres, A.; Pang, H.; Karthik, R.; Nugent, P.; McManamay, R.; Stewart, R.; Bhaduri, B. L.

2017-12-01

Interactive data analytics are playing an increasingly vital role in the generation of new, critical insights regarding the complex dynamics of the energy/water nexus (EWN) and its interactions with climate variability and change. Integration of impacts, adaptation, and vulnerability (IAV) science with emerging, and increasingly critical, data science capabilities offers a promising potential to meet the needs of the EWN community. To enable the exploration of pertinent research questions, a web-based geospatial visualization platform is being built that integrates a data analysis toolbox with advanced data fusion and data visualization capabilities to create a knowledge discovery framework for the EWN. The system, when fully built out, will offer several geospatial visualization capabilities including statistical visual analytics, clustering, principal-component analysis, dynamic time warping, support uncertainty visualization and the exploration of data provenance, as well as support machine learning discoveries to render diverse types of geospatial data and facilitate interactive analysis. Key components in the system architecture includes NASA's WebWorldWind, the Globus toolkit, postgresql, as well as other custom built software modules.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

PubMed

Hartman, Amber L; Riddle, Sean; McPhillips, Timothy; Ludäscher, Bertram; Eisen, Jonathan A

2010-06-12

For more than two decades microbiologists have used a highly conserved microbial gene as a phylogenetic marker for bacteria and archaea. The small-subunit ribosomal RNA gene, also known as 16 S rRNA, is encoded by ribosomal DNA, 16 S rDNA, and has provided a powerful comparative tool to microbial ecologists. Over time, the microbial ecology field has matured from small-scale studies in a select number of environments to massive collections of sequence data that are paired with dozens of corresponding collection variables. As the complexity of data and tool sets have grown, the need for flexible automation and maintenance of the core processes of 16 S rDNA sequence analysis has increased correspondingly. We present WATERS, an integrated approach for 16 S rDNA analysis that bundles a suite of publicly available 16 S rDNA analysis software tools into a single software package. The "toolkit" includes sequence alignment, chimera removal, OTU determination, taxonomy assignment, phylogentic tree construction as well as a host of ecological analysis and visualization tools. WATERS employs a flexible, collection-oriented 'workflow' approach using the open-source Kepler system as a platform. By packaging available software tools into a single automated workflow, WATERS simplifies 16 S rDNA analyses, especially for those without specialized bioinformatics, programming expertise. In addition, WATERS, like some of the newer comprehensive rRNA analysis tools, allows researchers to minimize the time dedicated to carrying out tedious informatics steps and to focus their attention instead on the biological interpretation of the results. One advantage of WATERS over other comprehensive tools is that the use of the Kepler workflow system facilitates result interpretation and reproducibility via a data provenance sub-system. Furthermore, new "actors" can be added to the workflow as desired and we see WATERS as an initial seed for a sizeable and growing repository of interoperable, easy-to-combine tools for asking increasingly complex microbial ecology questions.

Evaluating the decision accuracy and speed of clinical data visualizations.

PubMed

Pieczkiewicz, David S; Finkelstein, Stanley M

2010-01-01

Clinicians face an increasing volume of biomedical data. Assessing the efficacy of systems that enable accurate and timely clinical decision making merits corresponding attention. This paper discusses the multiple-reader multiple-case (MRMC) experimental design and linear mixed models as means of assessing and comparing decision accuracy and latency (time) for decision tasks in which clinician readers must interpret visual displays of data. These tools can assess and compare decision accuracy and latency (time). These experimental and statistical techniques, used extensively in radiology imaging studies, offer a number of practical and analytic advantages over more traditional quantitative methods such as percent-correct measurements and ANOVAs, and are recommended for their statistical efficiency and generalizability. An example analysis using readily available, free, and commercial statistical software is provided as an appendix. While these techniques are not appropriate for all evaluation questions, they can provide a valuable addition to the evaluative toolkit of medical informatics research.

Integrating hidden Markov model and PRAAT: a toolbox for robust automatic speech transcription

NASA Astrophysics Data System (ADS)

Kabir, A.; Barker, J.; Giurgiu, M.

2010-09-01

An automatic time-aligned phone transcription toolbox of English speech corpora has been developed. Especially the toolbox would be very useful to generate robust automatic transcription and able to produce phone level transcription using speaker independent models as well as speaker dependent models without manual intervention. The system is based on standard Hidden Markov Models (HMM) approach and it was successfully experimented over a large audiovisual speech corpus namely GRID corpus. One of the most powerful features of the toolbox is the increased flexibility in speech processing where the speech community would be able to import the automatic transcription generated by HMM Toolkit (HTK) into a popular transcription software, PRAAT, and vice-versa. The toolbox has been evaluated through statistical analysis on GRID data which shows that automatic transcription deviates by an average of 20 ms with respect to manual transcription.

A coupling strategy for nonlocal and local diffusion models with mixed volume constraints and boundary conditions

DOE PAGES

D'Elia, Marta; Perego, Mauro; Bochev, Pavel B.; ...

2015-12-21

We develop and analyze an optimization-based method for the coupling of nonlocal and local diffusion problems with mixed volume constraints and boundary conditions. The approach formulates the coupling as a control problem where the states are the solutions of the nonlocal and local equations, the objective is to minimize their mismatch on the overlap of the nonlocal and local domains, and the controls are virtual volume constraints and boundary conditions. When some assumptions on the kernel functions hold, we prove that the resulting optimization problem is well-posed and discuss its implementation using Sandia’s agile software components toolkit. As a result,more » the latter provides the groundwork for the development of engineering analysis tools, while numerical results for nonlocal diffusion in three-dimensions illustrate key properties of the optimization-based coupling method.« less

An Automated Ab Initio Framework for Identifying New Ferroelectrics

NASA Astrophysics Data System (ADS)

Smidt, Tess; Reyes-Lillo, Sebastian E.; Jain, Anubhav; Neaton, Jeffrey B.

Ferroelectric materials have a wide-range of technological applications including non-volatile RAM and optoelectronics. In this work, we present an automated first-principles search for ferroelectrics. We integrate density functional theory, crystal structure databases, symmetry tools, workflow software, and a custom analysis toolkit to build a library of known and proposed ferroelectrics. We screen thousands of candidates using symmetry relations between nonpolar and polar structure pairs. We use two search strategies 1) polar-nonpolar pairs with the same composition and 2) polar-nonpolar structure type pairs. Results are automatically parsed, stored in a database, and accessible via a web interface showing distortion animations and plots of polarization and total energy as a function of distortion. We benchmark our results against experimental data, present new ferroelectric candidates found through our search, and discuss future work on expanding this search methodology to other material classes such as anti-ferroelectrics and multiferroics.

Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer

PubMed Central

Gutman, David A.; Dunn, William D.; Cobb, Jake; Stoner, Richard M.; Kalpathy-Cramer, Jayashree; Erickson, Bradley

2014-01-01

Advances in web technologies now allow direct visualization of imaging data sets without necessitating the download of large file sets or the installation of software. This allows centralization of file storage and facilitates image review and analysis. XNATView is a light framework recently developed in our lab to visualize DICOM images stored in The Extensible Neuroimaging Archive Toolkit (XNAT). It consists of a PyXNAT-based framework to wrap around the REST application programming interface (API) and query the data in XNAT. XNATView was developed to simplify quality assurance, help organize imaging data, and facilitate data sharing for intra- and inter-laboratory collaborations. Its zero-footprint design allows the user to connect to XNAT from a web browser, navigate through projects, experiments, and subjects, and view DICOM images with accompanying metadata all within a single viewing instance. PMID:24904399

Development of Fuel Shuffling Module for PHISICS

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

Allan Mabe; Andrea Alfonsi; Cristian Rabiti

2013-06-01

PHISICS (Parallel and Highly Innovative Simulation for the INL Code System) [4] code toolkit has been in development at the Idaho National Laboratory. This package is intended to provide a modern analysis tool for reactor physics investigation. It is designed with the mindset to maximize accuracy for a given availability of computational resources and to give state of the art tools to the modern nuclear engineer. This is obtained by implementing several different algorithms and meshing approaches among which the user will be able to choose, in order to optimize his computational resources and accuracy needs. The software is completelymore » modular in order to simplify the independent development of modules by different teams and future maintenance. The package is coupled with the thermo-hydraulic code RELAP5-3D [3]. In the following the structure of the different PHISICS modules is briefly recalled, focusing on the new shuffling module (SHUFFLE), object of this paper.« less

TriageTools: tools for partitioning and prioritizing analysis of high-throughput sequencing data.

PubMed

Fimereli, Danai; Detours, Vincent; Konopka, Tomasz

2013-04-01

High-throughput sequencing is becoming a popular research tool but carries with it considerable costs in terms of computation time, data storage and bandwidth. Meanwhile, some research applications focusing on individual genes or pathways do not necessitate processing of a full sequencing dataset. Thus, it is desirable to partition a large dataset into smaller, manageable, but relevant pieces. We present a toolkit for partitioning raw sequencing data that includes a method for extracting reads that are likely to map onto pre-defined regions of interest. We show the method can be used to extract information about genes of interest from DNA or RNA sequencing samples in a fraction of the time and disk space required to process and store a full dataset. We report speedup factors between 2.6 and 96, depending on settings and samples used. The software is available at http://www.sourceforge.net/projects/triagetools/.

Remote Visualization and Remote Collaboration On Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Watson, Val; Lasinski, T. A. (Technical Monitor)

1995-01-01

A new technology has been developed for remote visualization that provides remote, 3D, high resolution, dynamic, interactive viewing of scientific data (such as fluid dynamics simulations or measurements). Based on this technology, some World Wide Web sites on the Internet are providing fluid dynamics data for educational or testing purposes. This technology is also being used for remote collaboration in joint university, industry, and NASA projects in computational fluid dynamics and wind tunnel testing. Previously, remote visualization of dynamic data was done using video format (transmitting pixel information) such as video conferencing or MPEG movies on the Internet. The concept for this new technology is to send the raw data (e.g., grids, vectors, and scalars) along with viewing scripts over the Internet and have the pixels generated by a visualization tool running on the viewer's local workstation. The visualization tool that is currently used is FAST (Flow Analysis Software Toolkit).

Studying groundwater and surface water interactions using airborne remote sensing in Heihe River basin, northwest China

NASA Astrophysics Data System (ADS)

Liu, C.; Liu, J.; Hu, Y.; Zheng, C.

2015-05-01

Managing surface water and groundwater as a unified system is important for water resource exploitation and aquatic ecosystem conservation. The unified approach to water management needs accurate characterization of surface water and groundwater interactions. Temperature is a natural tracer for identifying surface water and groundwater interactions, and the use of remote sensing techniques facilitates basin-scale temperature measurement. This study focuses on the Heihe River basin, the second largest inland river basin in the arid and semi-arid northwest of China where surface water and groundwater undergoes dynamic exchanges. The spatially continuous river-surface temperature of the midstream section of the Heihe River was obtained by using an airborne pushbroom hyperspectral thermal sensor system. By using the hot spot analysis toolkit in the ArcGIS software, abnormally cold water zones were identified as indicators of the spatial pattern of groundwater discharge to the river.

Image-guided navigation: a cost effective practical introduction using the Image-Guided Surgery Toolkit (IGSTK).

PubMed

Güler, Özgür; Yaniv, Ziv

2012-01-01

Teaching the key technical aspects of image-guided interventions using a hands-on approach is a challenging task. This is primarily due to the high cost and lack of accessibility to imaging and tracking systems. We provide a software and data infrastructure which addresses both challenges. Our infrastructure allows students, patients, and clinicians to develop an understanding of the key technologies by using them, and possibly by developing additional components and integrating them into a simple navigation system which we provide. Our approach requires minimal hardware, LEGO blocks to construct a phantom for which we provide CT scans, and a webcam which when combined with our software provides the functionality of a tracking system. A premise of this approach is that tracking accuracy is sufficient for our purpose. We evaluate the accuracy provided by a consumer grade webcam and show that it is sufficient for educational use. We provide an open source implementation of all the components required for a basic image-guided navigation as part of the Image-Guided Surgery Toolkit (IGSTK). It has long been known that in education there is no substitute for hands-on experience, to quote Sophocles, "One must learn by doing the thing; for though you think you know it, you have no certainty, until you try.". Our work provides this missing capability in the context of image-guided navigation. Enabling a wide audience to learn and experience the use of a navigation system.

To generate a finite element model of human thorax using the VCH dataset

NASA Astrophysics Data System (ADS)

Shi, Hui; Liu, Qian

2009-10-01

Purpose: To generate a three-dimensional (3D) finite element (FE) model of human thorax which may provide the basis of biomechanics simulation for the study of design effect and mechanism of safety belt when vehicle collision. Methods: Using manually or semi-manually segmented method, the interested area can be segmented from the VCH (Visible Chinese Human) dataset. The 3D surface model of thorax is visualized by using VTK (Visualization Toolkit) and further translated into (Stereo Lithography) STL format, which approximates the geometry of solid model by representing the boundaries with triangular facets. The data in STL format need to be normalized into NURBS surfaces and IGES format using software such as Geomagic Studio to provide archetype for reverse engineering. The 3D FE model was established using Ansys software. Results: The generated 3D FE model was an integrated thorax model which could reproduce human's complicated structure morphology including clavicle, ribs, spine and sternum. It was consisted of 1 044 179 elements in total. Conclusions: Compared with the previous thorax model, this FE model enhanced the authenticity and precision of results analysis obviously, which can provide a sound basis for analysis of human thorax biomechanical research. Furthermore, using the method above, we can also establish 3D FE models of some other organizes and tissues utilizing the VCH dataset.

Visualization techniques to aid in the analysis of multispectral astrophysical data sets

NASA Technical Reports Server (NTRS)

Brugel, E. W.; Domik, Gitta O.; Ayres, T. R.

1993-01-01

The goal of this project was to support the scientific analysis of multi-spectral astrophysical data by means of scientific visualization. Scientific visualization offers its greatest value if it is not used as a method separate or alternative to other data analysis methods but rather in addition to these methods. Together with quantitative analysis of data, such as offered by statistical analysis, image or signal processing, visualization attempts to explore all information inherent in astrophysical data in the most effective way. Data visualization is one aspect of data analysis. Our taxonomy as developed in Section 2 includes identification and access to existing information, preprocessing and quantitative analysis of data, visual representation and the user interface as major components to the software environment of astrophysical data analysis. In pursuing our goal to provide methods and tools for scientific visualization of multi-spectral astrophysical data, we therefore looked at scientific data analysis as one whole process, adding visualization tools to an already existing environment and integrating the various components that define a scientific data analysis environment. As long as the software development process of each component is separate from all other components, users of data analysis software are constantly interrupted in their scientific work in order to convert from one data format to another, or to move from one storage medium to another, or to switch from one user interface to another. We also took an in-depth look at scientific visualization and its underlying concepts, current visualization systems, their contributions and their shortcomings. The role of data visualization is to stimulate mental processes different from quantitative data analysis, such as the perception of spatial relationships or the discovery of patterns or anomalies while browsing through large data sets. Visualization often leads to an intuitive understanding of the meaning of data values and their relationships by sacrificing accuracy in interpreting the data values. In order to be accurate in the interpretation, data values need to be measured, computed on, and compared to theoretical or empirical models (quantitative analysis). If visualization software hampers quantitative analysis (which happens with some commercial visualization products), its use is greatly diminished for astrophysical data analysis. The software system STAR (Scientific Toolkit for Astrophysical Research) was developed as a prototype during the course of the project to better understand the pragmatic concerns raised in the project. STAR led to a better understanding on the importance of collaboration between astrophysicists and computer scientists. Twenty-one examples of the use of visualization for astrophysical data are included with this report. Sixteen publications related to efforts performed during or initiated through work on this project are listed at the end of this report.

Real-time control using open source RTOS

NASA Astrophysics Data System (ADS)

Irwin, Philip C.; Johnson, Richard L., Jr.

2002-12-01

Complex telescope systems such as interferometers tend to rely heavily on hard real-time operating systems (RTOS). It has been standard practice at NASA's Jet Propulsion Laboratory (JPL) and many other institutions to use costly commercial RTOSs and hardware. After developing a real-time toolkit for VxWorks on the PowerPC platform (dubbed RTC), the interferometry group at JPL is porting this code to the real-time Application Interface (RTAI), an open source RTOS that is essentially an extension to the Linux kernel. This port has the potential to reduce software and hardware costs for future projects, while increasing the level of performance. The goals of this paper are to briefly describe the RTC toolkit, highlight the successes and pitfalls of porting the toolkit from VxWorks to Linux-RTAI, and to discuss future enhancements that will be implemented as a direct result of this port. The first port of any body of code is always the most difficult since it uncovers the OS-specific calls and forces "red flags" into those portions of the code. For this reason, It has also been a huge benefit that the project chose a generic, platform independent OS extension, ACE, and its CORBA counterpart, TAO. This port of RTC will pave the way for conversions to other environments, the most interesting of which is a non-real-time simulation environment, currently being considered by the Space Interferometry Mission (SIM) and the Terrestrial Planet Finder (TPF) Projects.

The Orthanc Ecosystem for Medical Imaging.

PubMed

Jodogne, Sébastien

2018-05-03

This paper reviews the components of Orthanc, a free and open-source, highly versatile ecosystem for medical imaging. At the core of the Orthanc ecosystem, the Orthanc server is a lightweight vendor neutral archive that provides PACS managers with a powerful environment to automate and optimize the imaging flows that are very specific to each hospital. The Orthanc server can be extended with plugins that provide solutions for teleradiology, digital pathology, or enterprise-ready databases. It is shown how software developers and research engineers can easily develop external software or Web portals dealing with medical images, with minimal knowledge of the DICOM standard, thanks to the advanced programming interface of the Orthanc server. The paper concludes by introducing the Stone of Orthanc, an innovative toolkit for the cross-platform rendering of medical images.

Methodology for the development of a taxonomy and toolkit to evaluate health-related habits and lifestyle (eVITAL)

PubMed Central

2010-01-01

Background Chronic diseases cause an ever-increasing percentage of morbidity and mortality, but many have modifiable risk factors. Many behaviors that predispose or protect an individual to chronic disease are interrelated, and therefore are best approached using an integrated model of health and the longevity paradigm, using years lived without disability as the endpoint. Findings This study used a 4-phase mixed qualitative design to create a taxonomy and related online toolkit for the evaluation of health-related habits. Core members of a working group conducted a literature review and created a framing document that defined relevant constructs. This document was revised, first by a working group and then by a series of multidisciplinary expert groups. The working group and expert panels also designed a systematic evaluation of health behaviors and risks, which was computerized and evaluated for feasibility. A demonstration study of the toolkit was performed in 11 healthy volunteers. Discussion In this protocol, we used forms of the community intelligence approach, including frame analysis, feasibility, and demonstration, to develop a clinical taxonomy and an online toolkit with standardized procedures for screening and evaluation of multiple domains of health, with a focus on longevity and the goal of integrating the toolkit into routine clinical practice. Trial Registration IMSERSO registry 200700012672 PMID:20334642

Implementing a Breastfeeding Toolkit for Nursing Education.

PubMed

Folker-Maglaya, Catherine; Pylman, Maureen E; Couch, Kimberly A; Spatz, Diane L; Marzalik, Penny R

All health professional organizations recommend exclusive breastfeeding for at least 6 months, with continued breastfeeding for 1 year or more after birth. Women cite lack of support from health professionals as a barrier to breastfeeding. Meanwhile, breastfeeding education is not considered essential to basic nursing education and students are not adequately prepared to support breastfeeding women. Therefore, a toolkit of comprehensive evidence-based breastfeeding educational materials was developed to provide essential breastfeeding knowledge. A study was performed to determine the effectiveness of the breastfeeding toolkit education in an associate degree nursing program. A pretest/posttest survey design with intervention and comparison groups was used. One hundred fourteen students completed pre- and posttests. Student knowledge was measured using a 12-item survey derived with minor modifications from Marzalik's 2004 instrument measuring breastfeeding knowledge. When pre- and posttests scores were compared within groups, both groups' knowledge scores increased. A change score was calculated with a significantly higher mean score for the intervention group. When regression analysis was used to control for the pretest score, belonging to the intervention group increased student scores but not significantly. The toolkit was developed to provide a curriculum that demonstrates enhanced learning to prepare nursing students for practice. The toolkit could be used in other settings, such as to educate staff nurses working with childbearing families.

Planetary Space Weather Services for the Europlanet 2020 Research Infrastructure

NASA Astrophysics Data System (ADS)

André, Nicolas; Grande, Manuel

2016-04-01

Under Horizon 2020, the Europlanet 2020 Research Infrastructure (EPN2020-RI) will include an entirely new Virtual Access Service, WP5 VA1 "Planetary Space Weather Services" (PSWS) that will extend the concepts of space weather and space situational awareness to other planets in our Solar System and in particular to spacecraft that voyage through it. VA1 will make five entirely new 'toolkits' accessible to the research community and to industrial partners planning for space missions: a general planetary space weather toolkit, as well as three toolkits dedicated to the following key planetary environments: Mars (in support ExoMars), comets (building on the expected success of the ESA Rosetta mission), and outer planets (in preparation for the ESA JUICE mission to be launched in 2022). This will give the European planetary science community new methods, interfaces, functionalities and/or plugins dedicated to planetary space weather in the tools and models available within the partner institutes. It will also create a novel event-diary toolkit aiming at predicting and detecting planetary events like meteor showers and impacts. A variety of tools (in the form of web applications, standalone software, or numerical models in various degrees of implementation) are available for tracing propagation of planetary and/or solar events through the Solar System and modelling the response of the planetary environment (surfaces, atmospheres, ionospheres, and magnetospheres) to those events. But these tools were not originally designed for planetary event prediction and space weather applications. So WP10 JRA4 "Planetary Space Weather Services" (PSWS) will provide the additional research and tailoring required to apply them for these purposes. The overall objectives of this Joint Research Aactivities will be to review, test, improve and adapt methods and tools available within the partner institutes in order to make prototype planetary event and space weather services operational in Europe at the end of the programme. Europlanet 2020 RI has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 654208.

CAPRI: Using a Geometric Foundation for Computational Analysis and Design

NASA Technical Reports Server (NTRS)

Haimes, Robert

2002-01-01

CAPRI (Computational Analysis Programming Interface) is a software development tool intended to make computerized design, simulation and analysis faster and more efficient. The computational steps traditionally taken for most engineering analysis (Computational Fluid Dynamics (CFD), structural analysis, etc.) are: Surface Generation, usually by employing a Computer Aided Design (CAD) system; Grid Generation, preparing the volume for the simulation; Flow Solver, producing the results at the specified operational point; Post-processing Visualization, interactively attempting to understand the results. It should be noted that the structures problem is more tractable than CFD; there are fewer mesh topologies used and the grids are not as fine (this problem space does not have the length scaling issues of fluids). For CFD, these steps have worked well in the past for simple steady-state simulations at the expense of much user interaction. The data was transmitted between phases via files. In most cases, the output from a CAD system could go IGES files. The output from Grid Generators and Solvers do not really have standards though there are a couple of file formats that can be used for a subset of the gridding (i.e. PLOT3D) data formats and the upcoming CGNS). The user would have to patch up the data or translate from one format to another to move to the next step. Sometimes this could take days. Instead of the serial approach to analysis, CAPRI takes a geometry centric approach. CAPRI is a software building tool-kit that refers to two ideas: (1) A simplified, object-oriented, hierarchical view of a solid part integrating both geometry and topology definitions, and (2) programming access to this part or assembly and any attached data. The connection to the geometry is made through an Application Programming Interface (API) and not a file system.

netCDF Operators for Rapid Analysis of Measured and Modeled Swath-like Data

NASA Astrophysics Data System (ADS)

Zender, C. S.

2015-12-01

Swath-like data (hereafter SLD) are defined by non-rectangular and/or time-varying spatial grids in which one or more coordinates are multi-dimensional. It is often challenging and time-consuming to work with SLD, including all Level 2 satellite-retrieved data, non-rectangular subsets of Level 3 data, and model data on curvilinear grids. Researchers and data centers want user-friendly, fast, and powerful methods to specify, extract, serve, manipulate, and thus analyze, SLD. To meet these needs, large research-oriented agencies and modeling center such as NASA, DOE, and NOAA increasingly employ the netCDF Operators (NCO), an open-source scientific data analysis software package applicable to netCDF and HDF data. NCO includes extensive, fast, parallelized regridding features to facilitate analysis and intercomparison of SLD and model data. Remote sensing, weather and climate modeling and analysis communities face similar problems in handling SLD including how to easily: 1. Specify and mask irregular regions such as ocean basins and political boundaries in SLD (and rectangular) grids. 2. Bin, interpolate, average, or re-map SLD to regular grids. 3. Derive secondary data from given quality levels of SLD. These common tasks require a data extraction and analysis toolkit that is SLD-friendly and, like NCO, familiar in all these communities. With NCO users can 1. Quickly project SLD onto the most useful regular grids for intercomparison. 2. Access sophisticated statistical and regridding functions that are robust to missing data and allow easy specification of quality control metrics. These capabilities improve interoperability, software-reuse, and, because they apply to SLD, minimize transmission, storage, and handling of unwanted data. While SLD analysis still poses many challenges compared to regularly gridded, rectangular data, the custom analyses scripts SLD once required are now shorter, more powerful, and user-friendly.

Comparison of 3D reconstruction of mandible for pre-operative planning using commercial and open-source software

NASA Astrophysics Data System (ADS)

Abdullah, Johari Yap; Omar, Marzuki; Pritam, Helmi Mohd Hadi; Husein, Adam; Rajion, Zainul Ahmad

2016-12-01

3D printing of mandible is important for pre-operative planning, diagnostic purposes, as well as for education and training. Currently, the processing of CT data is routinely performed with commercial software which increases the cost of operation and patient management for a small clinical setting. Usage of open-source software as an alternative to commercial software for 3D reconstruction of the mandible from CT data is scarce. The aim of this study is to compare two methods of 3D reconstruction of the mandible using commercial Materialise Mimics software and open-source Medical Imaging Interaction Toolkit (MITK) software. Head CT images with a slice thickness of 1 mm and a matrix of 512x512 pixels each were retrieved from the server located at the Radiology Department of Hospital Universiti Sains Malaysia. The CT data were analysed and the 3D models of mandible were reconstructed using both commercial Materialise Mimics and open-source MITK software. Both virtual 3D models were saved in STL format and exported to 3matic and MeshLab software for morphometric and image analyses. Both models were compared using Wilcoxon Signed Rank Test and Hausdorff Distance. No significant differences were obtained between the 3D models of the mandible produced using Mimics and MITK software. The 3D model of the mandible produced using MITK open-source software is comparable to the commercial MIMICS software. Therefore, open-source software could be used in clinical setting for pre-operative planning to minimise the operational cost.

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig

PubMed Central

Sahoo, Satya S.; Wei, Annan; Valdez, Joshua; Wang, Li; Zonjy, Bilal; Tatsuoka, Curtis; Loparo, Kenneth A.; Lhatoo, Samden D.

2016-01-01

The recent advances in neurological imaging and sensing technologies have led to rapid increase in the volume, rate of data generation, and variety of neuroscience data. This “neuroscience Big data” represents a significant opportunity for the biomedical research community to design experiments using data with greater timescale, large number of attributes, and statistically significant data size. The results from these new data-driven research techniques can advance our understanding of complex neurological disorders, help model long-term effects of brain injuries, and provide new insights into dynamics of brain networks. However, many existing neuroinformatics data processing and analysis tools were not built to manage large volume of data, which makes it difficult for researchers to effectively leverage this available data to advance their research. We introduce a new toolkit called NeuroPigPen that was developed using Apache Hadoop and Pig data flow language to address the challenges posed by large-scale electrophysiological signal data. NeuroPigPen is a modular toolkit that can process large volumes of electrophysiological signal data, such as Electroencephalogram (EEG), Electrocardiogram (ECG), and blood oxygen levels (SpO2), using a new distributed storage model called Cloudwave Signal Format (CSF) that supports easy partitioning and storage of signal data on commodity hardware. NeuroPigPen was developed with three design principles: (a) Scalability—the ability to efficiently process increasing volumes of data; (b) Adaptability—the toolkit can be deployed across different computing configurations; and (c) Ease of programming—the toolkit can be easily used to compose multi-step data processing pipelines using high-level programming constructs. The NeuroPigPen toolkit was evaluated using 750 GB of electrophysiological signal data over a variety of Hadoop cluster configurations ranging from 3 to 30 Data nodes. The evaluation results demonstrate that the toolkit is highly scalable and adaptable, which makes it suitable for use in neuroscience applications as a scalable data processing toolkit. As part of the ongoing extension of NeuroPigPen, we are developing new modules to support statistical functions to analyze signal data for brain connectivity research. In addition, the toolkit is being extended to allow integration with scientific workflow systems. NeuroPigPen is released under BSD license at: https://sites.google.com/a/case.edu/neuropigpen/. PMID:27375472

NeuroPigPen: A Scalable Toolkit for Processing Electrophysiological Signal Data in Neuroscience Applications Using Apache Pig.

PubMed

Sahoo, Satya S; Wei, Annan; Valdez, Joshua; Wang, Li; Zonjy, Bilal; Tatsuoka, Curtis; Loparo, Kenneth A; Lhatoo, Samden D

2016-01-01

The recent advances in neurological imaging and sensing technologies have led to rapid increase in the volume, rate of data generation, and variety of neuroscience data. This "neuroscience Big data" represents a significant opportunity for the biomedical research community to design experiments using data with greater timescale, large number of attributes, and statistically significant data size. The results from these new data-driven research techniques can advance our understanding of complex neurological disorders, help model long-term effects of brain injuries, and provide new insights into dynamics of brain networks. However, many existing neuroinformatics data processing and analysis tools were not built to manage large volume of data, which makes it difficult for researchers to effectively leverage this available data to advance their research. We introduce a new toolkit called NeuroPigPen that was developed using Apache Hadoop and Pig data flow language to address the challenges posed by large-scale electrophysiological signal data. NeuroPigPen is a modular toolkit that can process large volumes of electrophysiological signal data, such as Electroencephalogram (EEG), Electrocardiogram (ECG), and blood oxygen levels (SpO2), using a new distributed storage model called Cloudwave Signal Format (CSF) that supports easy partitioning and storage of signal data on commodity hardware. NeuroPigPen was developed with three design principles: (a) Scalability-the ability to efficiently process increasing volumes of data; (b) Adaptability-the toolkit can be deployed across different computing configurations; and (c) Ease of programming-the toolkit can be easily used to compose multi-step data processing pipelines using high-level programming constructs. The NeuroPigPen toolkit was evaluated using 750 GB of electrophysiological signal data over a variety of Hadoop cluster configurations ranging from 3 to 30 Data nodes. The evaluation results demonstrate that the toolkit is highly scalable and adaptable, which makes it suitable for use in neuroscience applications as a scalable data processing toolkit. As part of the ongoing extension of NeuroPigPen, we are developing new modules to support statistical functions to analyze signal data for brain connectivity research. In addition, the toolkit is being extended to allow integration with scientific workflow systems. NeuroPigPen is released under BSD license at: https://sites.google.com/a/case.edu/neuropigpen/.

Stroke

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Software Technology for Adaptable, Reliable Systems (STARS) (User Manual). Ada Command Environment (ACE) Version 8.0 Sun OS Implementation

DTIC Science & Technology

1990-10-29

the equivalent type names in the basic X libary . 37. Intrinsics Contains the type declarations common to all Xt toolkit routines. 38. Widget-Package...Memory-Size constant Integer 1; MinInt constant I-reger Integer’First; MaxInt const-i’ integer Integer’Last; -- Max- Digits constant Integer 1; -- MaxMan...connection between some type names used by Xt routines and the equivalent type names in the basic X libary . .package RenamedXlibTypes is P;’ge 65 29

The Virtual Environment for Reactor Applications (VERA): Design and architecture

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

Turner, John A., E-mail: turnerja@ornl.gov; Clarno, Kevin; Sieger, Matt

VERA, the Virtual Environment for Reactor Applications, is the system of physics capabilities being developed and deployed by the Consortium for Advanced Simulation of Light Water Reactors (CASL). CASL was established for the modeling and simulation of commercial nuclear reactors. VERA consists of integrating and interfacing software together with a suite of physics components adapted and/or refactored to simulate relevant physical phenomena in a coupled manner. VERA also includes the software development environment and computational infrastructure needed for these components to be effectively used. We describe the architecture of VERA from both software and numerical perspectives, along with the goalsmore » and constraints that drove major design decisions, and their implications. We explain why VERA is an environment rather than a framework or toolkit, why these distinctions are relevant (particularly for coupled physics applications), and provide an overview of results that demonstrate the use of VERA tools for a variety of challenging applications within the nuclear industry.« less

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

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

Varicose Veins

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Automated model integration at source code level: An approach for implementing models into the NASA Land Information System

NASA Astrophysics Data System (ADS)

Wang, S.; Peters-Lidard, C. D.; Mocko, D. M.; Kumar, S.; Nearing, G. S.; Arsenault, K. R.; Geiger, J. V.

2014-12-01

Model integration bridges the data flow between modeling frameworks and models. However, models usually do not fit directly into a particular modeling environment, if not designed for it. An example includes implementing different types of models into the NASA Land Information System (LIS), a software framework for land-surface modeling and data assimilation. Model implementation requires scientific knowledge and software expertise and may take a developer months to learn LIS and model software structure. Debugging and testing of the model implementation is also time-consuming due to not fully understanding LIS or the model. This time spent is costly for research and operational projects. To address this issue, an approach has been developed to automate model integration into LIS. With this in mind, a general model interface was designed to retrieve forcing inputs, parameters, and state variables needed by the model and to provide as state variables and outputs to LIS. Every model can be wrapped to comply with the interface, usually with a FORTRAN 90 subroutine. Development efforts need only knowledge of the model and basic programming skills. With such wrappers, the logic is the same for implementing all models. Code templates defined for this general model interface could be re-used with any specific model. Therefore, the model implementation can be done automatically. An automated model implementation toolkit was developed with Microsoft Excel and its built-in VBA language. It allows model specifications in three worksheets and contains FORTRAN 90 code templates in VBA programs. According to the model specification, the toolkit generates data structures and procedures within FORTRAN modules and subroutines, which transfer data between LIS and the model wrapper. Model implementation is standardized, and about 80 - 90% of the development load is reduced. In this presentation, the automated model implementation approach is described along with LIS programming interfaces, the general model interface and five case studies, including a regression model, Noah-MP, FASST, SAC-HTET/SNOW-17, and FLake. These different models vary in complexity with software structure. Also, we will describe how these complexities were overcome through using this approach and results of model benchmarks within LIS.

[A preliminary mapping methodology for occupational hazards and biomechanical risk evaluation: presentation of a simple, computerized tool kit for ergonomic hazards identification and risk assessment].

PubMed

Colombini, Daniela; Occhipinti, E; Di Leone, G

2011-01-01

During the last Congress of the International Ergonomics Association (IEA), Beijing, August 2009, an international group was founded with the task of developing a "toolkit for MSD prevention" under the IEA and in collaboration with the World Health Organization. The possible users of toolkits are: members of health and safety committees; health and safety representatives; line supervisors; foremen; workers; government representatives; health workers providing basic occupational health services; occupational health and safety specialists. According to the ISO standard 11228 series and the new Draft CD ISO 12259-2009: Application document guides for the potential user, our group developed a preliminary "mapping" methodology of occupational hazards in the craft industry, supported by software (Excel). The proposed methodology, using specific key enters and quick assessment criteria, allows a simple ergonomics hazards identification and risk estimation to be made. It is thus possible to decide for which occupational hazards a more exhaustive risk assessment will be necessary and which occupational consultant should be involved (occupational physician, safety engineer, industrial hygienist, etc.).

The design of an intelligent human-computer interface for the test, control and monitor system

NASA Technical Reports Server (NTRS)

Shoaff, William D.

1988-01-01

The graphical intelligence and assistance capabilities of a human-computer interface for the Test, Control, and Monitor System at Kennedy Space Center are explored. The report focuses on how a particular commercial off-the-shelf graphical software package, Data Views, can be used to produce tools that build widgets such as menus, text panels, graphs, icons, windows, and ultimately complete interfaces for monitoring data from an application; controlling an application by providing input data to it; and testing an application by both monitoring and controlling it. A complete set of tools for building interfaces is described in a manual for the TCMS toolkit. Simple tools create primitive widgets such as lines, rectangles and text strings. Intermediate level tools create pictographs from primitive widgets, and connect processes to either text strings or pictographs. Other tools create input objects; Data Views supports output objects directly, thus output objects are not considered. Finally, a set of utilities for executing, monitoring use, editing, and displaying the content of interfaces is included in the toolkit.

G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures.

PubMed

Lee, Hui Sun; Im, Wonpil

2017-01-01

Recent advances in high-throughput structure determination and computational protein structure prediction have significantly enriched the universe of protein structure. However, there is still a large gap between the number of available protein structures and that of proteins with annotated function in high accuracy. Computational structure-based protein function prediction has emerged to reduce this knowledge gap. The identification of a ligand binding site and its structure is critical to the determination of a protein's molecular function. We present a computational methodology for predicting small molecule ligand binding site and ligand structure using G-LoSA, our protein local structure alignment and similarity measurement tool. All the computational procedures described here can be easily implemented using G-LoSA Toolkit, a package of standalone software programs and preprocessed PDB structure libraries. G-LoSA and G-LoSA Toolkit are freely available to academic users at http://compbio.lehigh.edu/GLoSA . We also illustrate a case study to show the potential of our template-based approach harnessing G-LoSA for protein function prediction.

Tribal Green Building Toolkit

EPA Pesticide Factsheets

This Tribal Green Building Toolkit (Toolkit) is designed to help tribal officials, community members, planners, developers, and architects develop and adopt building codes to support green building practices. Anyone can use this toolkit!

Improving linear transport infrastructure efficiency by automated learning and optimised predictive maintenance techniques (INFRALERT)

NASA Astrophysics Data System (ADS)

Jiménez-Redondo, Noemi; Calle-Cordón, Alvaro; Kandler, Ute; Simroth, Axel; Morales, Francisco J.; Reyes, Antonio; Odelius, Johan; Thaduri, Aditya; Morgado, Joao; Duarte, Emmanuele

2017-09-01

The on-going H2020 project INFRALERT aims to increase rail and road infrastructure capacity in the current framework of increased transportation demand by developing and deploying solutions to optimise maintenance interventions planning. It includes two real pilots for road and railways infrastructure. INFRALERT develops an ICT platform (the expert-based Infrastructure Management System, eIMS) which follows a modular approach including several expert-based toolkits. This paper presents the methodologies and preliminary results of the toolkits for i) nowcasting and forecasting of asset condition, ii) alert generation, iii) RAMS & LCC analysis and iv) decision support. The results of these toolkits in a meshed road network in Portugal under the jurisdiction of Infraestruturas de Portugal (IP) are presented showing the capabilities of the approaches.

Find an Interventional Radiologist

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Society of Interventional Radiology

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Hereditary Hemorrhagic Telangiectasia - HHT

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

Child Abuse - Multiple Languages

MedlinePlus

... Section Healthy Living Toolkit: Violence In the Home - English PDF Healthy Living Toolkit: Violence In the Home - ... Section Healthy Living Toolkit: Violence In the Home - English PDF Healthy Living Toolkit: Violence In the Home - ...

Wind Integration National Dataset Toolkit | Grid Modernization | NREL

Science.gov Websites

information, share tips The WIND Toolkit includes meteorological conditions and turbine power for more than Integration National Dataset Toolkit Wind Integration National Dataset Toolkit The Wind Integration National Dataset (WIND) Toolkit is an update and expansion of the Eastern Wind Integration Data Set and

A new open-source Python-based Space Weather data access, visualization, and analysis toolkit

NASA Astrophysics Data System (ADS)

de Larquier, S.; Ribeiro, A.; Frissell, N. A.; Spaleta, J.; Kunduri, B.; Thomas, E. G.; Ruohoniemi, J.; Baker, J. B.

2013-12-01

Space weather research relies heavily on combining and comparing data from multiple observational platforms. Current frameworks exist to aggregate some of the data sources, most based on file downloads via web or ftp interfaces. Empirical models are mostly fortran based and lack interfaces with more useful scripting languages. In an effort to improve data and model access, the SuperDARN community has been developing a Python-based Space Science Data Visualization Toolkit (DaViTpy). At the center of this development was a redesign of how our data (from 30 years of SuperDARN radars) was made available. Several access solutions are now wrapped into one convenient Python interface which probes local directories, a new remote NoSQL database, and an FTP server to retrieve the requested data based on availability. Motivated by the efficiency of this interface and the inherent need for data from multiple instruments, we implemented similar modules for other space science datasets (POES, OMNI, Kp, AE...), and also included fundamental empirical models with Python interfaces to enhance data analysis (IRI, HWM, MSIS...). All these modules and more are gathered in a single convenient toolkit, which is collaboratively developed and distributed using Github and continues to grow. While still in its early stages, we expect this toolkit will facilitate multi-instrument space weather research and improve scientific productivity.

The Virtual Astronomical Observatory: Re-engineering access to astronomical data

NASA Astrophysics Data System (ADS)

Hanisch, R. J.; Berriman, G. B.; Lazio, T. J. W.; Emery Bunn, S.; Evans, J.; McGlynn, T. A.; Plante, R.

2015-06-01

The US Virtual Astronomical Observatory was a software infrastructure and development project designed both to begin the establishment of an operational Virtual Observatory (VO) and to provide the US coordination with the international VO effort. The concept of the VO is to provide the means by which an astronomer is able to discover, access, and process data seamlessly, regardless of its physical location. This paper describes the origins of the VAO, including the predecessor efforts within the US National Virtual Observatory, and summarizes its main accomplishments. These accomplishments include the development of both scripting toolkits that allow scientists to incorporate VO data directly into their reduction and analysis environments and high-level science applications for data discovery, integration, analysis, and catalog cross-comparison. Working with the international community, and based on the experience from the software development, the VAO was a major contributor to international standards within the International Virtual Observatory Alliance. The VAO also demonstrated how an operational virtual observatory could be deployed, providing a robust operational environment in which VO services worldwide were routinely checked for aliveness and compliance with international standards. Finally, the VAO engaged in community outreach, developing a comprehensive web site with on-line tutorials, announcements, links to both US and internationally developed tools and services, and exhibits and hands-on training at annual meetings of the American Astronomical Society and through summer schools and community days. All digital products of the VAO Project, including software, documentation, and tutorials, are stored in a repository for community access. The enduring legacy of the VAO is an increasing expectation that new telescopes and facilities incorporate VO capabilities during the design of their data management systems.

Trinity | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Trinity Cancer Transcriptome Analysis Toolkit (CTAT) including de novo transcriptome assembly with downstream support for expression analysis and focused analyses on cancer transcriptomes, incorporating mutation and fusion transcript discovery, and single cell analysis.

Chronic pelvic pain (pelvic congestion syndrome)

MedlinePlus

... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ... GUIDELINES, CLINICAL TOPIC ACKNOWLEDGEMENTS MACRA MATTERS HEALTH POLICY, ECONOMICS, CODING REIMBURSEMENT AND APPEALS TOOLKITS UFE AWARENESS TOOLKIT ...

KinImmerse: Macromolecular VR for NMR ensembles

PubMed Central

Block, Jeremy N; Zielinski, David J; Chen, Vincent B; Davis, Ian W; Vinson, E Claire; Brady, Rachael; Richardson, Jane S; Richardson, David C

2009-01-01

Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment) or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR) models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs). Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis. PMID:19222844

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

PubMed Central

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

2009-01-01

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

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

PubMed

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

2009-06-16

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

Monte Carlo treatment planning with modulated electron radiotherapy: framework development and application

NASA Astrophysics Data System (ADS)

Alexander, Andrew William

Within the field of medical physics, Monte Carlo radiation transport simulations are considered to be the most accurate method for the determination of dose distributions in patients. The McGill Monte Carlo treatment planning system (MMCTP), provides a flexible software environment to integrate Monte Carlo simulations with current and new treatment modalities. A developing treatment modality called energy and intensity modulated electron radiotherapy (MERT) is a promising modality, which has the fundamental capabilities to enhance the dosimetry of superficial targets. An objective of this work is to advance the research and development of MERT with the end goal of clinical use. To this end, we present the MMCTP system with an integrated toolkit for MERT planning and delivery of MERT fields. Delivery is achieved using an automated "few leaf electron collimator" (FLEC) and a controller. Aside from the MERT planning toolkit, the MMCTP system required numerous add-ons to perform the complex task of large-scale autonomous Monte Carlo simulations. The first was a DICOM import filter, followed by the implementation of DOSXYZnrc as a dose calculation engine and by logic methods for submitting and updating the status of Monte Carlo simulations. Within this work we validated the MMCTP system with a head and neck Monte Carlo recalculation study performed by a medical dosimetrist. The impact of MMCTP lies in the fact that it allows for systematic and platform independent large-scale Monte Carlo dose calculations for different treatment sites and treatment modalities. In addition to the MERT planning tools, various optimization algorithms were created external to MMCTP. The algorithms produced MERT treatment plans based on dose volume constraints that employ Monte Carlo pre-generated patient-specific kernels. The Monte Carlo kernels are generated from patient-specific Monte Carlo dose distributions within MMCTP. The structure of the MERT planning toolkit software and optimization algorithms are demonstrated. We investigated the clinical significance of MERT on spinal irradiation, breast boost irradiation, and a head and neck sarcoma cancer site using several parameters to analyze the treatment plans. Finally, we investigated the idea of mixed beam photon and electron treatment planning. Photon optimization treatment planning tools were included within the MERT planning toolkit for the purpose of mixed beam optimization. In conclusion, this thesis work has resulted in the development of an advanced framework for photon and electron Monte Carlo treatment planning studies and the development of an inverse planning system for photon, electron or mixed beam radiotherapy (MBRT). The justification and validation of this work is found within the results of the planning studies, which have demonstrated dosimetric advantages to using MERT or MBRT in comparison to clinical treatment alternatives.

TECA: A Parallel Toolkit for Extreme Climate Analysis

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

Prabhat, Mr; Ruebel, Oliver; Byna, Surendra

2012-03-12

We present TECA, a parallel toolkit for detecting extreme events in large climate datasets. Modern climate datasets expose parallelism across a number of dimensions: spatial locations, timesteps and ensemble members. We design TECA to exploit these modes of parallelism and demonstrate a prototype implementation for detecting and tracking three classes of extreme events: tropical cyclones, extra-tropical cyclones and atmospheric rivers. We process a modern TB-sized CAM5 simulation dataset with TECA, and demonstrate good runtime performance for the three case studies.

Integration Toolkit and Methods (ITKM) Corporate Data Integration Tools (CDIT). Review of the State-of-the-Art with Respect to Integration Toolkits and Methods (ITKM)

DTIC Science & Technology

1992-06-01

system capabilities \\Jch as memory management and network communications are provided by a virtual machine-type operating environment. Various human ...thinking. The elements of this substrate include representational formality, genericity, a method of formal analysis, and augmentation of human analytical...the form of identifying: the data entity itself; its aliases (including how the data is presented th programs or human users in the form of copy

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework.

PubMed

Zheng, Qi; Grice, Elizabeth A

2016-10-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost's algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost.

Filling the gaps between tools and users: a tool comparator, using protein-protein interaction as an example.

PubMed

Kano, Yoshinobu; Nguyen, Ngan; Saetre, Rune; Yoshida, Kazuhiro; Miyao, Yusuke; Tsuruoka, Yoshimasa; Matsubayashi, Yuichiro; Ananiadou, Sophia; Tsujii, Jun'ichi

2008-01-01

Recently, several text mining programs have reached a near-practical level of performance. Some systems are already being used by biologists and database curators. However, it has also been recognized that current Natural Language Processing (NLP) and Text Mining (TM) technology is not easy to deploy, since research groups tend to develop systems that cater specifically to their own requirements. One of the major reasons for the difficulty of deployment of NLP/TM technology is that re-usability and interoperability of software tools are typically not considered during development. While some effort has been invested in making interoperable NLP/TM toolkits, the developers of end-to-end systems still often struggle to reuse NLP/TM tools, and often opt to develop similar programs from scratch instead. This is particularly the case in BioNLP, since the requirements of biologists are so diverse that NLP tools have to be adapted and re-organized in a much more extensive manner than was originally expected. Although generic frameworks like UIMA (Unstructured Information Management Architecture) provide promising ways to solve this problem, the solution that they provide is only partial. In order for truly interoperable toolkits to become a reality, we also need sharable type systems and a developer-friendly environment for software integration that includes functionality for systematic comparisons of available tools, a simple I/O interface, and visualization tools. In this paper, we describe such an environment that was developed based on UIMA, and we show its feasibility through our experience in developing a protein-protein interaction (PPI) extraction system.

An evaluation of a toolkit for the early detection, management, and control of carbapenemase-producing Enterobacteriaceae: a survey of acute hospital trusts in England.

PubMed

Coope, C M; Verlander, N Q; Schneider, A; Hopkins, S; Welfare, W; Johnson, A P; Patel, B; Oliver, I

2018-03-09

Following hospital outbreaks of carbapenemase-producing Enterobacteriaceae (CPE), Public Health England published a toolkit in December 2013 to promote the early detection, management, and control of CPE colonization and infection in acute hospital settings. To examine awareness, uptake, implementation and usefulness of the CPE toolkit and identify potential barriers and facilitators to its adoption in order to inform future guidance. A cross-sectional survey of National Health Service (NHS) acute trusts was conducted in May 2016. Descriptive analysis and multivariable regression models were conducted, and narrative responses were analysed thematically and informed using behaviour change theory. Most (92%) acute trusts had a written CPE plan. Fewer (75%) reported consistent compliance with screening and isolation of CPE risk patients. Lower prioritization and weaker senior management support for CPE prevention were associated with poorer compliance. Awareness of the CPE toolkit was high and all trusts with patients infected or colonized with CPE had used the toolkit either as provided (32%), or to inform (65%) their own local CPE plan. Despite this, many respondents (80%) did not believe that the CPE toolkit guidance offered an effective means to prevent CPE or was practical to follow. CPE prevention and control requires robust IPC measures. Successful implementation can be hindered by a complex set of factors related to their practical execution, insufficient resources and a lack of confidence in the effectiveness of the guidance. Future CPE guidance would benefit from substantive user involvement, processes for ongoing feedback, and regular guidance updates. Copyright © 2018 The Healthcare Infection Society. All rights reserved.

Computer Games as Therapy for Persons with Stroke.

PubMed

Lauterbach, Sarah A; Foreman, Matt H; Engsberg, Jack R

2013-02-01

Stroke affects approximately 800,000 individuals each year, with 65% having residual impairments. Studies have demonstrated that mass practice leads to regaining motor function in affected extremities; however, traditional therapy does not include the repetitions needed for this recovery. Videogames have been shown to be good motivators to complete repetitions. Advances in technology and low-cost hardware bring new opportunities to use computer games during stroke therapy. This study examined the use of the Microsoft (Redmond, WA) Kinect™ and Flexible Action and Articulated Skeleton Toolkit (FAAST) software as a therapy tool to play existing free computer games on the Internet. Three participants attended a 1-hour session where they played two games with upper extremity movements as game controls. Video was taken for analysis of movement repetitions, and questions were answered about participant history and their perceptions of the games. Participants remained engaged through both games; regardless of previous computer use all participants successfully played two games. Five minutes of game play averaged 34 repetitions of the affected extremity. The Intrinsic Motivation Inventory showed a high level of satisfaction in two of the three participants. The Kinect Sensor with the FAAST software has the potential to be an economical tool to be used alongside traditional therapy to increase the number of repetitions completed in a motivating and engaging way for clients.

ASERA: A spectrum eye recognition assistant for quasar spectra

NASA Astrophysics Data System (ADS)

Yuan, Hailong; Zhang, Haotong; Zhang, Yanxia; Lei, Yajuan; Dong, Yiqiao; Zhao, Yongheng

2013-11-01

Spectral type recognition is an important and fundamental step of large sky survey projects in the data reduction for further scientific research, like parameter measurement and statistic work. It tends out to be a huge job to manually inspect the low quality spectra produced from the massive spectroscopic survey, where the automatic pipeline may not provide confident type classification results. In order to improve the efficiency and effectiveness of spectral classification, we develop a semi-automated toolkit named ASERA, ASpectrum Eye Recognition Assistant. The main purpose of ASERA is to help the user in quasar spectral recognition and redshift measurement. Furthermore it can also be used to recognize various types of spectra of stars, galaxies and AGNs (Active Galactic Nucleus). It is an interactive software allowing the user to visualize observed spectra, superimpose template spectra from the Sloan Digital Sky Survey (SDSS), and interactively access related spectral line information. It is an efficient and user-friendly toolkit for the accurate classification of spectra observed by LAMOST (the Large Sky Area Multi-object Fiber Spectroscopic Telescope). The toolkit is available in two modes: a Java standalone application and a Java applet. ASERA has a few functions, such as wavelength and flux scale setting, zoom in and out, redshift estimation, spectral line identification, which helps user to improve the spectral classification accuracy especially for low quality spectra and reduce the labor of eyeball check. The function and performance of this tool is displayed through the recognition of several quasar spectra and a late type stellar spectrum from the LAMOST Pilot survey. Its future expansion capabilities are discussed.

Get Your Atoms in Order--An Open-Source Implementation of a Novel and Robust Molecular Canonicalization Algorithm.

PubMed

Schneider, Nadine; Sayle, Roger A; Landrum, Gregory A

2015-10-26

Finding a canonical ordering of the atoms in a molecule is a prerequisite for generating a unique representation of the molecule. The canonicalization of a molecule is usually accomplished by applying some sort of graph relaxation algorithm, the most common of which is the Morgan algorithm. There are known issues with that algorithm that lead to noncanonical atom orderings as well as problems when it is applied to large molecules like proteins. Furthermore, each cheminformatics toolkit or software provides its own version of a canonical ordering, most based on unpublished algorithms, which also complicates the generation of a universal unique identifier for molecules. We present an alternative canonicalization approach that uses a standard stable-sorting algorithm instead of a Morgan-like index. Two new invariants that allow canonical ordering of molecules with dependent chirality as well as those with highly symmetrical cyclic graphs have been developed. The new approach proved to be robust and fast when tested on the 1.45 million compounds of the ChEMBL 20 data set in different scenarios like random renumbering of input atoms or SMILES round tripping. Our new algorithm is able to generate a canonical order of the atoms of protein molecules within a few milliseconds. The novel algorithm is implemented in the open-source cheminformatics toolkit RDKit. With this paper, we provide a reference Python implementation of the algorithm that could easily be integrated in any cheminformatics toolkit. This provides a first step toward a common standard for canonical atom ordering to generate a universal unique identifier for molecules other than InChI.

Every Place Counts Leadership Academy : transportation toolkit quick guide

DOT National Transportation Integrated Search

2016-12-01

This is a quick guide to the Transportation Toolkit. The Transportation Toolkit is meant to explain the transportation process to members of the public with no prior knowledge of transportation. The Toolkit is meant to demystify transportation and he...

Object Toolkit Version 4.3 User’s Manual

DTIC Science & Technology

2016-12-31

unlimited. (OPS-17-12855 dtd 19 Jan 2017) 13. SUPPLEMENTARY NOTES 14. ABSTRACT Object Toolkit is a finite - element model builder specifically designed for...INTRODUCTION 1 What Is Object Toolkit? Object Toolkit is a finite - element model builder specifically designed for creating representations of spacecraft...Nascap-2k and EPIC, the user is not required to purchase or learn expensive finite element generators to create system models. Second, Object Toolkit

Platform for Postprocessing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Don

2008-01-01

Taking advantage of the similarities that exist among all waveform-based non-destructive evaluation (NDE) methods, a common software platform has been developed containing multiple- signal and image-processing techniques for waveforms and images. The NASA NDE Signal and Image Processing software has been developed using the latest versions of LabVIEW, and its associated Advanced Signal Processing and Vision Toolkits. The software is useable on a PC with Windows XP and Windows Vista. The software has been designed with a commercial grade interface in which two main windows, Waveform Window and Image Window, are displayed if the user chooses a waveform file to display. Within these two main windows, most actions are chosen through logically conceived run-time menus. The Waveform Window has plots for both the raw time-domain waves and their frequency- domain transformations (fast Fourier transform and power spectral density). The Image Window shows the C-scan image formed from information of the time-domain waveform (such as peak amplitude) or its frequency-domain transformation at each scan location. The user also has the ability to open an image, or series of images, or a simple set of X-Y paired data set in text format. Each of the Waveform and Image Windows contains menus from which to perform many user actions. An option exists to use raw waves obtained directly from scan, or waves after deconvolution if system wave response is provided. Two types of deconvolution, time-based subtraction or inverse-filter, can be performed to arrive at a deconvolved wave set. Additionally, the menu on the Waveform Window allows preprocessing of waveforms prior to image formation, scaling and display of waveforms, formation of different types of images (including non-standard types such as velocity), gating of portions of waves prior to image formation, and several other miscellaneous and specialized operations. The menu available on the Image Window allows many further image processing and analysis operations, some of which are found in commercially-available image-processing software programs (such as Adobe Photoshop), and some that are not (removing outliers, Bscan information, region-of-interest analysis, line profiles, and precision feature measurements).

Supporting safe driving with arthritis: developing a driving toolkit for clinical practice and consumer use.

PubMed

Vrkljan, Brenda H; Cranney, Ann; Worswick, Julia; O'Donnell, Siobhan; Li, Linda C; Gélinas, Isabelle; Byszewski, Anna; Man-Son-Hing, Malcolm; Marshall, Shawn

2010-01-01

We conducted a series of focus groups to explore the information needs of clinicians and consumers related to arthritis and driving. An open coding analysis identified common themes across both consumer and clinician-based focus groups that underscored the importance of addressing driving-related concerns and the challenges associated with assessing safety. The results revealed that although driving is critical for maintaining independence and community mobility, drivers with arthritis experience several problems that can affect safe operation of a motor vehicle. Findings from this study are part of a broader research initiative that will inform the development of the Arthritis and Driving toolkit. This toolkit outlines strategies to support safe mobility for people with arthritis and will be an important resource in the coming years given the aging population.

Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities.

PubMed

Covington, Kelsie; McCreedy, Evan S; Chen, Min; Carass, Aaron; Aucoin, Nicole; Landman, Bennett A

2010-05-25

Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

DPOI: Distributed software system development platform for ocean information service

NASA Astrophysics Data System (ADS)

Guo, Zhongwen; Hu, Keyong; Jiang, Yongguo; Sun, Zhaosui

2015-02-01

Ocean information management is of great importance as it has been employed in many areas of ocean science and technology. However, the developments of Ocean Information Systems (OISs) often suffer from low efficiency because of repetitive work and continuous modifications caused by dynamic requirements. In this paper, the basic requirements of OISs are analyzed first, and then a novel platform DPOI is proposed to improve development efficiency and enhance software quality of OISs by providing off-the-shelf resources. In the platform, the OIS is decomposed hierarchically into a set of modules, which can be reused in different system developments. These modules include the acquisition middleware and data loader that collect data from instruments and files respectively, the database that stores data consistently, the components that support fast application generation, the web services that make the data from distributed sources syntactical by use of predefined schemas and the configuration toolkit that enables software customization. With the assistance of the development platform, the software development needs no programming and the development procedure is thus accelerated greatly. We have applied the development platform in practical developments and evaluated its efficiency in several development practices and different development approaches. The results show that DPOI significantly improves development efficiency and software quality.

Techniques in helical scanning, dynamic imaging and image segmentation for improved quantitative analysis with X-ray micro-CT

NASA Astrophysics Data System (ADS)

Sheppard, Adrian; Latham, Shane; Middleton, Jill; Kingston, Andrew; Myers, Glenn; Varslot, Trond; Fogden, Andrew; Sawkins, Tim; Cruikshank, Ron; Saadatfar, Mohammad; Francois, Nicolas; Arns, Christoph; Senden, Tim

2014-04-01

This paper reports on recent advances at the micro-computed tomography facility at the Australian National University. Since 2000 this facility has been a significant centre for developments in imaging hardware and associated software for image reconstruction, image analysis and image-based modelling. In 2010 a new instrument was constructed that utilises theoretically-exact image reconstruction based on helical scanning trajectories, allowing higher cone angles and thus better utilisation of the available X-ray flux. We discuss the technical hurdles that needed to be overcome to allow imaging with cone angles in excess of 60°. We also present dynamic tomography algorithms that enable the changes between one moment and the next to be reconstructed from a sparse set of projections, allowing higher speed imaging of time-varying samples. Researchers at the facility have also created a sizeable distributed-memory image analysis toolkit with capabilities ranging from tomographic image reconstruction to 3D shape characterisation. We show results from image registration and present some of the new imaging and experimental techniques that it enables. Finally, we discuss the crucial question of image segmentation and evaluate some recently proposed techniques for automated segmentation.

MoKey: A versatile exergame creator for everyday usage.

PubMed

Eckert, Martina; López, Marcos; Lázaro, Carlos; Meneses, Juan

2017-11-27

Currently, virtual applications for physical exercises are highly appreciated as rehabilitation instruments. This article presents a middleware called "MoKey" (Motion Keyboard), which converts standard off-the-shelf software into exergames (exercise games). A configurable set of gestures, captured by a motion capture camera, is translated into the key strokes required by the chosen software. The present study assesses the tool regarding usability and viability on a heterogeneous group of 11 participants, aged 5 to 51, with moderate to severe disabilities, and mostly bound to a wheelchair. In comparison with FAAST (The Flexible Action and Articulated Skeleton Toolkit), MoKey achieved better results in terms of ease of use and computational load. The viability as an exergame creator tool was proven with help of four applications (PowerPoint®, e-book reader, Skype®, and Tetris). Success rates of up to 91% have been achieved, subjective perception was rated with 4.5 points (from 0-5). The middleware provides increased motivation due to the use of favorite software and the advantage of exploiting it for exercise. Used together with communication software or online games, social inclusion can be stimulated. The therapists can employ the tool to monitor the correctness and progress of the exercises.

Frame Decoder for Consultative Committee for Space Data Systems (CCSDS)

NASA Technical Reports Server (NTRS)

Reyes, Miguel A. De Jesus

2014-01-01

GNU Radio is a free and open source development toolkit that provides signal processing to implement software radios. It can be used with low-cost external RF hardware to create software defined radios, or without hardware in a simulation-like environment. GNU Radio applications are primarily written in Python and C++. The Universal Software Radio Peripheral (USRP) is a computer-hosted software radio designed by Ettus Research. The USRP connects to a host computer via high-speed Gigabit Ethernet. Using the open source Universal Hardware Driver (UHD), we can run GNU Radio applications using the USRP. An SDR is a "radio in which some or all physical layer functions are software defined"(IEEE Definition). A radio is any kind of device that wirelessly transmits or receives radio frequency (RF) signals in the radio frequency. An SDR is a radio communication system where components that have been typically implemented in hardware are implemented in software. GNU Radio has a generic packet decoder block that is not optimized for CCSDS frames. Using this generic packet decoder will add bytes to the CCSDS frames and will not permit for bit error correction using Reed-Solomon. The CCSDS frames consist of 256 bytes, including a 32-bit sync marker (0x1ACFFC1D). This frames are generated by the Space Data Processor and GNU Radio will perform the modulation and framing operations, including frame synchronization.

A Racial Equity Toolkit for Midwifery Organizations.

PubMed

Gordon, Wendy M

2016-11-01

Midwifery associations are increasing awareness and commitment to racial equity in the profession and in the communities we serve. Moving these commitments from words into action may be facilitated by a racial equity toolkit to help guide midwifery organizations to consider all policies, initiatives, and actions with a racial equity lens. Racial equity impact analyses have been used in recent years by various governmental agencies in the United States and abroad with positive results, and emerging literature indicates that nonprofit organizations are having similarly positive results. This article proposes a framework for midwifery organizations to incorporate a racial equity toolkit, starting with explicit intentions of the organization with regard to racial equity in the profession. Indicators of success are elucidated as the next step, followed by the use of a racial equity impact analysis worksheet. This worksheet is applied by teams or committees when considering new policies or initiatives to examine those actions through a racial equity lens. An organizational change team and equity advisory groups are essential in assisting organizational leadership to forecast potential negative and positive impacts. Examples of the components of a midwifery-specific racial equity toolkit are included. © 2016 by the American College of Nurse-Midwives.

The effectiveness of toolkits as knowledge translation strategies for integrating evidence into clinical care: a systematic review

PubMed Central

Yamada, Janet; Shorkey, Allyson; Barwick, Melanie; Widger, Kimberley; Stevens, Bonnie J

2015-01-01

Objectives The aim of this systematic review was to evaluate the effectiveness of toolkits as a knowledge translation (KT) strategy for facilitating the implementation of evidence into clinical care. Toolkits include multiple resources for educating and/or facilitating behaviour change. Design Systematic review of the literature on toolkits. Methods A search was conducted on MEDLINE, EMBASE, PsycINFO and CINAHL. Studies were included if they evaluated the effectiveness of a toolkit to support the integration of evidence into clinical care, and if the KT goal(s) of the study were to inform, share knowledge, build awareness, change practice, change behaviour, and/or clinical outcomes in healthcare settings, inform policy, or to commercialise an innovation. Screening of studies, assessment of methodological quality and data extraction for the included studies were conducted by at least two reviewers. Results 39 relevant studies were included for full review; 8 were rated as moderate to strong methodologically with clinical outcomes that could be somewhat attributed to the toolkit. Three of the eight studies evaluated the toolkit as a single KT intervention, while five embedded the toolkit into a multistrategy intervention. Six of the eight toolkits were partially or mostly effective in changing clinical outcomes and six studies reported on implementation outcomes. The types of resources embedded within toolkits varied but included predominantly educational materials. Conclusions Future toolkits should be informed by high-quality evidence and theory, and should be evaluated using rigorous study designs to explain the factors underlying their effectiveness and successful implementation. PMID:25869686

VTK-m: Accelerating the Visualization Toolkit for Massively Threaded Architectures

DOE PAGES

Moreland, Kenneth; Sewell, Christopher; Usher, William; ...

2016-05-09

Here, one of the most critical challenges for high-performance computing (HPC) scientific visualization is execution on massively threaded processors. Of the many fundamental changes we are seeing in HPC systems, one of the most profound is a reliance on new processor types optimized for execution bandwidth over latency hiding. Our current production scientific visualization software is not designed for these new types of architectures. To address this issue, the VTK-m framework serves as a container for algorithms, provides flexible data representation, and simplifies the design of visualization algorithms on new and future computer architecture.

VTK-m: Accelerating the Visualization Toolkit for Massively Threaded Architectures

DOE PAGES

Moreland, Kenneth; Sewell, Christopher; Usher, William; ...

2016-05-09

Execution on massively threaded processors is one of the most critical challenges for high-performance computing (HPC) scientific visualization. Of the many fundamental changes we are seeing in HPC systems, one of the most profound is a reliance on new processor types optimized for execution bandwidth over latency hiding. Moreover, our current production scientific visualization software is not designed for these new types of architectures. In order to address this issue, the VTK-m framework serves as a container for algorithms, provides flexible data representation, and simplifies the design of visualization algorithms on new and future computer architecture.

Study on Web-Based Tool for Regional Agriculture Industry Structure Optimization Using Ajax

NASA Astrophysics Data System (ADS)

Huang, Xiaodong; Zhu, Yeping

According to the research status of regional agriculture industry structure adjustment information system and the current development of information technology, this paper takes web-based regional agriculture industry structure optimization tool as research target. This paper introduces Ajax technology and related application frameworks to build an auxiliary toolkit of decision support system for agricultural policy maker and economy researcher. The toolkit includes a “one page” style component of regional agriculture industry structure optimization which provides agile arguments setting method that enables applying sensitivity analysis and usage of data and comparative advantage analysis result, and a component that can solve the linear programming model and its dual problem by simplex method.

ITEP: an integrated toolkit for exploration of microbial pan-genomes.

PubMed

Benedict, Matthew N; Henriksen, James R; Metcalf, William W; Whitaker, Rachel J; Price, Nathan D

2014-01-03

Comparative genomics is a powerful approach for studying variation in physiological traits as well as the evolution and ecology of microorganisms. Recent technological advances have enabled sequencing large numbers of related genomes in a single project, requiring computational tools for their integrated analysis. In particular, accurate annotations and identification of gene presence and absence are critical for understanding and modeling the cellular physiology of newly sequenced genomes. Although many tools are available to compare the gene contents of related genomes, new tools are necessary to enable close examination and curation of protein families from large numbers of closely related organisms, to integrate curation with the analysis of gain and loss, and to generate metabolic networks linking the annotations to observed phenotypes. We have developed ITEP, an Integrated Toolkit for Exploration of microbial Pan-genomes, to curate protein families, compute similarities to externally-defined domains, analyze gene gain and loss, and generate draft metabolic networks from one or more curated reference network reconstructions in groups of related microbial species among which the combination of core and variable genes constitute the their "pan-genomes". The ITEP toolkit consists of: (1) a series of modular command-line scripts for identification, comparison, curation, and analysis of protein families and their distribution across many genomes; (2) a set of Python libraries for programmatic access to the same data; and (3) pre-packaged scripts to perform common analysis workflows on a collection of genomes. ITEP's capabilities include de novo protein family prediction, ortholog detection, analysis of functional domains, identification of core and variable genes and gene regions, sequence alignments and tree generation, annotation curation, and the integration of cross-genome analysis and metabolic networks for study of metabolic network evolution. ITEP is a powerful, flexible toolkit for generation and curation of protein families. ITEP's modular design allows for straightforward extension as analysis methods and tools evolve. By integrating comparative genomics with the development of draft metabolic networks, ITEP harnesses the power of comparative genomics to build confidence in links between genotype and phenotype and helps disambiguate gene annotations when they are evaluated in both evolutionary and metabolic network contexts.

3D Simulation of External Flooding Events for the RISMC Pathway

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

Prescott, Steven; Mandelli, Diego; Sampath, Ramprasad

2015-09-01

Incorporating 3D simulations as part of the Risk-Informed Safety Margins Characterization (RISMIC) Toolkit allows analysts to obtain a more complete picture of complex system behavior for events including external plant hazards. External events such as flooding have become more important recently – however these can be analyzed with existing and validated simulated physics toolkits. In this report, we describe these approaches specific to flooding-based analysis using an approach called Smoothed Particle Hydrodynamics. The theory, validation, and example applications of the 3D flooding simulation are described. Integrating these 3D simulation methods into computational risk analysis provides a spatial/visual aspect to themore » design, improves the realism of results, and can prove visual understanding to validate the analysis of flooding.« less

Measuring the Environmental Dimensions of Human Migration: The Demographer's Toolkit.

PubMed

Fussell, Elizabeth; Hunter, Lori M; Gray, Clark L

2014-09-01

In recent years, the empirical literature linking environmental factors and human migration has grown rapidly and gained increasing visibility among scholars and the policy community. Still, this body of research uses a wide range of methodological approaches for assessing environment-migration relationships. Without comparable data and measures across a range of contexts, it is impossible to make generalizations that would facilitate the development of future migration scenarios. Demographic researchers have a large methodological toolkit for measuring migration as well as modeling its drivers. This toolkit includes population censuses, household surveys, survival analysis and multi-level modeling. This paper's purpose is to introduce climate change researchers to demographic data and methods and to review exemplary studies of the environmental dimensions of human migration. Our intention is to foster interdisciplinary understanding and scholarship, and to promote high quality research on environment and migration that will lead toward broader knowledge of this association.

Measuring the Environmental Dimensions of Human Migration: The Demographer’s Toolkit

PubMed Central

Hunter, Lori M.; Gray, Clark L.

2014-01-01

In recent years, the empirical literature linking environmental factors and human migration has grown rapidly and gained increasing visibility among scholars and the policy community. Still, this body of research uses a wide range of methodological approaches for assessing environment-migration relationships. Without comparable data and measures across a range of contexts, it is impossible to make generalizations that would facilitate the development of future migration scenarios. Demographic researchers have a large methodological toolkit for measuring migration as well as modeling its drivers. This toolkit includes population censuses, household surveys, survival analysis and multi-level modeling. This paper’s purpose is to introduce climate change researchers to demographic data and methods and to review exemplary studies of the environmental dimensions of human migration. Our intention is to foster interdisciplinary understanding and scholarship, and to promote high quality research on environment and migration that will lead toward broader knowledge of this association. PMID:25177108

iQIST v0.7: An open source continuous-time quantum Monte Carlo impurity solver toolkit

NASA Astrophysics Data System (ADS)

Huang, Li

2017-12-01

In this paper, we present a new version of the iQIST software package, which is capable of solving various quantum impurity models by using the hybridization expansion (or strong coupling expansion) continuous-time quantum Monte Carlo algorithm. In the revised version, the software architecture is completely redesigned. New basis (intermediate representation or singular value decomposition representation) for the single-particle and two-particle Green's functions is introduced. A lot of useful physical observables are added, such as the charge susceptibility, fidelity susceptibility, Binder cumulant, and autocorrelation time. Especially, we optimize measurement for the two-particle Green's functions. Both the particle-hole and particle-particle channels are supported. In addition, the block structure of the two-particle Green's functions is exploited to accelerate the calculation. Finally, we fix some known bugs and limitations. The computational efficiency of the code is greatly enhanced.

When paradigms collide at the road rail interface: evaluation of a sociotechnical systems theory design toolkit for cognitive work analysis.

PubMed

Read, Gemma J M; Salmon, Paul M; Lenné, Michael G

2016-09-01

The Cognitive Work Analysis Design Toolkit (CWA-DT) is a recently developed approach that provides guidance and tools to assist in applying the outputs of CWA to design processes to incorporate the values and principles of sociotechnical systems theory. In this paper, the CWA-DT is evaluated based on an application to improve safety at rail level crossings. The evaluation considered the extent to which the CWA-DT met pre-defined methodological criteria and aligned with sociotechnical values and principles. Both process and outcome measures were taken based on the ratings of workshop participants and human factors experts. Overall, workshop participants were positive about the process and indicated that it met the methodological criteria and sociotechnical values. However, expert ratings suggested that the CWA-DT achieved only limited success in producing RLX designs that fully aligned with the sociotechnical approach. Discussion about the appropriateness of the sociotechnical approach in a public safety context is provided. Practitioner Summary: Human factors and ergonomics practitioners need evidence of the effectiveness of methods. A design toolkit for cognitive work analysis, incorporating values and principles from sociotechnical systems theory, was applied to create innovative designs for rail level crossings. Evaluation results based on the application are provided and discussed.

An algorithm to identify functional groups in organic molecules.

PubMed

Ertl, Peter

2017-06-07

The concept of functional groups forms a basis of organic chemistry, medicinal chemistry, toxicity assessment, spectroscopy and also chemical nomenclature. All current software systems to identify functional groups are based on a predefined list of substructures. We are not aware of any program that can identify all functional groups in a molecule automatically. The algorithm presented in this article is an attempt to solve this scientific challenge. An algorithm to identify functional groups in a molecule based on iterative marching through its atoms is described. The procedure is illustrated by extracting functional groups from the bioactive portion of the ChEMBL database, resulting in identification of 3080 unique functional groups. A new algorithm to identify all functional groups in organic molecules is presented. The algorithm is relatively simple and full details with examples are provided, therefore implementation in any cheminformatics toolkit should be relatively easy. The new method allows the analysis of functional groups in large chemical databases in a way that was not possible using previous approaches. Graphical abstract .

Quantity, Revisited: An Object-Oriented Reusable Class

NASA Technical Reports Server (NTRS)

Funston, Monica Gayle; Gerstle, Walter; Panthaki, Malcolm

1998-01-01

"Quantity", a prototype implementation of an object-oriented class, was developed for two reasons: to help engineers and scientists manipulate the many types of quantities encountered during routine analysis, and to create a reusable software component to for large domain-specific applications. From being used as a stand-alone application to being incorporated into an existing computational mechanics toolkit, "Quantity" appears to be a useful and powerful object. "Quantity" has been designed to maintain the full engineering meaning of values with respect to units and coordinate systems. A value is a scalar, vector, tensor, or matrix, each of which is composed of Value Components, each of which may be an integer, floating point number, fuzzy number, etc., and its associated physical unit. Operations such as coordinate transformation and arithmetic operations are handled by member functions of "Quantity". The prototype has successfully tested such characteristics as maintaining a numeric value, an associated unit, and an annotation. In this paper we further explore the design of "Quantity", with particular attention to coordinate systems.

StarTrax --- The Next Generation User Interface

NASA Astrophysics Data System (ADS)

Richmond, Alan; White, Nick

StarTrax is a software package to be distributed to end users for installation on their local computing infrastructure. It will provide access to many services of the HEASARC, i.e. bulletins, catalogs, proposal and analysis tools, initially for the ROSAT MIPS (Mission Information and Planning System), later for the Next Generation Browse. A user activating the GUI will reach all HEASARC capabilities through a uniform view of the system, independent of the local computing environment and of the networking method of accessing StarTrax. Use it if you prefer the point-and-click metaphor of modern GUI technology, to the classical command-line interfaces (CLI). Notable strengths include: easy to use; excellent portability; very robust server support; feedback button on every dialog; painstakingly crafted User Guide. It is designed to support a large number of input devices including terminals, workstations and personal computers. XVT's Portability Toolkit is used to build the GUI in C/C++ to run on: OSF/Motif (UNIX or VMS), OPEN LOOK (UNIX), or Macintosh, or MS-Windows (DOS), or character systems.

Optical Modeling Activities for NASA's James Webb Space Telescope (JWST): V. Operational Alignment Updates

NASA Technical Reports Server (NTRS)

Howard, Joseph M.; Ha, Kong Q.; Shiri, Ron; Smith, J. Scott; Mosier, Gary; Muheim, Danniella

2008-01-01

This paper is part five of a series on the ongoing optical modeling activities for the James Webb Space Telescope (JWST). The first two papers discussed modeling JWST on-orbit performance using wavefront sensitivities to predict line of sight motion induced blur, and stability during thermal transients. The third paper investigates the aberrations resulting from alignment and figure compensation of the controllable degrees of freedom (primary and secondary mirrors), which may be encountered during ground alignment and on-orbit commissioning of the observatory, and the fourth introduced the software toolkits used to perform much of the optical analysis for JWST. The work here models observatory operations by simulating line-of-sight image motion and alignment drifts over a two-week period. Alignment updates are then simulated using wavefront sensing and control processes to calculate and perform the corrections. A single model environment in Matlab is used for evaluating the predicted performance of the observatory during these operations.

Multimethod evaluation of the VA's peer-to-peer Toolkit for patient-centered medical home implementation.

PubMed

Luck, Jeff; Bowman, Candice; York, Laura; Midboe, Amanda; Taylor, Thomas; Gale, Randall; Asch, Steven

2014-07-01

Effective implementation of the patient-centered medical home (PCMH) in primary care practices requires training and other resources, such as online toolkits, to share strategies and materials. The Veterans Health Administration (VA) developed an online Toolkit of user-sourced tools to support teams implementing its Patient Aligned Care Team (PACT) medical home model. To present findings from an evaluation of the PACT Toolkit, including use, variation across facilities, effect of social marketing, and factors influencing use. The Toolkit is an online repository of ready-to-use tools created by VA clinic staff that physicians, nurses, and other team members may share, download, and adopt in order to more effectively implement PCMH principles and improve local performance on VA metrics. Multimethod evaluation using: (1) website usage analytics, (2) an online survey of the PACT community of practice's use of the Toolkit, and (3) key informant interviews. Survey respondents were PACT team members and coaches (n = 544) at 136 VA facilities. Interview respondents were Toolkit users and non-users (n = 32). For survey data, multivariable logistic models were used to predict Toolkit awareness and use. Interviews and open-text survey comments were coded using a "common themes" framework. The Consolidated Framework for Implementation Research (CFIR) guided data collection and analyses. The Toolkit was used by 6,745 staff in the first 19 months of availability. Among members of the target audience, 80 % had heard of the Toolkit, and of those, 70 % had visited the website. Tools had been implemented at 65 % of facilities. Qualitative findings revealed a range of user perspectives from enthusiastic support to lack of sufficient time to browse the Toolkit. An online Toolkit to support PCMH implementation was used at VA facilities nationwide. Other complex health care organizations may benefit from adopting similar online peer-to-peer resource libraries.

Web servers and services for electrostatics calculations with APBS and PDB2PQR

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

Unni, Samir; Huang, Yong; Hanson, Robert M.

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in currentmore » distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/.« less

The Virtual Environment for Reactor Applications (VERA): Design and architecture

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

Turner, John A.; Clarno, Kevin; Sieger, Matt

VERA, the Virtual Environment for Reactor Applications, is the system of physics capabilities being developed and deployed by the Consortium for Advanced Simulation of Light Water Reactors (CASL), the first DOE Hub, which was established in July 2010 for the modeling and simulation of commercial nuclear reactors. VERA consists of integrating and interfacing software together with a suite of physics components adapted and/or refactored to simulate relevant physical phenomena in a coupled manner. VERA also includes the software development environment and computational infrastructure needed for these components to be effectively used. We describe the architecture of VERA from both amore » software and a numerical perspective, along with the goals and constraints that drove the major design decisions and their implications. As a result, we explain why VERA is an environment rather than a framework or toolkit, why these distinctions are relevant (particularly for coupled physics applications), and provide an overview of results that demonstrate the application of VERA tools for a variety of challenging problems within the nuclear industry.« less

Web servers and services for electrostatics calculations with APBS and PDB2PQR

PubMed Central

Unni, Samir; Huang, Yong; Hanson, Robert; Tobias, Malcolm; Krishnan, Sriram; Li, Wilfred W.; Nielsen, Jens E.; Baker, Nathan A.

2011-01-01

APBS and PDB2PQR are widely utilized free software packages for biomolecular electrostatics calculations. Using the Opal toolkit, we have developed a Web services framework for these software packages that enables the use of APBS and PDB2PQR by users who do not have local access to the necessary amount of computational capabilities. This not only increases accessibility of the software to a wider range of scientists, educators, and students but it also increases the availability of electrostatics calculations on portable computing platforms. Users can access this new functionality in two ways. First, an Opal-enabled version of APBS is provided in current distributions, available freely on the web. Second, we have extended the PDB2PQR web server to provide an interface for the setup, execution, and visualization electrostatics potentials as calculated by APBS. This web interface also uses the Opal framework which ensures the scalability needed to support the large APBS user community. Both of these resources are available from the APBS/PDB2PQR website: http://www.poissonboltzmann.org/. PMID:21425296

Optical Modeling Activities for NASA's James Webb Space Telescope (JWST). 4; Overview and Introduction of Matlab Based Toolkits used to Interface with Optical Design Software

NASA Technical Reports Server (NTRS)

Howard, Joseph

2007-01-01

This is part four of a series on the ongoing optical modeling activities for James Webb Space Telescope (JWST). The first two discussed modeling JWST on-orbit performance using wavefront sensitivities to predict line of sight motion induced blur, and stability during thermal transients. The third investigates the aberrations resulting from alignment and figure compensation of the controllable degrees of freedom (primary and secondary mirrors), which may be encountered during ground alignment and on-orbit commissioning of the observatory. The work here introduces some of the math software tools used to perform the work of the previous three papers of this series. NASA has recently approved these in-house tools for public release as open source, so this presentation also serves as a quick tutorial on their use. The tools are collections of functions written in Matlab, which interface with optical design software (CodeV, OSLO, and Zemax) using either COM or DDE communication protocol. The functions are discussed, and examples are given.

The Virtual Environment for Reactor Applications (VERA): Design and architecture

DOE PAGES

Turner, John A.; Clarno, Kevin; Sieger, Matt; ...

2016-09-08

VERA, the Virtual Environment for Reactor Applications, is the system of physics capabilities being developed and deployed by the Consortium for Advanced Simulation of Light Water Reactors (CASL), the first DOE Hub, which was established in July 2010 for the modeling and simulation of commercial nuclear reactors. VERA consists of integrating and interfacing software together with a suite of physics components adapted and/or refactored to simulate relevant physical phenomena in a coupled manner. VERA also includes the software development environment and computational infrastructure needed for these components to be effectively used. We describe the architecture of VERA from both amore » software and a numerical perspective, along with the goals and constraints that drove the major design decisions and their implications. As a result, we explain why VERA is an environment rather than a framework or toolkit, why these distinctions are relevant (particularly for coupled physics applications), and provide an overview of results that demonstrate the application of VERA tools for a variety of challenging problems within the nuclear industry.« less

The MERMAID project

NASA Technical Reports Server (NTRS)

Cowderoy, A. J. C.; Jenkins, John O.; Poulymenakou, A

1992-01-01

The tendency for software development projects to be completed over schedule and over budget was documented extensively. Additionally many projects are completed within budgetary and schedule target only as a result of the customer agreeing to accept reduced functionality. In his classic book, The Mythical Man Month, Fred Brooks exposes the fallacy that effort and schedule are freely interchangeable. All current cost models are produced on the assumption that there is very limited scope for schedule compression unless there is a corresponding reduction in delivered functionality. The Metrication and Resources Modeling Aid (MERMAID) project, partially financed by the Commission of the European Communities (CEC) as Project 2046 began in Oct. 1988 and its goal were as follows: (1) improvement of understanding of the relationships between software development productivity and product and process metrics; (2) to facilitate the widespread technology transfer from the Consortium to the European Software Industry; and (3) to facilitate the widespread uptake of cost estimation techniques by the provision of prototype cost estimation tools. MERMAID developed a family of methods for cost estimation, many of which have had tools implemented in prototypes. These prototypes are best considered as toolkits or workbenches.

Optical modeling activities for NASA's James Webb Space Telescope (JWST): IV. Overview and introduction of MATLAB based toolkits used to interface with optical design software

NASA Astrophysics Data System (ADS)

Howard, Joseph M.

2007-09-01

This paper is part four of a series on the ongoing optical modeling activities for the James Webb Space Telescope (JWST). The first two papers discussed modeling JWST on-orbit performance using wavefront sensitivities to predict line of sight motion induced blur, and stability during thermal transients. The third paper investigates the aberrations resulting from alignment and figure compensation of the controllable degrees of freedom (primary and secondary mirrors), which may be encountered during ground alignment and on-orbit commissioning of the observatory. The work here introduces some of the math software tools used to perform the work of the previous three papers of this series. NASA has recently approved these in-house tools for public release as open source, so this presentation also serves as a quick tutorial on their use. The tools are collections of functions written for use in MATLAB to interface with optical design software (CODE V, OSLO, and ZEMAX) using either COM or DDE communication protocol. The functions are discussed, and examples are given.

Python-Based Scientific Analysis and Visualization of Precipitation Systems at NASA Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Lang, Timothy J.

2015-01-01

At NASA Marshall Space Flight Center (MSFC), Python is used several different ways to analyze and visualize precipitating weather systems. A number of different Python-based software packages have been developed, which are available to the larger scientific community. The approach in all these packages is to utilize pre-existing Python modules as well as to be object-oriented and scalable. The first package that will be described and demonstrated is the Python Advanced Microwave Precipitation Radiometer (AMPR) Data Toolkit, or PyAMPR for short. PyAMPR reads geolocated brightness temperature data from any flight of the AMPR airborne instrument over its 25-year history into a common data structure suitable for user-defined analyses. It features rapid, simplified (i.e., one line of code) production of quick-look imagery, including Google Earth overlays, swath plots of individual channels, and strip charts showing multiple channels at once. These plotting routines are also capable of significant customization for detailed, publication-ready figures. Deconvolution of the polarization-varying channels to static horizontally and vertically polarized scenes is also available. Examples will be given of PyAMPR's contribution toward real-time AMPR data display during the Integrated Precipitation and Hydrology Experiment (IPHEx), which took place in the Carolinas during May-June 2014. The second software package is the Marshall Multi-Radar/Multi-Sensor (MRMS) Mosaic Python Toolkit, or MMM-Py for short. MMM-Py was designed to read, analyze, and display three-dimensional national mosaicked reflectivity data produced by the NOAA National Severe Storms Laboratory (NSSL). MMM-Py can read MRMS mosaics from either their unique binary format or their converted NetCDF format. It can also read and properly interpret the current mosaic design (4 regional tiles) as well as mosaics produced prior to late July 2013 (8 tiles). MMM-Py can easily stitch multiple tiles together to provide a larger regional or national picture of precipitating weather systems. Composites, horizontal and vertical crosssections, and combinations thereof are easily displayed using as little as one line of code. MMM-Py can also write to the native MRMS binary format, and sub-sectioning of tiles (or multiple stitched tiles) is anticipated to be in place by the time of this meeting. Thus, MMM-Py also can be used to power the creation of custom mosaics for targeted regional studies. Overlays of other data (e.g., lightning observations) are easily accomplished. Demonstrations of MMM-Py, including the creation of animations, will be shown. Finally, Marshall has done significant work to interface Python-based analysis routines with the U.S. Department of Energy's Py-ART software package for radar data ingest, processing, and analysis. One example of this is the Python Turbulence Detection Algorithm (PyTDA), an MSFC-based implementation of the National Center for Atmospheric Research (NCAR) Turbulence Detection Algorithm (NTDA) for the purposes of convective-scale analysis, situational awareness, and forensic meteorology. PyTDA exploits Py-ART's radar data ingest routines and data model to rapidly produce aviation-relevant turbulence estimates from Doppler radar data. Work toward processing speed optimization and better integration within the Py-ART framework will be highlighted. Python-based analysis within the Py-ART framework is also being done for new research related to intercomparison of ground-based radar data with satellite estimates of ocean winds, as well as research on the electrification of pyrocumulus clouds.

GARLIC: a bioinformatic toolkit for aetiologically connecting diseases and cell type-specific regulatory maps

PubMed Central

Nikolić, Miloš; Papantonis, Argyris

2017-01-01

Abstract Genome-wide association studies (GWAS) have emerged as a powerful tool to uncover the genetic basis of human common diseases, which often show a complex, polygenic and multi-factorial aetiology. These studies have revealed that 70–90% of all single nucleotide polymorphisms (SNPs) associated with common complex diseases do not occur within genes (i.e. they are non-coding), making the discovery of disease-causative genetic variants and the elucidation of the underlying pathological mechanisms far from straightforward. Based on emerging evidences suggesting that disease-associated SNPs are frequently found within cell type-specific regulatory sequences, here we present GARLIC (GWAS-based Prediction Toolkit for Connecting Diseases and Cell Types), a user-friendly, multi-purpose software with an associated database and online viewer that, using global maps of cis-regulatory elements, can aetiologically connect human diseases with relevant cell types. Additionally, GARLIC can be used to retrieve potential disease-causative genetic variants overlapping regulatory sequences of interest. Overall, GARLIC can satisfy several important needs within the field of medical genetics, thus potentially assisting in the ultimate goal of uncovering the elusive and complex genetic basis of common human disorders. PMID:28007912

Planetary Space Weather Service: Part of the the Europlanet 2020 Research Infrastructure

NASA Astrophysics Data System (ADS)

Grande, Manuel; Andre, Nicolas

2016-07-01

Over the next four years the Europlanet 2020 Research Infrastructure will set up an entirely new European Planetary Space Weather service (PSWS). Europlanet RI is a part of of Horizon 2020 (EPN2020-RI, http://www.europlanet-2020-ri.eu). The Virtual Access Service, WP5 VA1 "Planetary Space Weather Services" will extend the concepts of space weather and space situational awareness to other planets in our Solar System and in particular to spacecraft that voyage through it. VA1 will make five entirely new 'toolkits' accessible to the research community and to industrial partners planning for space missions: a general planetary space weather toolkit, as well as three toolkits dedicated to the following key planetary environments: Mars (in support ExoMars), comets (building on the expected success of the ESA Rosetta mission), and outer planets (in preparation for the ESA JUICE mission to be launched in 2022). This will give the European planetary science community new methods, interfaces, functionalities and/or plugins dedicated to planetary space weather in the tools and models available within the partner institutes. It will also create a novel event-diary toolkit aiming at predicting and detecting planetary events like meteor showers and impacts. A variety of tools (in the form of web applications, standalone software, or numerical models in various degrees of implementation) are available for tracing propagation of planetary and/or solar events through the Solar System and modelling the response of the planetary environment (surfaces, atmospheres, ionospheres, and magnetospheres) to those events. But these tools were not originally designed for planetary event prediction and space weather applications. So WP10 JRA4 "Planetary Space Weather Services" (PSWS) will provide the additional research and tailoring required to apply them for these purposes. The overall objectives of this Joint Research Aactivities will be to review, test, improve and adapt methods and tools available within the partner institutes in order to make prototype planetary event and space weather services operational in Europe at the end of the programme. Europlanet 2020 RI has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 654208.

Evaluation of an Extension-Delivered Resource for Accelerating Progress in Childhood Obesity Prevention: The BEPA-Toolkit

ERIC Educational Resources Information Center

Gunter, Katherine B.; Abi Nader, Patrick; Armington, Amanda; Hicks, John C.; John, Deborah

2017-01-01

The Balanced Energy Physical Activity Toolkit, or the BEPA-Toolkit, supports physical activity (PA) programming via Extension in elementary schools. In a pilot study, we evaluated the effectiveness of the BEPA-Toolkit as used by teachers through Supplemental Nutrition Assistance Program Education partnerships. We surveyed teachers (n = 57)…

Big data and clinicians: a review on the state of the science.

PubMed

Wang, Weiqi; Krishnan, Eswar

2014-01-17

In the past few decades, medically related data collection saw a huge increase, referred to as big data. These huge datasets bring challenges in storage, processing, and analysis. In clinical medicine, big data is expected to play an important role in identifying causality of patient symptoms, in predicting hazards of disease incidence or reoccurrence, and in improving primary-care quality. The objective of this review was to provide an overview of the features of clinical big data, describe a few commonly employed computational algorithms, statistical methods, and software toolkits for data manipulation and analysis, and discuss the challenges and limitations in this realm. We conducted a literature review to identify studies on big data in medicine, especially clinical medicine. We used different combinations of keywords to search PubMed, Science Direct, Web of Knowledge, and Google Scholar for literature of interest from the past 10 years. This paper reviewed studies that analyzed clinical big data and discussed issues related to storage and analysis of this type of data. Big data is becoming a common feature of biological and clinical studies. Researchers who use clinical big data face multiple challenges, and the data itself has limitations. It is imperative that methodologies for data analysis keep pace with our ability to collect and store data.

Wavelet extractor: A Bayesian well-tie and wavelet extraction program

NASA Astrophysics Data System (ADS)

Gunning, James; Glinsky, Michael E.

2006-06-01

We introduce a new open-source toolkit for the well-tie or wavelet extraction problem of estimating seismic wavelets from seismic data, time-to-depth information, and well-log suites. The wavelet extraction model is formulated as a Bayesian inverse problem, and the software will simultaneously estimate wavelet coefficients, other parameters associated with uncertainty in the time-to-depth mapping, positioning errors in the seismic imaging, and useful amplitude-variation-with-offset (AVO) related parameters in multi-stack extractions. It is capable of multi-well, multi-stack extractions, and uses continuous seismic data-cube interpolation to cope with the problem of arbitrary well paths. Velocity constraints in the form of checkshot data, interpreted markers, and sonic logs are integrated in a natural way. The Bayesian formulation allows computation of full posterior uncertainties of the model parameters, and the important problem of the uncertain wavelet span is addressed uses a multi-model posterior developed from Bayesian model selection theory. The wavelet extraction tool is distributed as part of the Delivery seismic inversion toolkit. A simple log and seismic viewing tool is included in the distribution. The code is written in Java, and thus platform independent, but the Seismic Unix (SU) data model makes the inversion particularly suited to Unix/Linux environments. It is a natural companion piece of software to Delivery, having the capacity to produce maximum likelihood wavelet and noise estimates, but will also be of significant utility to practitioners wanting to produce wavelet estimates for other inversion codes or purposes. The generation of full parameter uncertainties is a crucial function for workers wishing to investigate questions of wavelet stability before proceeding to more advanced inversion studies.

AlignerBoost: A Generalized Software Toolkit for Boosting Next-Gen Sequencing Mapping Accuracy Using a Bayesian-Based Mapping Quality Framework

PubMed Central

Zheng, Qi; Grice, Elizabeth A.

2016-01-01

Accurate mapping of next-generation sequencing (NGS) reads to reference genomes is crucial for almost all NGS applications and downstream analyses. Various repetitive elements in human and other higher eukaryotic genomes contribute in large part to ambiguously (non-uniquely) mapped reads. Most available NGS aligners attempt to address this by either removing all non-uniquely mapping reads, or reporting one random or "best" hit based on simple heuristics. Accurate estimation of the mapping quality of NGS reads is therefore critical albeit completely lacking at present. Here we developed a generalized software toolkit "AlignerBoost", which utilizes a Bayesian-based framework to accurately estimate mapping quality of ambiguously mapped NGS reads. We tested AlignerBoost with both simulated and real DNA-seq and RNA-seq datasets at various thresholds. In most cases, but especially for reads falling within repetitive regions, AlignerBoost dramatically increases the mapping precision of modern NGS aligners without significantly compromising the sensitivity even without mapping quality filters. When using higher mapping quality cutoffs, AlignerBoost achieves a much lower false mapping rate while exhibiting comparable or higher sensitivity compared to the aligner default modes, therefore significantly boosting the detection power of NGS aligners even using extreme thresholds. AlignerBoost is also SNP-aware, and higher quality alignments can be achieved if provided with known SNPs. AlignerBoost’s algorithm is computationally efficient, and can process one million alignments within 30 seconds on a typical desktop computer. AlignerBoost is implemented as a uniform Java application and is freely available at https://github.com/Grice-Lab/AlignerBoost. PMID:27706155

The Bioperl Toolkit: Perl Modules for the Life Sciences

PubMed Central

Stajich, Jason E.; Block, David; Boulez, Kris; Brenner, Steven E.; Chervitz, Stephen A.; Dagdigian, Chris; Fuellen, Georg; Gilbert, James G.R.; Korf, Ian; Lapp, Hilmar; Lehväslaiho, Heikki; Matsalla, Chad; Mungall, Chris J.; Osborne, Brian I.; Pocock, Matthew R.; Schattner, Peter; Senger, Martin; Stein, Lincoln D.; Stupka, Elia; Wilkinson, Mark D.; Birney, Ewan

2002-01-01

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort. [Supplemental material is available online at www.genome.org. Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html). It is available for download at http://www.bioperl.org. Support inquiries should be addressed to bioperl-l@bioperl.org.] PMID:12368254

The HARNESS Workbench: Unified and Adaptive Access to Diverse HPC Platforms

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

Sunderam, Vaidy S.

2012-03-20

The primary goal of the Harness WorkBench (HWB) project is to investigate innovative software environments that will help enhance the overall productivity of applications science on diverse HPC platforms. Two complementary frameworks were designed: one, a virtualized command toolkit for application building, deployment, and execution, that provides a common view across diverse HPC systems, in particular the DOE leadership computing platforms (Cray, IBM, SGI, and clusters); and two, a unified runtime environment that consolidates access to runtime services via an adaptive framework for execution-time and post processing activities. A prototype of the first was developed based on the concept ofmore » a 'system-call virtual machine' (SCVM), to enhance portability of the HPC application deployment process across heterogeneous high-end machines. The SCVM approach to portable builds is based on the insertion of toolkit-interpretable directives into original application build scripts. Modifications resulting from these directives preserve the semantics of the original build instruction flow. The execution of the build script is controlled by our toolkit that intercepts build script commands in a manner transparent to the end-user. We have applied this approach to a scientific production code (Gamess-US) on the Cray-XT5 machine. The second facet, termed Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users perspectives. To achieve that, Unibus proposes a Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and soft and successive conditioning to enable automatic and user-transparent resource provisioning. A proof of concept implementation has demonstrated the viability of this approach on high end machines, grid systems and computing clouds.« less

Business intelligence from social media: a study from the VAST Box Office Challenge.

PubMed

Lu, Yafeng; Wang, Feng; Maciejewski, Ross

2014-01-01

With over 16 million tweets per hour, 600 new blog posts per minute, and 400 million active users on Facebook, businesses have begun searching for ways to turn real-time consumer-based posts into actionable intelligence. The goal is to extract information from this noisy, unstructured data and use it for trend analysis and prediction. Current practices support the idea that visual analytics (VA) can help enable the effective analysis of such data. However, empirical evidence demonstrating the effectiveness of a VA solution is still lacking. A proposed VA toolkit extracts data from Bitly and Twitter to predict movie revenue and ratings. Results from the 2013 VAST Box Office Challenge demonstrate the benefit of an interactive environment for predictive analysis, compared to a purely statistical modeling approach. The VA approach used by the toolkit is generalizable to other domains involving social media data, such as sales forecasting and advertisement analysis.

Genetic Code Analysis Toolkit: A novel tool to explore the coding properties of the genetic code and DNA sequences

NASA Astrophysics Data System (ADS)

Kraljić, K.; Strüngmann, L.; Fimmel, E.; Gumbel, M.

2018-01-01

The genetic code is degenerated and it is assumed that redundancy provides error detection and correction mechanisms in the translation process. However, the biological meaning of the code's structure is still under current research. This paper presents a Genetic Code Analysis Toolkit (GCAT) which provides workflows and algorithms for the analysis of the structure of nucleotide sequences. In particular, sets or sequences of codons can be transformed and tested for circularity, comma-freeness, dichotomic partitions and others. GCAT comes with a fertile editor custom-built to work with the genetic code and a batch mode for multi-sequence processing. With the ability to read FASTA files or load sequences from GenBank, the tool can be used for the mathematical and statistical analysis of existing sequence data. GCAT is Java-based and provides a plug-in concept for extensibility. Availability: Open source Homepage:http://www.gcat.bio/

Implementing a user-driven online quality improvement toolkit for cancer care.

PubMed

Luck, Jeff; York, Laura S; Bowman, Candice; Gale, Randall C; Smith, Nina; Asch, Steven M

2015-05-01

Peer-to-peer collaboration within integrated health systems requires a mechanism for sharing quality improvement lessons. The Veterans Health Administration (VA) developed online compendia of tools linked to specific cancer quality indicators. We evaluated awareness and use of the toolkits, variation across facilities, impact of social marketing, and factors influencing toolkit use. A diffusion of innovations conceptual framework guided the collection of user activity data from the Toolkit Series SharePoint site and an online survey of potential Lung Cancer Care Toolkit users. The VA Toolkit Series site had 5,088 unique visitors in its first 22 months; 5% of users accounted for 40% of page views. Social marketing communications were correlated with site usage. Of survey respondents (n = 355), 54% had visited the site, of whom 24% downloaded at least one tool. Respondents' awareness of the lung cancer quality performance of their facility, and facility participation in quality improvement collaboratives, were positively associated with Toolkit Series site use. Facility-level lung cancer tool implementation varied widely across tool types. The VA Toolkit Series achieved widespread use and a high degree of user engagement, although use varied widely across facilities. The most active users were aware of and active in cancer care quality improvement. Toolkit use seemed to be reinforced by other quality improvement activities. A combination of user-driven tool creation and centralized toolkit development seemed to be effective for leveraging health information technology to spread disease-specific quality improvement tools within an integrated health care system. Copyright © 2015 by American Society of Clinical Oncology.

Network Science Research Laboratory (NSRL) Discrete Event Toolkit

DTIC Science & Technology

2016-01-01

ARL-TR-7579 ● JAN 2016 US Army Research Laboratory Network Science Research Laboratory (NSRL) Discrete Event Toolkit by...Laboratory (NSRL) Discrete Event Toolkit by Theron Trout and Andrew J Toth Computational and Information Sciences Directorate, ARL...Research Laboratory (NSRL) Discrete Event Toolkit 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Theron Trout

Using prospective hazard analysis to assess an active shooter emergency operations plan.

PubMed

Card, Alan J; Harrison, Heidi; Ward, James; Clarkson, P John

2012-01-01

Most risk management activity in the healthcare sector is retrospective, based on learning from experience. This is feasible where the risks are routine, but emergency operations plans (EOP) guide the response to events that are both high risk and rare. Under these circumstances, it is important to get the response right the first time, but learning from experience is usually not an option. This case study presents the rationale for taking a proactive approach to improving healthcare organizations' EOP. It demonstrates how the Prospective Hazard Analysis (PHA) Toolkit can drive organizational learning and argues that this toolkit may lead to more efficient improvement than drills and exercises. © 2012 American Society for Healthcare Risk Management of the American Hospital Association.