ReGaTE: Registration of Galaxy Tools in Elixir.

PubMed

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

2017-06-01

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

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

PubMed

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

2007-11-01

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

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

Open source cardiology electronic health record development for DIGICARDIAC implementation

NASA Astrophysics Data System (ADS)

Dugarte, Nelson; Medina, Rubén.; Huiracocha, Lourdes; Rojas, Rubén.

2015-12-01

This article presents the development of a Cardiology Electronic Health Record (CEHR) system. Software consists of a structured algorithm designed under Health Level-7 (HL7) international standards. Novelty of the system is the integration of high resolution ECG (HRECG) signal acquisition and processing tools, patient information management tools and telecardiology tools. Acquisition tools are for management and control of the DIGICARDIAC electrocardiograph functions. Processing tools allow management of HRECG signal analysis searching for indicative patterns of cardiovascular pathologies. Telecardiology tools incorporation allows system communication with other health care centers decreasing access time to the patient information. CEHR system was completely developed using open source software. Preliminary results of process validation showed the system efficiency.

Parallel software tools at Langley Research Center

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Tennille, Geoffrey M.; Lakeotes, Christopher D.; Randall, Donald P.; Arthur, Jarvis J.; Hammond, Dana P.; Mall, Gerald H.

1993-01-01

This document gives a brief overview of parallel software tools available on the Intel iPSC/860 parallel computer at Langley Research Center. It is intended to provide a source of information that is somewhat more concise than vendor-supplied material on the purpose and use of various tools. Each of the chapters on tools is organized in a similar manner covering an overview of the functionality, access information, how to effectively use the tool, observations about the tool and how it compares to similar software, known problems or shortfalls with the software, and reference documentation. It is primarily intended for users of the iPSC/860 at Langley Research Center and is appropriate for both the experienced and novice user.

Distributed and Collaborative Software Analysis

NASA Astrophysics Data System (ADS)

Ghezzi, Giacomo; Gall, Harald C.

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

Tools for open geospatial science

NASA Astrophysics Data System (ADS)

Petras, V.; Petrasova, A.; Mitasova, H.

2017-12-01

Open science uses open source to deal with reproducibility challenges in data and computational sciences. However, just using open source software or making the code public does not make the research reproducible. Moreover, the scientists face the challenge of learning new unfamiliar tools and workflows. In this contribution, we will look at a graduate-level course syllabus covering several software tools which make validation and reuse by a wider professional community possible. For the novices in the open science arena, we will look at how scripting languages such as Python and Bash help us reproduce research (starting with our own work). Jupyter Notebook will be introduced as a code editor, data exploration tool, and a lab notebook. We will see how Git helps us not to get lost in revisions and how Docker is used to wrap all the parts together using a single text file so that figures for a scientific paper or a technical report can be generated with a single command. We will look at examples of software and publications in the geospatial domain which use these tools and principles. Scientific contributions to GRASS GIS, a powerful open source desktop GIS and geoprocessing backend, will serve as an example of why and how to publish new algorithms and tools as part of a bigger open source project.

The GenABEL Project for statistical genomics.

PubMed

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

2016-01-01

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

Software for Real-Time Analysis of Subsonic Test Shot Accuracy

DTIC Science & Technology

2014-03-01

used the C++ programming language, the Open Source Computer Vision ( OpenCV ®) software library, and Microsoft Windows® Application Programming...video for comparison through OpenCV image analysis tools. Based on the comparison, the software then computed the coordinates of each shot relative to...DWB researchers wanted to use the Open Source Computer Vision ( OpenCV ) software library for capturing and analyzing frames of video. OpenCV contains

Generating DEM from LIDAR data - comparison of available software tools

NASA Astrophysics Data System (ADS)

Korzeniowska, K.; Lacka, M.

2011-12-01

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

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

PubMed

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

2016-01-01

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

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

NASA Astrophysics Data System (ADS)

Frigeri, A.

2012-12-01

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

Automated verification of flight software. User's manual

NASA Technical Reports Server (NTRS)

Saib, S. H.

1982-01-01

(Automated Verification of Flight Software), a collection of tools for analyzing source programs written in FORTRAN and AED is documented. The quality and the reliability of flight software are improved by: (1) indented listings of source programs, (2) static analysis to detect inconsistencies in the use of variables and parameters, (3) automated documentation, (4) instrumentation of source code, (5) retesting guidance, (6) analysis of assertions, (7) symbolic execution, (8) generation of verification conditions, and (9) simplification of verification conditions. Use of AVFS in the verification of flight software is described.

Strengthening Software Authentication with the ROSE Software Suite

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

White, G

2006-06-15

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

Using Rose and Compass for Authentication

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

White, G

2009-07-09

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

Software Engineering Laboratory (SEL) data and information policy

NASA Technical Reports Server (NTRS)

Mcgarry, Frank

1991-01-01

The policies and overall procedures that are used in distributing and in making available products of the Software Engineering Laboratory (SEL) are discussed. The products include project data and measures, project source code, reports, and software tools.

Finding the Right Educational Software for Your Child.

ERIC Educational Resources Information Center

Moore, Jack

1990-01-01

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

The GenABEL Project for statistical genomics

PubMed Central

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

2016-01-01

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

Software Model Checking Without Source Code

NASA Technical Reports Server (NTRS)

Chaki, Sagar; Ivers, James

2009-01-01

We present a framework, called AIR, for verifying safety properties of assembly language programs via software model checking. AIR extends the applicability of predicate abstraction and counterexample guided abstraction refinement to the automated verification of low-level software. By working at the assembly level, AIR allows verification of programs for which source code is unavailable-such as legacy and COTS software-and programs that use features-such as pointers, structures, and object-orientation-that are problematic for source-level software verification tools. In addition, AIR makes no assumptions about the underlying compiler technology. We have implemented a prototype of AIR and present encouraging results on several non-trivial examples.

Requirements UML Tool (RUT) Expanded for Extreme Programming (CI02)

NASA Technical Reports Server (NTRS)

McCoy, James R.

2003-01-01

A procedure for capturing and managing system requirements that incorporates XP user stories. Because costs associated with identifying problems in requirements increase dramatically over the lifecycle of a project, a method for identifying sources of software risks in user stories is urgently needed. This initiative aims to determine a set of guide-lines for user stories that will result in high-quality requirement. To further this initiative, a tool is needed to analyze user stories that can assess the quality of individual user stories, detect sources cf software risk's, produce software metrics, and identify areas in user stories that can be improved.

SU-E-T-254: Development of a HDR-BT QA Tool for Verification of Source Position with Oncentra Applicator Modeling

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

Kumazaki, Y; Miyaura, K; Hirai, R

2015-06-15

Purpose: To develop a High Dose Rate Brachytherapy (HDR-BT) quality assurance (QA) tool for verification of source position with Oncentra applicator modeling, and to report the results of radiation source positions with this tool. Methods: We developed a HDR-BT QA phantom and automated analysis software for verification of source position with Oncentra applicator modeling for the Fletcher applicator used in the MicroSelectron HDR system. This tool is intended for end-to-end tests that mimic the clinical 3D image-guided brachytherapy (3D-IGBT) workflow. The phantom is a 30x30x3 cm cuboid phantom with radiopaque markers, which are inserted into the phantom to evaluate applicatormore » tips and reference source positions; positions are laterally shifted 10 mm from the applicator axis. The markers are lead-based and scatter radiation to expose the films. Gafchromic RTQA2 films are placed on the applicators. The phantom includes spaces to embed the applicators. The source position is determined as the distance between the exposed source position and center position of two pairs of the first radiopaque markers. We generated a 3D-IGBT plan with applicator modeling. The first source position was 6 mm from the applicator tips, and the second source position was 10 mm from the first source position. Results: All source positions were consistent with the exposed positions within 1 mm for all Fletcher applicators using in-house software. Moreover, the distance between source positions was in good agreement with the reference distance. Applicator offset, determined as the distance from the applicator tips at the first source position in the treatment planning system, was accurate. Conclusion: Source position accuracy of applicator modeling used in 3D-IGBT was acceptable. This phantom and software will be useful as a HDR-BT QA tool for verification of source position with Oncentra applicator modeling.« less

Near-Infrared Neuroimaging with NinPy

PubMed Central

Strangman, Gary E.; Zhang, Quan; Zeffiro, Thomas

2009-01-01

There has been substantial recent growth in the use of non-invasive optical brain imaging in studies of human brain function in health and disease. Near-infrared neuroimaging (NIN) is one of the most promising of these techniques and, although NIN hardware continues to evolve at a rapid pace, software tools supporting optical data acquisition, image processing, statistical modeling, and visualization remain less refined. Python, a modular and computationally efficient development language, can support functional neuroimaging studies of diverse design and implementation. In particular, Python's easily readable syntax and modular architecture allow swift prototyping followed by efficient transition to stable production systems. As an introduction to our ongoing efforts to develop Python software tools for structural and functional neuroimaging, we discuss: (i) the role of non-invasive diffuse optical imaging in measuring brain function, (ii) the key computational requirements to support NIN experiments, (iii) our collection of software tools to support NIN, called NinPy, and (iv) future extensions of these tools that will allow integration of optical with other structural and functional neuroimaging data sources. Source code for the software discussed here will be made available at www.nmr.mgh.harvard.edu/Neural_SystemsGroup/software.html. PMID:19543449

PyPedal, an open source software package for pedigree analysis

USDA-ARS?s Scientific Manuscript database

The open source software package PyPedal (http://pypedal.sourceforge.net/) was first released in 2002, and provided users with a set of simple tools for manipulating pedigrees. Its flexibility has been demonstrated by its used in a number of settings for large and small populations. After substantia...

Methodology of decreasing software complexity using ontology

NASA Astrophysics Data System (ADS)

DÄ browska-Kubik, Katarzyna

2015-09-01

In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

The Application of Function Points to Predict Source Lines of Code for Software Development

DTIC Science & Technology

1992-09-01

there are some disadvantages. Software estimating tools are expensive. A single tool may cost more than $15,000 due to the high market value of the...term and Lang variables simultaneously onlN added marginal improvements over models with these terms included singularly. Using all the available

Anatomy of BioJS, an open source community for the life sciences.

PubMed

Yachdav, Guy; Goldberg, Tatyana; Wilzbach, Sebastian; Dao, David; Shih, Iris; Choudhary, Saket; Crouch, Steve; Franz, Max; García, Alexander; García, Leyla J; Grüning, Björn A; Inupakutika, Devasena; Sillitoe, Ian; Thanki, Anil S; Vieira, Bruno; Villaveces, José M; Schneider, Maria V; Lewis, Suzanna; Pettifer, Steve; Rost, Burkhard; Corpas, Manuel

2015-07-08

BioJS is an open source software project that develops visualization tools for different types of biological data. Here we report on the factors that influenced the growth of the BioJS user and developer community, and outline our strategy for building on this growth. The lessons we have learned on BioJS may also be relevant to other open source software projects.

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

PubMed

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

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

Role of Social Software Tools in Education: A Literature Review

ERIC Educational Resources Information Center

Minocha, Shailey

2009-01-01

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

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants

PubMed Central

Byrska-Bishop, Marta; Wallace, John; Frase, Alexander T; Ritchie, Marylyn D

2018-01-01

Abstract Motivation BioBin is an automated bioinformatics tool for the multi-level biological binning of sequence variants. Herein, we present a significant update to BioBin which expands the software to facilitate a comprehensive rare variant analysis and incorporates novel features and analysis enhancements. Results In BioBin 2.3, we extend our software tool by implementing statistical association testing, updating the binning algorithm, as well as incorporating novel analysis features providing for a robust, highly customizable, and unified rare variant analysis tool. Availability and implementation The BioBin software package is open source and freely available to users at http://www.ritchielab.com/software/biobin-download Contact mdritchie@geisinger.edu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28968757

CellProfiler and KNIME: open source tools for high content screening.

PubMed

Stöter, Martin; Niederlein, Antje; Barsacchi, Rico; Meyenhofer, Felix; Brandl, Holger; Bickle, Marc

2013-01-01

High content screening (HCS) has established itself in the world of the pharmaceutical industry as an essential tool for drug discovery and drug development. HCS is currently starting to enter the academic world and might become a widely used technology. Given the diversity of problems tackled in academic research, HCS could experience some profound changes in the future, mainly with more imaging modalities and smart microscopes being developed. One of the limitations in the establishment of HCS in academia is flexibility and cost. Flexibility is important to be able to adapt the HCS setup to accommodate the multiple different assays typical of academia. Many cost factors cannot be avoided, but the costs of the software packages necessary to analyze large datasets can be reduced by using Open Source software. We present and discuss the Open Source software CellProfiler for image analysis and KNIME for data analysis and data mining that provide software solutions which increase flexibility and keep costs low.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Improving mass measurement accuracy in mass spectrometry based proteomics by combining open source tools for chromatographic alignment and internal calibration.

PubMed

Palmblad, Magnus; van der Burgt, Yuri E M; Dalebout, Hans; Derks, Rico J E; Schoenmaker, Bart; Deelder, André M

2009-05-02

Accurate mass determination enhances peptide identification in mass spectrometry based proteomics. We here describe the combination of two previously published open source software tools to improve mass measurement accuracy in Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). The first program, msalign, aligns one MS/MS dataset with one FTICRMS dataset. The second software, recal2, uses peptides identified from the MS/MS data for automated internal calibration of the FTICR spectra, resulting in sub-ppm mass measurement errors.

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

PubMed

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

2015-03-01

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

Analyzing huge pathology images with open source software.

PubMed

Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

2013-06-06

Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here:http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272.

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5955513929846272 PMID:23829479

Software Assurance: Five Essential Considerations for Acquisition Officials

DTIC Science & Technology

2007-05-01

May 2007 www.stsc.hill.af.mil 17 2 • address security concerns in the software development life cycle ( SDLC )? • Are there formal software quality...What threat modeling process, if any, is used when designing the software ? What analysis, design, and construction tools are used by your software design...the-shelf (COTS), government off-the-shelf (GOTS), open- source, embedded, and legacy software . Attackers exploit unintentional vulnerabil- ities or

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

NASA Astrophysics Data System (ADS)

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

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

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

PubMed

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

2017-08-01

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

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

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

2008-11-01

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

User Guide for the Plotting Software for the Los Alamos National Laboratory Nuclear Weapons Analysis Tools Version 2.0

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

Cleland, Timothy James

The Los Alamos National Laboratory Plotting Software for the Nuclear Weapons Analysis Tools is a Java™ application based upon the open source library JFreeChart. The software provides a capability for plotting data on graphs with a rich variety of display options while allowing the viewer interaction via graph manipulation and scaling to best view the data. The graph types include XY plots, Date XY plots, Bar plots and Histogram plots.

Automated real-time software development

NASA Technical Reports Server (NTRS)

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

1993-01-01

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

Software Tools for Software Maintenance

DTIC Science & Technology

1988-10-01

Cobol ! ASTEC I --------------- ----. -... . . . ---------. P . .---------- I-.... IBM Main DOS None Spec I CA-Converter I A -------- -------------I...none ASTEC Source: VSM Company: MAINTEC, Inc. Change-Han Phone: (612) 831-2122 Company: SERENA Consulting Function: RF Phone: (800) 621-0851

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

Ensemble: an Architecture for Mission-Operations Software

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

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

PubMed Central

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

2013-01-01

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

3D reconstruction software comparison for short sequences

NASA Astrophysics Data System (ADS)

Strupczewski, Adam; Czupryński, BłaŻej

2014-11-01

Large scale multiview reconstruction is recently a very popular area of research. There are many open source tools that can be downloaded and run on a personal computer. However, there are few, if any, comparisons between all the available software in terms of accuracy on small datasets that a single user can create. The typical datasets for testing of the software are archeological sites or cities, comprising thousands of images. This paper presents a comparison of currently available open source multiview reconstruction software for small datasets. It also compares the open source solutions with a simple structure from motion pipeline developed by the authors from scratch with the use of OpenCV and Eigen libraries.

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

PubMed

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

2017-08-15

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

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

PubMed Central

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

2017-01-01

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

An approach to software cost estimation

NASA Technical Reports Server (NTRS)

Mcgarry, F.; Page, J.; Card, D.; Rohleder, M.; Church, V.

1984-01-01

A general procedure for software cost estimation in any environment is outlined. The basic concepts of work and effort estimation are explained, some popular resource estimation models are reviewed, and the accuracy of source estimates is discussed. A software cost prediction procedure based on the experiences of the Software Engineering Laboratory in the flight dynamics area and incorporating management expertise, cost models, and historical data is described. The sources of information and relevant parameters available during each phase of the software life cycle are identified. The methodology suggested incorporates these elements into a customized management tool for software cost prediction. Detailed guidelines for estimation in the flight dynamics environment developed using this methodology are presented.

An online open-source tool for automated quantification of liver and myocardial iron concentrations by T2* magnetic resonance imaging.

PubMed

Git, K-A; Fioravante, L A B; Fernandes, J L

2015-09-01

To assess whether an online open-source tool would provide accurate calculations of T2(*) values for iron concentrations in the liver and heart compared with a standard reference software. An online open-source tool, written in pure HTML5/Javascript, was tested in 50 patients (age 26.0 ± 18.9 years, 46% males) who underwent T2(*) MRI of the liver and heart for iron overload assessment as part of their routine workup. Automated truncation correction was the default with optional manual adjustment provided if needed. The results were compared against a standard reference measurement using commercial software with manual truncation (CVI(42)(®) v. 5.1; Circle Cardiovascular Imaging; Calgary, AB). The mean liver T2(*) values calculated with the automated tool was 4.3 ms [95% confidence interval (CI) 3.1 to 5.5 ms] vs 4.26 ms using the reference software (95% CI 3.1 to 5.4 ms) without any significant differences (p = 0.71). In the liver, the mean difference was 0.036 ms (95% CI -0.1609 to 0.2329 ms) with a regression correlation coefficient of 0.97. For the heart, the automated T2(*) value was 26.0 ms (95% CI 22.9 to 29.0 ms) vs 25.3 ms (95% CI 22.3 to 28.3 ms), p = 0.28. The mean difference was 0.72 ms (95% CI 0.08191 to 1.3621 ms) with a correlation coefficient of 0.96. The automated online tool provides similar T2(*) values for the liver and myocardial iron concentrations as compared with a standard reference software. The online program provides an open-source tool for the calculation of T2(*) values, incorporating an automated correction algorithm in a simple and easy-to-use interface.

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

NASA Technical Reports Server (NTRS)

Gilbertson, Christian; Welch, Bryan

2017-01-01

Orbit propagation is fundamental to almost every space-based analysis. Currently, many system analysts use commercial software to predict the future positions of orbiting satellites. This is one of many capabilities that can replicated, with great accuracy, without using expensive, proprietary software. NASAs SCaN (Space Communication and Navigation) Center for Engineering, Networks, Integration, and Communications (SCENIC) project plans to provide its analysis capabilities using a combination of internal and open-source software, allowing for a much greater measure of customization and flexibility, while reducing recurring software license costs. MATLAB and the open-source Orbit Determination Toolbox created by Goddard Space Flight Center (GSFC) were utilized to develop tools with the capability to propagate orbits, perform line-of-sight (LOS) availability analyses, and visualize the results. The developed programs are modular and can be applied for mission planning and viability analysis in a variety of Solar System applications. The tools can perform 2 and N-body orbit propagation, find inter-satellite and satellite to ground station LOS access (accounting for intermediate oblate spheroid body blocking, geometric restrictions of the antenna field-of-view (FOV), and relativistic corrections), and create animations of planetary movement, satellite orbits, and LOS accesses. The code is the basis for SCENICs broad analysis capabilities including dynamic link analysis, dilution-of-precision navigation analysis, and orbital availability calculations.

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

NASA Astrophysics Data System (ADS)

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

2013-12-01

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

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

PubMed Central

Busby, Ben; Lesko, Matthew; Federer, Lisa

2016-01-01

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

Pilot Study of an Open-source Image Analysis Software for Automated Screening of Conventional Cervical Smears.

PubMed

Sanyal, Parikshit; Ganguli, Prosenjit; Barui, Sanghita; Deb, Prabal

2018-01-01

The Pap stained cervical smear is a screening tool for cervical cancer. Commercial systems are used for automated screening of liquid based cervical smears. However, there is no image analysis software used for conventional cervical smears. The aim of this study was to develop and test the diagnostic accuracy of a software for analysis of conventional smears. The software was developed using Python programming language and open source libraries. It was standardized with images from Bethesda Interobserver Reproducibility Project. One hundred and thirty images from smears which were reported Negative for Intraepithelial Lesion or Malignancy (NILM), and 45 images where some abnormality has been reported, were collected from the archives of the hospital. The software was then tested on the images. The software was able to segregate images based on overall nuclear: cytoplasmic ratio, coefficient of variation (CV) in nuclear size, nuclear membrane irregularity, and clustering. 68.88% of abnormal images were flagged by the software, as well as 19.23% of NILM images. The major difficulties faced were segmentation of overlapping cell clusters and separation of neutrophils. The software shows potential as a screening tool for conventional cervical smears; however, further refinement in technique is required.

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

PubMed Central

2012-01-01

Background In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. Results We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. Conclusions We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback. PMID:22490389

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

PubMed

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

2012-04-10

In the past 20 years, society has witnessed the following landmark scientific advances: (i) the sequencing of the human genome, (ii) the distribution of software by the open source movement, and (iii) the invention of the World Wide Web. Together, these advances have provided a new impetus for clinical software development: developers now translate the products of human genomic research into clinical software tools; they use open-source programs to build them; and they use the Web to deliver them. Whilst this open-source component-based approach has undoubtedly made clinical software development easier, clinical software projects are still hampered by problems that traditionally accompany the software process. This study describes the development of the BOADICEA Web Application, a computer program used by clinical geneticists to assess risks to patients with a family history of breast and ovarian cancer. The key challenge of the BOADICEA Web Application project was to deliver a program that was safe, secure and easy for healthcare professionals to use. We focus on the software process, problems faced, and lessons learned. Our key objectives are: (i) to highlight key clinical software development issues; (ii) to demonstrate how software engineering tools and techniques can facilitate clinical software development for the benefit of individuals who lack software engineering expertise; and (iii) to provide a clinical software development case report that can be used as a basis for discussion at the start of future projects. We developed the BOADICEA Web Application using an evolutionary software process. Our approach to Web implementation was conservative and we used conventional software engineering tools and techniques. The principal software development activities were: requirements, design, implementation, testing, documentation and maintenance. The BOADICEA Web Application has now been widely adopted by clinical geneticists and researchers. BOADICEA Web Application version 1 was released for general use in November 2007. By May 2010, we had > 1200 registered users based in the UK, USA, Canada, South America, Europe, Africa, Middle East, SE Asia, Australia and New Zealand. We found that an evolutionary software process was effective when we developed the BOADICEA Web Application. The key clinical software development issues identified during the BOADICEA Web Application project were: software reliability, Web security, clinical data protection and user feedback.

A Roadmap for using Agile Development in a Traditional System

NASA Technical Reports Server (NTRS)

Streiffert, Barbara; Starbird, Thomas

2006-01-01

I. Ensemble Development Group: a) Produces activity planning software for in spacecraft; b) Built on Eclipse Rich Client Platform (open source development and runtime software); c) Funded by multiple sources including the Mars Technology Program; d) Incorporated the use of Agile Development. II. Next Generation Uplink Planning System: a) Researches the Activity Planning and Sequencing Subsystem for Mars Science Laboratory (APSS); b) APSS includes Ensemble, Activity Modeling, Constraint Checking, Command Editing and Sequencing tools plus other uplink generation utilities; c) Funded by the Mars Technology Program; d) Integrates all of the tools for APSS.

Decision Analysis Tools for Volcano Observatories

NASA Astrophysics Data System (ADS)

Hincks, T. H.; Aspinall, W.; Woo, G.

2005-12-01

Staff at volcano observatories are predominantly engaged in scientific activities related to volcano monitoring and instrumentation, data acquisition and analysis. Accordingly, the academic education and professional training of observatory staff tend to focus on these scientific functions. From time to time, however, staff may be called upon to provide decision support to government officials responsible for civil protection. Recognizing that Earth scientists may have limited technical familiarity with formal decision analysis methods, specialist software tools that assist decision support in a crisis should be welcome. A review is given of two software tools that have been under development recently. The first is for probabilistic risk assessment of human and economic loss from volcanic eruptions, and is of practical use in short and medium-term risk-informed planning of exclusion zones, post-disaster response, etc. A multiple branch event-tree architecture for the software, together with a formalism for ascribing probabilities to branches, have been developed within the context of the European Community EXPLORIS project. The second software tool utilizes the principles of the Bayesian Belief Network (BBN) for evidence-based assessment of volcanic state and probabilistic threat evaluation. This is of practical application in short-term volcano hazard forecasting and real-time crisis management, including the difficult challenge of deciding when an eruption is over. An open-source BBN library is the software foundation for this tool, which is capable of combining synoptically different strands of observational data from diverse monitoring sources. A conceptual vision is presented of the practical deployment of these decision analysis tools in a future volcano observatory environment. Summary retrospective analyses are given of previous volcanic crises to illustrate the hazard and risk insights gained from use of these tools.

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research.

PubMed

Campagnola, Luke; Kratz, Megan B; Manis, Paul B

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org.

Information Extraction for System-Software Safety Analysis: Calendar Year 2008 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2009-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

SpectraFox: A free open-source data management and analysis tool for scanning probe microscopy and spectroscopy

NASA Astrophysics Data System (ADS)

Ruby, Michael

In the last decades scanning probe microscopy and spectroscopy have become well-established tools in nanotechnology and surface science. This opened the market for many commercial manufacturers, each with different hardware and software standards. Besides the advantage of a wide variety of available hardware, the diversity may software-wise complicate the data exchange between scientists, and the data analysis for groups working with hardware developed by different manufacturers. Not only the file format differs between manufacturers, but also the data often requires further numerical treatment before publication. SpectraFox is an open-source and independent tool which manages, processes, and evaluates scanning probe spectroscopy and microscopy data. It aims at simplifying the documentation in parallel to measurement, and it provides solid evaluation tools for a large number of data.

GIS-Based Noise Simulation Open Source Software: N-GNOIS

NASA Astrophysics Data System (ADS)

Vijay, Ritesh; Sharma, A.; Kumar, M.; Shende, V.; Chakrabarti, T.; Gupta, Rajesh

2015-12-01

Geographical information system (GIS)-based noise simulation software (N-GNOIS) has been developed to simulate the noise scenario due to point and mobile sources considering the impact of geographical features and meteorological parameters. These have been addressed in the software through attenuation modules of atmosphere, vegetation and barrier. N-GNOIS is a user friendly, platform-independent and open geospatial consortia (OGC) compliant software. It has been developed using open source technology (QGIS) and open source language (Python). N-GNOIS has unique features like cumulative impact of point and mobile sources, building structure and honking due to traffic. Honking is the most common phenomenon in developing countries and is frequently observed on any type of roads. N-GNOIS also helps in designing physical barrier and vegetation cover to check the propagation of noise and acts as a decision making tool for planning and management of noise component in environmental impact assessment (EIA) studies.

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.

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

World Wind Tools Reveal Environmental Change

NASA Technical Reports Server (NTRS)

2012-01-01

Originally developed under NASA's Learning Technologies program as a tool to engage and inspire students, World Wind software was released under the NASA Open Source Agreement license. Honolulu, Hawaii based Intelesense Technologies is one of the companies currently making use of the technology for environmental, public health, and other monitoring applications for nonprofit organizations and Government agencies. The company saved about $1 million in development costs by using the NASA software.

Systems biology driven software design for the research enterprise.

PubMed

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

2008-06-25

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

Open source tools for fluorescent imaging.

PubMed

Hamilton, Nicholas A

2012-01-01

As microscopy becomes increasingly automated and imaging expands in the spatial and time dimensions, quantitative analysis tools for fluorescent imaging are becoming critical to remove both bottlenecks in throughput as well as fully extract and exploit the information contained in the imaging. In recent years there has been a flurry of activity in the development of bio-image analysis tools and methods with the result that there are now many high-quality, well-documented, and well-supported open source bio-image analysis projects with large user bases that cover essentially every aspect from image capture to publication. These open source solutions are now providing a viable alternative to commercial solutions. More importantly, they are forming an interoperable and interconnected network of tools that allow data and analysis methods to be shared between many of the major projects. Just as researchers build on, transmit, and verify knowledge through publication, open source analysis methods and software are creating a foundation that can be built upon, transmitted, and verified. Here we describe many of the major projects, their capabilities, and features. We also give an overview of the current state of open source software for fluorescent microscopy analysis and the many reasons to use and develop open source methods. Copyright © 2012 Elsevier Inc. All rights reserved.

28 CFR 802.4 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Administration COURT SERVICES AND OFFENDER SUPERVISION AGENCY FOR THE DISTRICT OF COLUMBIA DISCLOSURE OF RECORDS... proprietary interest in the information. (e) Computer software means tools by which records are created, stored, and retrieved. Normally, computer software, including source code, object code, and listings of...

Introducing a new open source GIS user interface for the SWAT model

USDA-ARS?s Scientific Manuscript database

The Soil and Water Assessment Tool (SWAT) model is a robust watershed modelling tool. It typically uses the ArcSWAT interface to create its inputs. ArcSWAT is public domain software which works in the licensed ArcGIS environment. The aim of this paper was to develop an open source user interface ...

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

Science.gov Websites

. Development Tools View list of tools for build automation, version control, and high-level or specialized scripting. Toolchains Learn about the available toolchains to build applications from source code

Data and Tools | Integrated Energy Solutions | NREL

Science.gov Websites

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

Basic to Advanced InSAR Processing: GMTSAR

NASA Astrophysics Data System (ADS)

Sandwell, D. T.; Xu, X.; Baker, S.; Hogrelius, A.; Mellors, R. J.; Tong, X.; Wei, M.; Wessel, P.

2017-12-01

Monitoring crustal deformation using InSAR is becoming a standard technique for the science and application communities. Optimal use of the new data streams from Sentinel-1 and NISAR will require open software tools as well as education on the strengths and limitations of the InSAR methods. Over the past decade we have developed freely available, open-source software for processing InSAR data. The software relies on the Generic Mapping Tools (GMT) for the back-end data analysis and display and is thus called GMTSAR. With startup funding from NSF, we accelerated the development of GMTSAR to include more satellite data sources and provide better integration and distribution with GMT. In addition, with support from UNAVCO we have offered 6 GMTSAR short courses to educate mostly novice InSAR users. Currently, the software is used by hundreds of scientists and engineers around the world to study deformation at more than 4300 different sites. The most challenging aspect of the recent software development was the transition from image alignment using the cross-correlation method to a completely new alignment algorithm that uses only the precise orbital information to geometrically align images to an accuracy of better than 7 cm. This development was needed to process a new data type that is being acquired by the Sentinel-1A/B satellites. This combination of software and open data is transforming radar interferometry from a research tool into a fully operational time series analysis tool. Over the next 5 years we are planning to continue to broaden the user base through: improved software delivery methods; code hardening; better integration with data archives; support for high level products being developed for NISAR; and continued education and outreach.

AKM in Open Source Communities

NASA Astrophysics Data System (ADS)

Stamelos, Ioannis; Kakarontzas, George

Previous chapters in this book have dealt with Architecture Knowledge Management in traditional Closed Source Software (CSS) projects. This chapterwill attempt to examine the ways that knowledge is shared among participants in Free Libre Open Source Software (FLOSS 1) projects and how architectural knowledge is managed w.r.t. CSS. FLOSS projects are organized and developed in a fundamentally different way than CSS projects. FLOSS projects simply do not develop code as CSS projects do. As a consequence, their knowledge management mechanisms are also based on different concepts and tools.

TiConverter: A training image converting tool for multiple-point geostatistics

NASA Astrophysics Data System (ADS)

Fadlelmula F., Mohamed M.; Killough, John; Fraim, Michael

2016-11-01

TiConverter is a tool developed to ease the application of multiple-point geostatistics whether by the open source Stanford Geostatistical Modeling Software (SGeMS) or other available commercial software. TiConverter has a user-friendly interface and it allows the conversion of 2D training images into numerical representations in four different file formats without the need for additional code writing. These are the ASCII (.txt), the geostatistical software library (GSLIB) (.txt), the Isatis (.dat), and the VTK formats. It performs the conversion based on the RGB color system. In addition, TiConverter offers several useful tools including image resizing, smoothing, and segmenting tools. The purpose of this study is to introduce the TiConverter, and to demonstrate its application and advantages with several examples from the literature.

A Tale of Two Observing Systems: Interoperability in the World of Microsoft Windows

NASA Astrophysics Data System (ADS)

Babin, B. L.; Hu, L.

2008-12-01

Louisiana Universities Marine Consortium's (LUMCON) and Dauphin Island Sea Lab's (DISL) Environmental Monitoring System provide a unified coastal ocean observing system. These two systems are mirrored to maintain autonomy while offering an integrated data sharing environment. Both systems collect data via Campbell Scientific Data loggers, store the data in Microsoft SQL servers, and disseminate the data in real- time on the World Wide Web via Microsoft Internet Information Servers and Active Server Pages (ASP). The utilization of Microsoft Windows technologies presented many challenges to these observing systems as open source tools for interoperability grow. The current open source tools often require the installation of additional software. In order to make data available through common standards formats, "home grown" software has been developed. One example of this is the development of software to generate xml files for transmission to the National Data Buoy Center (NDBC). OOSTethys partners develop, test and implement easy-to-use, open-source, OGC-compliant software., and have created a working prototype of networked, semantically interoperable, real-time data systems. Partnering with OOSTethys, we are developing a cookbook to implement OGC web services. The implementation will be written in ASP, will run in a Microsoft operating system environment, and will serve data via Sensor Observation Services (SOS). This cookbook will give observing systems running Microsoft Windows the tools to easily participate in the Open Geospatial Consortium (OGC) Oceans Interoperability Experiment (OCEANS IE).

SeisCode: A seismological software repository for discovery and collaboration

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Automation for System Safety Analysis

NASA Technical Reports Server (NTRS)

Malin, Jane T.; Fleming, Land; Throop, David; Thronesbery, Carroll; Flores, Joshua; Bennett, Ted; Wennberg, Paul

2009-01-01

This presentation describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis and simulation to identify and evaluate possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations and scenarios; and 4) identify resulting candidate scenarios for software integration testing. There has been significant technical progress in model extraction from Orion program text sources, architecture model derivation (components and connections) and documentation of extraction sources. Models have been derived from Internal Interface Requirements Documents (IIRDs) and FMEA documents. Linguistic text processing is used to extract model parts and relationships, and the Aerospace Ontology also aids automated model development from the extracted information. Visualizations of these models assist analysts in requirements overview and in checking consistency and completeness.

Proceedings Papers of the AFSC (Air Force Systems Command) Avionics Standardization Conference (2nd) Held at Dayton, Ohio on 30 November-2 December 1982. Volume 1.

DTIC Science & Technology

1982-11-01

Avionic Systems Integration Facilities, Mark van den Broek 1113 and Paul M. Vicen, AFLC/LOE Planning of Operational Software Implementation Tool...classified as software tools, including: * o" Operating System " Language Processors (compilers, assem’blers, link editors) o Source Editors " Debug Systems ...o Data Base Systems o Utilities o Etc . This talk addresses itself to the current set of tools provided JOVIAL iJ73 1750A application programmners by

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

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

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

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

PubMed Central

2013-01-01

Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data. PMID:24341380

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

PubMed

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

2013-10-25

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

Techniques to Access Databases and Integrate Data for Hydrologic Modeling

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

Whelan, Gene; Tenney, Nathan D.; Pelton, Mitchell A.

2009-06-17

This document addresses techniques to access and integrate data for defining site-specific conditions and behaviors associated with ground-water and surface-water radionuclide transport applicable to U.S. Nuclear Regulatory Commission reviews. Environmental models typically require input data from multiple internal and external sources that may include, but are not limited to, stream and rainfall gage data, meteorological data, hydrogeological data, habitat data, and biological data. These data may be retrieved from a variety of organizations (e.g., federal, state, and regional) and source types (e.g., HTTP, FTP, and databases). Available data sources relevant to hydrologic analyses for reactor licensing are identified and reviewed.more » The data sources described can be useful to define model inputs and parameters, including site features (e.g., watershed boundaries, stream locations, reservoirs, site topography), site properties (e.g., surface conditions, subsurface hydraulic properties, water quality), and site boundary conditions, input forcings, and extreme events (e.g., stream discharge, lake levels, precipitation, recharge, flood and drought characteristics). Available software tools for accessing established databases, retrieving the data, and integrating it with models were identified and reviewed. The emphasis in this review was on existing software products with minimal required modifications to enable their use with the FRAMES modeling framework. The ability of four of these tools to access and retrieve the identified data sources was reviewed. These four software tools were the Hydrologic Data Acquisition and Processing System (HDAPS), Integrated Water Resources Modeling System (IWRMS) External Data Harvester, Data for Environmental Modeling Environmental Data Download Tool (D4EM EDDT), and the FRAMES Internet Database Tools. The IWRMS External Data Harvester and the D4EM EDDT were identified as the most promising tools based on their ability to access and retrieve the required data, and their ability to integrate the data into environmental models using the FRAMES environment.« less

CWA 15793 2011 Planning and Implementation Tool

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

Gross, Alan; Nail, George

This software, built on an open source platform called Electron (runs on Chromium and Node.js), is designed to assist organizations in the implementation of a biorisk management system consistent with the requirements of the international, publicly available guidance document CEN Workshop Agreement 15793:2011 (CWA 15793). The software includes tools for conducting organizational gap analysis against CWA 15793 requirements, planning tools to support the implementation of CWA 15793 requirements, and performance monitoring support. The gap analysis questions are based on the text of CWA 15793, and its associated guidance document, CEN Workshop Agreement 16393:2012. The authors have secured permission from themore » publisher of CWA 15793, the European Committee for Standardization (CEN), to use language from the document in the software, with the understanding that the software will be made available freely, without charge.« less

Meta-tools for software development and knowledge acquisition

NASA Technical Reports Server (NTRS)

Eriksson, Henrik; Musen, Mark A.

1992-01-01

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

SNPversity: A web-based tool for visualizing diversity

USDA-ARS?s Scientific Manuscript database

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

Test-driven programming

NASA Astrophysics Data System (ADS)

Georgiev, Bozhidar; Georgieva, Adriana

2013-12-01

In this paper, are presented some possibilities concerning the implementation of a test-driven development as a programming method. Here is offered a different point of view for creation of advanced programming techniques (build tests before programming source with all necessary software tools and modules respectively). Therefore, this nontraditional approach for easier programmer's work through building tests at first is preferable way of software development. This approach allows comparatively simple programming (applied with different object-oriented programming languages as for example JAVA, XML, PYTHON etc.). It is predictable way to develop software tools and to provide help about creating better software that is also easier to maintain. Test-driven programming is able to replace more complicated casual paradigms, used by many programmers.

Technology Infusion of CodeSonar into the Space Network Ground Segment (RII07)

NASA Technical Reports Server (NTRS)

Benson, Markland

2008-01-01

The NASA Software Assurance Research Program (in part) performs studies as to the feasibility of technologies for improving the safety, quality, reliability, cost, and performance of NASA software. This study considers the application of commercial automated source code analysis tools to mission critical ground software that is in the operations and sustainment portion of the product lifecycle.

PsyToolkit: a software package for programming psychological experiments using Linux.

PubMed

Stoet, Gijsbert

2010-11-01

PsyToolkit is a set of software tools for programming psychological experiments on Linux computers. Given that PsyToolkit is freely available under the Gnu Public License, open source, and designed such that it can easily be modified and extended for individual needs, it is suitable not only for technically oriented Linux users, but also for students, researchers on small budgets, and universities in developing countries. The software includes a high-level scripting language, a library for the programming language C, and a questionnaire presenter. The software easily integrates with other open source tools, such as the statistical software package R. PsyToolkit is designed to work with external hardware (including IoLab and Cedrus response keyboards and two common digital input/output boards) and to support millisecond timing precision. Four in-depth examples explain the basic functionality of PsyToolkit. Example 1 demonstrates a stimulus-response compatibility experiment. Example 2 demonstrates a novel mouse-controlled visual search experiment. Example 3 shows how to control light emitting diodes using PsyToolkit, and Example 4 shows how to build a light-detection sensor. The last two examples explain the electronic hardware setup such that they can even be used with other software packages.

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

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

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

Watershed Deposition Tool for air quality impacts

EPA Pesticide Factsheets

The WDT is a software tool for mapping deposition estimates from the CMAQ model to watersheds. It provides users with the linkage of air and water needed for the total maximum daily load (TMDL) and related nonpoint-source watershed analyses.

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

NASA Technical Reports Server (NTRS)

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

2006-01-01

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

ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research

PubMed Central

Campagnola, Luke; Kratz, Megan B.; Manis, Paul B.

2014-01-01

The complexity of modern neurophysiology experiments requires specialized software to coordinate multiple acquisition devices and analyze the collected data. We have developed ACQ4, an open-source software platform for performing data acquisition and analysis in experimental neurophysiology. This software integrates the tasks of acquiring, managing, and analyzing experimental data. ACQ4 has been used primarily for standard patch-clamp electrophysiology, laser scanning photostimulation, multiphoton microscopy, intrinsic imaging, and calcium imaging. The system is highly modular, which facilitates the addition of new devices and functionality. The modules included with ACQ4 provide for rapid construction of acquisition protocols, live video display, and customizable analysis tools. Position-aware data collection allows automated construction of image mosaics and registration of images with 3-dimensional anatomical atlases. ACQ4 uses free and open-source tools including Python, NumPy/SciPy for numerical computation, PyQt for the user interface, and PyQtGraph for scientific graphics. Supported hardware includes cameras, patch clamp amplifiers, scanning mirrors, lasers, shutters, Pockels cells, motorized stages, and more. ACQ4 is available for download at http://www.acq4.org. PMID:24523692

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.

What's New in Software? Hot New Tool: The Hypertext.

ERIC Educational Resources Information Center

Hedley, Carolyn N.

1989-01-01

This article surveys recent developments in hypertext software, a highly interactive nonsequential reading/writing/database approach to research and teaching that allows paths to be created through related materials including text, graphics, video, and animation sources. Described are uses, advantages, and problems of hypertext. (PB)

Global Situational Awareness with Free Tools

DTIC Science & Technology

2015-01-15

Client Technical Solutions • Software Engineering Measurement and Analysis • Architecture Practices • Product Line Practice • Team Software Process...multiple data sources • Snort (Snorby on Security Onion ) • Nagios • SharePoint RSS • Flow • Others • Leverage standard data formats • Keyhole Markup Language

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

NASA Astrophysics Data System (ADS)

Tonini, Roberto; Selva, Jacopo

2013-04-01

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

Open-source Software for Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis.

PubMed

Mohammed, Emad A; Naugler, Christopher

2017-01-01

Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. This tool will allow anyone with historic test volume data to model future demand.

Open-source Software for Demand Forecasting of Clinical Laboratory Test Volumes Using Time-series Analysis

PubMed Central

Mohammed, Emad A.; Naugler, Christopher

2017-01-01

Background: Demand forecasting is the area of predictive analytics devoted to predicting future volumes of services or consumables. Fair understanding and estimation of how demand will vary facilitates the optimal utilization of resources. In a medical laboratory, accurate forecasting of future demand, that is, test volumes, can increase efficiency and facilitate long-term laboratory planning. Importantly, in an era of utilization management initiatives, accurately predicted volumes compared to the realized test volumes can form a precise way to evaluate utilization management initiatives. Laboratory test volumes are often highly amenable to forecasting by time-series models; however, the statistical software needed to do this is generally either expensive or highly technical. Method: In this paper, we describe an open-source web-based software tool for time-series forecasting and explain how to use it as a demand forecasting tool in clinical laboratories to estimate test volumes. Results: This tool has three different models, that is, Holt-Winters multiplicative, Holt-Winters additive, and simple linear regression. Moreover, these models are ranked and the best one is highlighted. Conclusion: This tool will allow anyone with historic test volume data to model future demand. PMID:28400996

Data Mining Meets HCI: Making Sense of Large Graphs

DTIC Science & Technology

2012-07-01

graph algo- rithms, won the Open Source Software World Challenge, Silver Award. We have released Pegasus as free , open-source software, downloaded by...METIS [77], spectral clustering [108], and the parameter- free “Cross-associations” (CA) [26]. Belief Propagation can also be used for clus- tering, as...number of tools have been developed to support “ landscape ” views of information. These include WebBook and Web- Forager [23], which use a book metaphor

Systems biology driven software design for the research enterprise

PubMed Central

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

2008-01-01

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

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

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

2017-03-01

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

Share Repository Framework: Component Specification and Otology

DTIC Science & Technology

2008-04-23

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

SwarmSight: Measuring the Temporal Progression of Animal Group Activity Levels from Natural Scene and Laboratory Videos

PubMed Central

Birgiolas, Justas; Jernigan, Christopher M.; Smith, Brian H.; Crook, Sharon M.

2016-01-01

We describe SwarmSight (available at: https://github.com/justasb/SwarmSight), a novel, open-source, Microsoft Windows software tool for quantitative assessment of the temporal progression of animal group activity levels from recorded videos. The tool utilizes a background subtraction machine vision algorithm and provides an activity metric that can be used to quantitatively assess and compare animal group behavior. Here we demonstrate the tool utility by analyzing defensive bee behavior as modulated by alarm pheromones, wild bird feeding onset and interruption, and cockroach nest finding activity. While more sophisticated, commercial software packages are available, SwarmSight provides a low-cost, open-source, and easy-to-use alternative that is suitable for a wide range of users, including minimally trained research technicians and behavioral science undergraduate students in classroom laboratory settings. PMID:27130170

Information Extraction for System-Software Safety Analysis: Calendar Year 2007 Year-End Report

NASA Technical Reports Server (NTRS)

Malin, Jane T.

2008-01-01

This annual report describes work to integrate a set of tools to support early model-based analysis of failures and hazards due to system-software interactions. The tools perform and assist analysts in the following tasks: 1) extract model parts from text for architecture and safety/hazard models; 2) combine the parts with library information to develop the models for visualization and analysis; 3) perform graph analysis on the models to identify possible paths from hazard sources to vulnerable entities and functions, in nominal and anomalous system-software configurations; 4) perform discrete-time-based simulation on the models to investigate scenarios where these paths may play a role in failures and mishaps; and 5) identify resulting candidate scenarios for software integration testing. This paper describes new challenges in a NASA abort system case, and enhancements made to develop the integrated tool set.

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

PubMed

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

2012-08-01

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

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

PubMed

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

2016-08-30

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

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

PubMed

Espino, Jeremy U; Wagner, M; Szczepaniak, C; Tsui, F C; Su, H; Olszewski, R; Liu, Z; Chapman, W; Zeng, X; Ma, L; Lu, Z; Dara, J

2004-09-24

Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

Apache Open Climate Workbench: Building Open Source Climate Science Tools and Community at the Apache Software Foundation

NASA Astrophysics Data System (ADS)

Joyce, M.; Ramirez, P.; Boustani, M.; Mattmann, C. A.; Khudikyan, S.; McGibbney, L. J.; Whitehall, K. D.

2014-12-01

Apache Open Climate Workbench (OCW; https://climate.apache.org/) is a Top-Level Project at the Apache Software Foundation that aims to provide a suite of tools for performing climate science evaluations using model outputs from a multitude of different sources (ESGF, CORDEX, U.S. NCA, NARCCAP) with remote sensing data from NASA, NOAA, and other agencies. Apache OCW is the second NASA project to become a Top-Level Project at the Apache Software Foundation. It grew out of the Jet Propulsion Laboratory's (JPL) Regional Climate Model Evaluation System (RCMES) project, a collaboration between JPL and the University of California, Los Angeles' Joint Institute for Regional Earth System Science and Engineering (JIFRESSE). Apache OCW provides scientists and developers with tools for data manipulation, metrics for dataset comparisons, and a visualization suite. In addition to a powerful low-level API, Apache OCW also supports a web application for quick, browser-controlled evaluations, a command line application for local evaluations, and a virtual machine for isolated experimentation with minimal setup. This talk will look at the difficulties and successes of moving a closed community research project out into the wild world of open source. We'll explore the growing pains Apache OCW went through to become a Top-Level Project at the Apache Software Foundation as well as the benefits gained by opening up development to the broader climate and computer science communities.

WILDFIRE IGNITION RESISTANCE ESTIMATOR WIZARD SOFTWARE DEVELOPMENT REPORT

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

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

2012-10-10

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

The Core Flight System (cFS) Community: Providing Low Cost Solutions for Small Spacecraft

NASA Technical Reports Server (NTRS)

McComas, David; Wilmot, Jonathan; Cudmore, Alan

2016-01-01

In February 2015 the NASA Goddard Space Flight Center (GSFC) completed the open source release of the entire Core Flight Software (cFS) suite. After the open source release a multi-NASA center Configuration Control Board (CCB) was established that has managed multiple cFS product releases. The cFS was developed and is being maintained in compliance with the NASA Class B software development process requirements and the open source release includes all Class B artifacts. The cFS is currently running on three operational science spacecraft and is being used on multiple spacecraft and instrument development efforts. While the cFS itself is a viable flight software (FSW) solution, we have discovered that the cFS community is a continuous source of innovation and growth that provides products and tools that serve the entire FSW lifecycle and future mission needs. This paper summarizes the current state of the cFS community, the key FSW technologies being pursued, the development/verification tools and opportunities for the small satellite community to become engaged. The cFS is a proven high quality and cost-effective solution for small satellites with constrained budgets.

Approaches in highly parameterized inversion—PEST++ Version 3, a Parameter ESTimation and uncertainty analysis software suite optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; White, Jeremy T.; Hunt, Randall J.; Doherty, John E.

2015-09-18

The PEST++ Version 3 software suite can be compiled for Microsoft Windows®4 and Linux®5 operating systems; the source code is available in a Microsoft Visual Studio®6 2013 solution; Linux Makefiles are also provided. PEST++ Version 3 continues to build a foundation for an open-source framework capable of producing robust and efficient parameter estimation tools for large environmental models.

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

RTSPM: real-time Linux control software for scanning probe microscopy.

PubMed

Chandrasekhar, V; Mehta, M M

2013-01-01

Real time computer control is an essential feature of scanning probe microscopes, which have become important tools for the characterization and investigation of nanometer scale samples. Most commercial (and some open-source) scanning probe data acquisition software uses digital signal processors to handle the real time data processing and control, which adds to the expense and complexity of the control software. We describe here scan control software that uses a single computer and a data acquisition card to acquire scan data. The computer runs an open-source real time Linux kernel, which permits fast acquisition and control while maintaining a responsive graphical user interface. Images from a simulated tuning-fork based microscope as well as a standard topographical sample are also presented, showing some of the capabilities of the software.

Nurturing reliable and robust open-source scientific software

NASA Astrophysics Data System (ADS)

Uieda, L.; Wessel, P.

2017-12-01

Scientific results are increasingly the product of software. The reproducibility and validity of published results cannot be ensured without access to the source code of the software used to produce them. Therefore, the code itself is a fundamental part of the methodology and must be published along with the results. With such a reliance on software, it is troubling that most scientists do not receive formal training in software development. Tools such as version control, continuous integration, and automated testing are routinely used in industry to ensure the correctness and robustness of software. However, many scientist do not even know of their existence (although efforts like Software Carpentry are having an impact on this issue; software-carpentry.org). Publishing the source code is only the first step in creating an open-source project. For a project to grow it must provide documentation, participation guidelines, and a welcoming environment for new contributors. Expanding the project community is often more challenging than the technical aspects of software development. Maintainers must invest time to enforce the rules of the project and to onboard new members, which can be difficult to justify in the context of the "publish or perish" mentality. This problem will continue as long as software contributions are not recognized as valid scholarship by hiring and tenure committees. Furthermore, there are still unsolved problems in providing attribution for software contributions. Many journals and metrics of academic productivity do not recognize citations to sources other than traditional publications. Thus, some authors choose to publish an article about the software and use it as a citation marker. One issue with this approach is that updating the reference to include new contributors involves writing and publishing a new article. A better approach would be to cite a permanent archive of individual versions of the source code in services such as Zenodo (zenodo.org). However, citations to these sources are not always recognized when computing citation metrics. In summary, the widespread development of reliable and robust open-source software relies on the creation of formal training programs in software development best practices and the recognition of software as a valid form of scholarship.

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

PubMed

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

2011-03-08

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

BIAS: Bioinformatics Integrated Application Software.

PubMed

Finak, G; Godin, N; Hallett, M; Pepin, F; Rajabi, Z; Srivastava, V; Tang, Z

2005-04-15

We introduce a development platform especially tailored to Bioinformatics research and software development. BIAS (Bioinformatics Integrated Application Software) provides the tools necessary for carrying out integrative Bioinformatics research requiring multiple datasets and analysis tools. It follows an object-relational strategy for providing persistent objects, allows third-party tools to be easily incorporated within the system and supports standards and data-exchange protocols common to Bioinformatics. BIAS is an OpenSource project and is freely available to all interested users at http://www.mcb.mcgill.ca/~bias/. This website also contains a paper containing a more detailed description of BIAS and a sample implementation of a Bayesian network approach for the simultaneous prediction of gene regulation events and of mRNA expression from combinations of gene regulation events. hallett@mcb.mcgill.ca.

SU-E-T-103: Development and Implementation of Web Based Quality Control Software

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

Studinski, R; Taylor, R; Angers, C

Purpose: Historically many radiation medicine programs have maintained their Quality Control (QC) test results in paper records or Microsoft Excel worksheets. Both these approaches represent significant logistical challenges, and are not predisposed to data review and approval. It has been our group's aim to develop and implement web based software designed not just to record and store QC data in a centralized database, but to provide scheduling and data review tools to help manage a radiation therapy clinics Equipment Quality control program. Methods: The software was written in the Python programming language using the Django web framework. In order tomore » promote collaboration and validation from other centres the code was made open source and is freely available to the public via an online source code repository. The code was written to provide a common user interface for data entry, formalize the review and approval process, and offer automated data trending and process control analysis of test results. Results: As of February 2014, our installation of QAtrack+ has 180 tests defined in its database and has collected ∼22 000 test results, all of which have been reviewed and approved by a physicist via QATrack+'s review tools. These results include records for quality control of Elekta accelerators, CT simulators, our brachytherapy programme, TomoTherapy and Cyberknife units. Currently at least 5 other centres are known to be running QAtrack+ clinically, forming the start of an international user community. Conclusion: QAtrack+ has proven to be an effective tool for collecting radiation therapy QC data, allowing for rapid review and trending of data for a wide variety of treatment units. As free and open source software, all source code, documentation and a bug tracker are available to the public at https://bitbucket.org/tohccmedphys/qatrackplus/.« less

Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information.

PubMed

Khushi, Matloob; Edwards, Georgina; de Marcos, Diego Alonso; Carpenter, Jane E; Graham, J Dinny; Clarke, Christine L

2013-02-12

Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient's clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www.abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934.

BEANS - a software package for distributed Big Data analysis

NASA Astrophysics Data System (ADS)

Hypki, Arkadiusz

2018-07-01

BEANS software is a web-based, easy to install and maintain, new tool to store and analyse in a distributed way a massive amount of data. It provides a clear interface for querying, filtering, aggregating, and plotting data from an arbitrary number of data sets. Its main purpose is to simplify the process of storing, examining, and finding new relations in huge data sets. The software is an answer to a growing need of the astronomical community to have a versatile tool to store, analyse, and compare the complex astrophysical numerical simulations with observations (e.g. simulations of the Galaxy or star clusters with the Gaia archive). However, this software was built in a general form and it is ready to use in any other research field. It can be used as a building block for other open-source software too.

BEANS - a software package for distributed Big Data analysis

NASA Astrophysics Data System (ADS)

Hypki, Arkadiusz

2018-03-01

BEANS software is a web based, easy to install and maintain, new tool to store and analyse in a distributed way a massive amount of data. It provides a clear interface for querying, filtering, aggregating, and plotting data from an arbitrary number of datasets. Its main purpose is to simplify the process of storing, examining and finding new relations in huge datasets. The software is an answer to a growing need of the astronomical community to have a versatile tool to store, analyse and compare the complex astrophysical numerical simulations with observations (e.g. simulations of the Galaxy or star clusters with the Gaia archive). However, this software was built in a general form and it is ready to use in any other research field. It can be used as a building block for other open source software too.

APT: Aperture Photometry Tool

NASA Astrophysics Data System (ADS)

Laher, Russ

2012-08-01

Aperture Photometry Tool (APT) is software for astronomers and students interested in manually exploring the photometric qualities of astronomical images. It has a graphical user interface (GUI) which allows the image data associated with aperture photometry calculations for point and extended sources to be visualized and, therefore, more effectively analyzed. Mouse-clicking on a source in the displayed image draws a circular or elliptical aperture and sky annulus around the source and computes the source intensity and its uncertainty, along with several commonly used measures of the local sky background and its variability. The results are displayed and can be optionally saved to an aperture-photometry-table file and plotted on graphs in various ways using functions available in the software. APT is geared toward processing sources in a small number of images and is not suitable for bulk processing a large number of images, unlike other aperture photometry packages (e.g., SExtractor). However, APT does have a convenient source-list tool that enables calculations for a large number of detections in a given image. The source-list tool can be run either in automatic mode to generate an aperture photometry table quickly or in manual mode to permit inspection and adjustment of the calculation for each individual detection. APT displays a variety of useful graphs, including image histogram, and aperture slices, source scatter plot, sky scatter plot, sky histogram, radial profile, curve of growth, and aperture-photometry-table scatter plots and histograms. APT has functions for customizing calculations, including outlier rejection, pixel “picking” and “zapping,” and a selection of source and sky models. The radial-profile-interpolation source model, accessed via the radial-profile-plot panel, allows recovery of source intensity from pixels with missing data and can be especially beneficial in crowded fields.

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

PubMed Central

2016-01-01

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome. PMID:27051515

The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

PubMed

Nickerson, David; Atalag, Koray; de Bono, Bernard; Geiger, Jörg; Goble, Carole; Hollmann, Susanne; Lonien, Joachim; Müller, Wolfgang; Regierer, Babette; Stanford, Natalie J; Golebiewski, Martin; Hunter, Peter

2016-04-06

Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

Launching GUPPI: the Green Bank Ultimate Pulsar Processing Instrument

NASA Astrophysics Data System (ADS)

DuPlain, Ron; Ransom, Scott; Demorest, Paul; Brandt, Patrick; Ford, John; Shelton, Amy L.

2008-08-01

The National Radio Astronomy Observatory (NRAO) is launching the Green Bank Ultimate Pulsar Processing Instrument (GUPPI), a prototype flexible digital signal processor designed for pulsar observations with the Robert C. Byrd Green Bank Telescope (GBT). GUPPI uses field programmable gate array (FPGA) hardware and design tools developed by the Center for Astronomy Signal Processing and Electronics Research (CASPER) at the University of California, Berkeley. The NRAO has been concurrently developing GUPPI software and hardware using minimal software resources. The software handles instrument monitor and control, data acquisition, and hardware interfacing. GUPPI is currently an expert-only spectrometer, but supports future integration with the full GBT production system. The NRAO was able to take advantage of the unique flexibility of the CASPER FPGA hardware platform, develop hardware and software in parallel, and build a suite of software tools for monitoring, controlling, and acquiring data with a new instrument over a short timeline of just a few months. The NRAO interacts regularly with CASPER and its users, and GUPPI stands as an example of what reconfigurable computing and open-source development can do for radio astronomy. GUPPI is modular for portability, and the NRAO provides the results of development as an open-source resource.

Prototyping with Data Dictionaries for Requirements Analysis.

DTIC Science & Technology

1985-03-01

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

Survivability as a Tool for Evaluating Open Source Software

DTIC Science & Technology

2015-06-01

the thesis limited the program development, so it is only able to process project issues (bugs or feature requests), which is an important metric for...Ideally, these insights may provide an analytic framework to generate guidance for decision makers that may support the inclusion of OSS to more...refine their efforts to build quality software and to strengthen their software development communities. 1.4 Research Questions This thesis addresses

NASA Operational Simulator for Small Satellites: Tools for Software Based Validation and Verification of Small Satellites

NASA Technical Reports Server (NTRS)

Grubb, Matt

2016-01-01

The NASA Operational Simulator for Small Satellites (NOS3) is a suite of tools to aid in areas such as software development, integration test (IT), mission operations training, verification and validation (VV), and software systems check-out. NOS3 provides a software development environment, a multi-target build system, an operator interface-ground station, dynamics and environment simulations, and software-based hardware models. NOS3 enables the development of flight software (FSW) early in the project life cycle, when access to hardware is typically not available. For small satellites there are extensive lead times on many of the commercial-off-the-shelf (COTS) components as well as limited funding for engineering test units (ETU). Considering the difficulty of providing a hardware test-bed to each developer tester, hardware models are modeled based upon characteristic data or manufacturers data sheets for each individual component. The fidelity of each hardware models is such that FSW executes unaware that physical hardware is not present. This allows binaries to be compiled for both the simulation environment, and the flight computer, without changing the FSW source code. For hardware models that provide data dependent on the environment, such as a GPS receiver or magnetometer, an open-source tool from NASA GSFC (42 Spacecraft Simulation) is used to provide the necessary data. The underlying infrastructure used to transfer messages between FSW and the hardware models can also be used to monitor, intercept, and inject messages, which has proven to be beneficial for VV of larger missions such as James Webb Space Telescope (JWST). As hardware is procured, drivers can be added to the environment to enable hardware-in-the-loop (HWIL) testing. When strict time synchronization is not vital, any number of combinations of hardware components and software-based models can be tested. The open-source operator interface used in NOS3 is COSMOS from Ball Aerospace. For testing, plug-ins are implemented in COSMOS to control the NOS3 simulations, while the command and telemetry tools available in COSMOS are used to communicate with FSW. NOS3 is actively being used for FSW development and component testing of the Simulation-to-Flight 1 (STF-1) CubeSat. As NOS3 matures, hardware models have been added for common CubeSat components such as Novatel GPS receivers, ClydeSpace electrical power systems and batteries, ISISpace antenna systems, etc. In the future, NASA IVV plans to distribute NOS3 to other CubeSat developers and release the suite to the open-source community.

Updates in metabolomics tools and resources: 2014-2015.

PubMed

Misra, Biswapriya B; van der Hooft, Justin J J

2016-01-01

Data processing and interpretation represent the most challenging and time-consuming steps in high-throughput metabolomic experiments, regardless of the analytical platforms (MS or NMR spectroscopy based) used for data acquisition. Improved machinery in metabolomics generates increasingly complex datasets that create the need for more and better processing and analysis software and in silico approaches to understand the resulting data. However, a comprehensive source of information describing the utility of the most recently developed and released metabolomics resources--in the form of tools, software, and databases--is currently lacking. Thus, here we provide an overview of freely-available, and open-source, tools, algorithms, and frameworks to make both upcoming and established metabolomics researchers aware of the recent developments in an attempt to advance and facilitate data processing workflows in their metabolomics research. The major topics include tools and researches for data processing, data annotation, and data visualization in MS and NMR-based metabolomics. Most in this review described tools are dedicated to untargeted metabolomics workflows; however, some more specialist tools are described as well. All tools and resources described including their analytical and computational platform dependencies are summarized in an overview Table. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Developing an Intelligent Diagnosis and Assessment E-Learning Tool for Introductory Programming

ERIC Educational Resources Information Center

Huang, Chenn-Jung; Chen, Chun-Hua; Luo, Yun-Cheng; Chen, Hong-Xin; Chuang, Yi-Ta

2008-01-01

Recently, a lot of open source e-learning platforms have been offered for free in the Internet. We thus incorporate the intelligent diagnosis and assessment tool into an open software e-learning platform developed for programming language courses, wherein the proposed learning diagnosis assessment tools based on text mining and machine learning…

Streamlined sign-out of capillary protein electrophoresis using middleware and an open-source macro application.

PubMed

Mathur, Gagan; Haugen, Thomas H; Davis, Scott L; Krasowski, Matthew D

2014-01-01

Interfacing of clinical laboratory instruments with the laboratory information system (LIS) via "middleware" software is increasingly common. Our clinical laboratory implemented capillary electrophoresis using a Sebia(®) Capillarys-2™ (Norcross, GA, USA) instrument for serum and urine protein electrophoresis. Using Data Innovations Instrument Manager, an interface was established with the LIS (Cerner) that allowed for bi-directional transmission of numeric data. However, the text of the interpretive pathology report was not properly transferred. To reduce manual effort and possibility for error in text data transfer, we developed scripts in AutoHotkey, a free, open-source macro-creation and automation software utility. Scripts were written to create macros that automated mouse and key strokes. The scripts retrieve the specimen accession number, capture user input text, and insert the text interpretation in the correct patient record in the desired format. The scripts accurately and precisely transfer narrative interpretation into the LIS. Combined with bar-code reading by the electrophoresis instrument, the scripts transfer data efficiently to the correct patient record. In addition, the AutoHotKey script automated repetitive key strokes required for manual entry into the LIS, making protein electrophoresis sign-out easier to learn and faster to use by the pathology residents. Scripts allow for either preliminary verification by residents or final sign-out by the attending pathologist. Using the open-source AutoHotKey software, we successfully improved the transfer of text data between capillary electrophoresis software and the LIS. The use of open-source software tools should not be overlooked as tools to improve interfacing of laboratory instruments.

An Embedded Systems Course for Engineering Students Using Open-Source Platforms in Wireless Scenarios

ERIC Educational Resources Information Center

Rodriguez-Sanchez, M. C.; Torrado-Carvajal, Angel; Vaquero, Joaquin; Borromeo, Susana; Hernandez-Tamames, Juan A.

2016-01-01

This paper presents a case study analyzing the advantages and disadvantages of using project-based learning (PBL) combined with collaborative learning (CL) and industry best practices, integrated with information communication technologies, open-source software, and open-source hardware tools, in a specialized microcontroller and embedded systems…

Structure and software tools of AIDA.

PubMed

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

1987-01-01

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

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

2013-08-29

In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

Background In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods. PMID:23987653

Mocking the weak lensing universe: The LensTools Python computing package

NASA Astrophysics Data System (ADS)

Petri, A.

2016-10-01

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

pyLIMA : an open source microlensing software

NASA Astrophysics Data System (ADS)

Bachelet, Etienne

2017-01-01

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

Software engineering capability for Ada (GRASP/Ada Tool)

NASA Technical Reports Server (NTRS)

Cross, James H., II

1995-01-01

The GRASP/Ada project (Graphical Representations of Algorithms, Structures, and Processes for Ada) has successfully created and prototyped a new algorithmic level graphical representation 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 has been 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. A new Motif compliant graphical user interface has been developed for the GRASP/Ada prototype.

Evaluating Uncertainty in Integrated Environmental Models: A Review of Concepts and Tools

EPA Science Inventory

This paper reviews concepts for evaluating integrated environmental models and discusses a list of relevant software-based tools. A simplified taxonomy for sources of uncertainty and a glossary of key terms with standard definitions are provided in the context of integrated appro...

Multimedia Tools for Teaching Economics.

ERIC Educational Resources Information Center

Pereira-Ford, Clara V.

1998-01-01

Describes one professor's experience in researching the use of multimedia tools for teaching principles of economics. Provides a list of resources consulted, including universities and colleges, books, software, laserdiscs and VHS tapes, Web sites, and journal sources. Found the students generally to be receptive to the introduction of new tools…

Quantifying Uncertainties in Navigation and Orbit Propagation Analyses

NASA Technical Reports Server (NTRS)

Krieger, Andrew W.; Welch, Bryan W.

2017-01-01

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

Defining Geodetic Reference Frame using Matlab®: PlatEMotion 2.0

NASA Astrophysics Data System (ADS)

Cannavò, Flavio; Palano, Mimmo

2016-03-01

We describe the main features of the developed software tool, namely PlatE-Motion 2.0 (PEM2), which allows inferring the Euler pole parameters by inverting the observed velocities at a set of sites located on a rigid block (inverse problem). PEM2 allows also calculating the expected velocity value for any point located on the Earth providing an Euler pole (direct problem). PEM2 is the updated version of a previous software tool initially developed for easy-to-use file exchange with the GAMIT/GLOBK software package. The software tool is developed in Matlab® framework and, as the previous version, includes a set of MATLAB functions (m-files), GUIs (fig-files), map data files (mat-files) and user's manual as well as some example input files. New changes in PEM2 include (1) some bugs fixed, (2) improvements in the code, (3) improvements in statistical analysis, (4) new input/output file formats. In addition, PEM2 can be now run under the majority of operating systems. The tool is open source and freely available for the scientific community.

Improving the Product Documentation Process of a Small Software Company

NASA Astrophysics Data System (ADS)

Valtanen, Anu; Ahonen, Jarmo J.; Savolainen, Paula

Documentation is an important part of the software process, even though it is often neglected in software companies. The eternal question is how much documentation is enough. In this article, we present a practical implementation of lightweight product documentation process resulting from SPI efforts in a small company. Small companies’ financial and human resources are often limited. The documentation process described here, offers a template for creating adequate documentation consuming minimal amount of resources. The key element of the documentation process is an open source web-based bugtracking system that was customized to be used as a documentation tool. The use of the tool enables iterative and well structured documentation. The solution best serves the needs of a small company with off-the-shelf software products and striving for SPI.

Software reuse in spacecraft planning and scheduling systems

NASA Technical Reports Server (NTRS)

Mclean, David; Tuchman, Alan; Broseghini, Todd; Yen, Wen; Page, Brenda; Johnson, Jay; Bogovich, Lynn; Burkhardt, Chris; Mcintyre, James; Klein, Scott

1993-01-01

The use of a software toolkit and development methodology that supports software reuse is described. The toolkit includes source-code-level library modules and stand-alone tools which support such tasks as data reformatting and report generation, simple relational database applications, user interfaces, tactical planning, strategic planning and documentation. The current toolkit is written in C and supports applications that run on IBM-PC's under DOS and UNlX-based workstations under OpenLook and Motif. The toolkit is fully integrated for building scheduling systems that reuse AI knowledge base technology. A typical scheduling scenario and three examples of applications that utilize the reuse toolkit will be briefly described. In addition to the tools themselves, a description of the software evolution and reuse methodology that was used is presented.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Modular Analytical Multicomponent Analysis in Gas Sensor Aarrays

PubMed Central

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

2006-01-01

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

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

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

2017-02-01

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

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.

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

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

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

2011-11-01

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

General guidelines for biomedical software development

PubMed Central

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

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

1993-11-01

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

Community-driven computational biology with Debian Linux.

PubMed

Möller, Steffen; Krabbenhöft, Hajo Nils; Tille, Andreas; Paleino, David; Williams, Alan; Wolstencroft, Katy; Goble, Carole; Holland, Richard; Belhachemi, Dominique; Plessy, Charles

2010-12-21

The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers.

SEURAT: visual analytics for the integrated analysis of microarray data.

PubMed

Gribov, Alexander; Sill, Martin; Lück, Sonja; Rücker, Frank; Döhner, Konstanze; Bullinger, Lars; Benner, Axel; Unwin, Antony

2010-06-03

In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data.

Global GIS database; digital atlas of South Pacific

USGS Publications Warehouse

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

2001-01-01

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

Global GIS database; digital atlas of Africa

USGS Publications Warehouse

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

2001-01-01

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

Global GIS database; digital atlas of South Asia

USGS Publications Warehouse

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

2001-01-01

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

Baseliner: an open source, interactive tool for processing sap flux data from thermal dissipation probes.

Treesearch

Andrew C. Oishi; David Hawthorne; Ram Oren

2016-01-01

Estimating transpiration from woody plants using thermal dissipation sap flux sensors requires careful data processing. Currently, researchers accomplish this using spreadsheets, or by personally writing scripts for statistical software programs (e.g., R, SAS). We developed the Baseliner software to help establish a standardized protocol for processing sap...

Open Source Seismic Software in NOAA's Next Generation Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Baker, B. I.; Hagerty, M. T.; Leifer, J. M.; Lisowski, S.; Thies, D. A.; Donnelly, B. K.; Griffith, F. P.

2014-12-01

The Tsunami Information technology Modernization (TIM) is a project spearheaded by National Oceanic and Atmospheric Administration to update the United States' Tsunami Warning System software currently employed at the Pacific Tsunami Warning Center (Eva Beach, Hawaii) and the National Tsunami Warning Center (Palmer, Alaska). This entirely open source software project will integrate various seismic processing utilities with the National Weather Service Weather Forecast Office's core software, AWIPS2. For the real-time and near real-time seismic processing aspect of this project, NOAA has elected to integrate the open source portions of GFZ's SeisComP 3 (SC3) processing system into AWIPS2. To provide for better tsunami threat assessments we are developing open source tools for magnitude estimations (e.g., moment magnitude, energy magnitude, surface wave magnitude), detection of slow earthquakes with the Theta discriminant, moment tensor inversions (e.g. W-phase and teleseismic body waves), finite fault inversions, and array processing. With our reliance on common data formats such as QuakeML and seismic community standard messaging systems, all new facilities introduced into AWIPS2 and SC3 will be available as stand-alone tools or could be easily integrated into other real time seismic monitoring systems such as Earthworm, Antelope, etc. Additionally, we have developed a template based design paradigm so that the developer or scientist can efficiently create upgrades, replacements, and/or new metrics to the seismic data processing with only a cursory knowledge of the underlying SC3.

Prepare for Impact

ERIC Educational Resources Information Center

Waters, John K.

2010-01-01

Open source software is poised to make a profound impact on K-12 education. For years industry experts have been predicting the widespread adoption of open source tools by K-12 school districts. They're about to be proved right. The impact may not yet have been profound, but it's fair to say that some open source systems and non-proprietary…

Open Source software and social networks: disruptive alternatives for medical imaging.

PubMed

Ratib, Osman; Rosset, Antoine; Heuberger, Joris

2011-05-01

In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate and exchange information is a new model that is particularly suitable for some specific groups of healthcare professional and for physicians. It has also changed the expectations of how patients wish to communicate with their physicians. Emerging disruptive technologies and innovative paradigm such as Open Source software are leading the way to a new generation of information systems that slowly will change the way physicians and healthcare providers as well as patients will interact and communicate in the future. The impact of these new technologies is particularly effective in image communication, PACS and teleradiology. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Informed-Proteomics: open-source software package for top-down proteomics

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

Park, Jungkap; Piehowski, Paul D.; Wilkins, Christopher

Top-down proteomics involves the analysis of intact proteins. This approach is very attractive as it allows for analyzing proteins in their endogenous form without proteolysis, preserving valuable information about post-translation modifications, isoforms, proteolytic processing or their combinations collectively called proteoforms. Moreover, the quality of the top-down LC-MS/MS datasets is rapidly increasing due to advances in the liquid chromatography and mass spectrometry instrumentation and sample processing protocols. However, the top-down mass spectra are substantially more complex compare to the more conventional bottom-up data. To take full advantage of the increasing quality of the top-down LC-MS/MS datasets there is an urgent needmore » to develop algorithms and software tools for confident proteoform identification and quantification. In this study we present a new open source software suite for top-down proteomics analysis consisting of an LC-MS feature finding algorithm, a database search algorithm, and an interactive results viewer. The presented tool along with several other popular tools were evaluated using human-in-mouse xenograft luminal and basal breast tumor samples that are known to have significant differences in protein abundance based on bottom-up analysis.« less

Antibiogramj: A tool for analysing images from disk diffusion tests.

PubMed

Alonso, C A; Domínguez, C; Heras, J; Mata, E; Pascual, V; Torres, C; Zarazaga, M

2017-05-01

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed

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

2018-02-01

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

Harnessing the power of emerging petascale platforms

NASA Astrophysics Data System (ADS)

Mellor-Crummey, John

2007-07-01

As part of the US Department of Energy's Scientific Discovery through Advanced Computing (SciDAC-2) program, science teams are tackling problems that require computational simulation and modeling at the petascale. A grand challenge for computer science is to develop software technology that makes it easier to harness the power of these systems to aid scientific discovery. As part of its activities, the SciDAC-2 Center for Scalable Application Development Software (CScADS) is building open source software tools to support efficient scientific computing on the emerging leadership-class platforms. In this paper, we describe two tools for performance analysis and tuning that are being developed as part of CScADS: a tool for analyzing scalability and performance, and a tool for optimizing loop nests for better node performance. We motivate these tools by showing how they apply to S3D, a turbulent combustion code under development at Sandia National Laboratory. For S3D, our node performance analysis tool helped uncover several performance bottlenecks. Using our loop nest optimization tool, we transformed S3D's most costly loop nest to reduce execution time by a factor of 2.94 for a processor working on a 503 domain.

OpenCFU, a new free and open-source software to count cell colonies and other circular objects.

PubMed

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net.

The ALMA common software: dispatch from the trenches

NASA Astrophysics Data System (ADS)

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

2008-07-01

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

GOTCHA

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

Poliakoff, David; Legendre, Matt

2017-03-29

GOTCHA is a runtime API intercepting function calls between shared libraries. It is intended to be used by HPC Tools (i.e., performance analysis tools like Open/SpeedShop, HPCToolkit, TAU, etc.). 2:18 PMThese other tools can use Gotch to intercept interesting functions, such as MPI functions, and collect performance metrics about those functions. We intend for this to be open-source software that gets adopted by other open-s0urse tools that are used at LLNL.

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.

The Complexity Analysis Tool

DTIC Science & Technology

1988-10-01

overview of the complexity analysis tool ( CAT ), an automated tool which will analyze mission critical computer resources (MCCR) software. CAT is based...84 MAR UNCLASSIFIED SECURITY CLASSIFICATION OF THIS PAGE 19. ABSTRACT: (cont) CAT automates the metric for BASIC (HP-71), ATLAS (EQUATE), Ada (subset...UNIX 5.2). CAT analyzes source code and computes complexity on a module basis. CAT also generates graphic representations of the logic flow paths and

LSDCat: Detection and cataloguing of emission-line sources in integral-field spectroscopy datacubes

NASA Astrophysics Data System (ADS)

Herenz, Edmund Christian; Wisotzki, Lutz

2017-06-01

We present a robust, efficient, and user-friendly algorithm for detecting faint emission-line sources in large integral-field spectroscopic datacubes together with the public release of the software package Line Source Detection and Cataloguing (LSDCat). LSDCat uses a three-dimensional matched filter approach, combined with thresholding in signal-to-noise, to build a catalogue of individual line detections. In a second pass, the detected lines are grouped into distinct objects, and positions, spatial extents, and fluxes of the detected lines are determined. LSDCat requires only a small number of input parameters, and we provide guidelines for choosing appropriate values. The software is coded in Python and capable of processing very large datacubes in a short time. We verify the implementation with a source insertion and recovery experiment utilising a real datacube taken with the MUSE instrument at the ESO Very Large Telescope. The LSDCat software is available for download at http://muse-vlt.eu/science/tools and via the Astrophysics Source Code Library at http://ascl.net/1612.002

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

NASA Technical Reports Server (NTRS)

Truong, Long V.

1995-01-01

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

WaveAR: A software tool for calculating parameters for water waves with incident and reflected components

NASA Astrophysics Data System (ADS)

Landry, Blake J.; Hancock, Matthew J.; Mei, Chiang C.; García, Marcelo H.

2012-09-01

The ability to determine wave heights and phases along a spatial domain is vital to understanding a wide range of littoral processes. The software tool presented here employs established Stokes wave theory and sampling methods to calculate parameters for the incident and reflected components of a field of weakly nonlinear waves, monochromatic at first order in wave slope and propagating in one horizontal dimension. The software calculates wave parameters over an entire wave tank and accounts for reflection, weak nonlinearity, and a free second harmonic. Currently, no publicly available program has such functionality. The included MATLAB®-based open source code has also been compiled for Windows®, Mac® and Linux® operating systems. An additional companion program, VirtualWave, is included to generate virtual wave fields for WaveAR. Together, the programs serve as ideal analysis and teaching tools for laboratory water wave systems.

The MATH--Open Source Application for Easier Learning of Numerical Mathematics

ERIC Educational Resources Information Center

Glaser-Opitz, Henrich; Budajová, Kristina

2016-01-01

The article introduces a software application (MATH) supporting an education of Applied Mathematics, with focus on Numerical Mathematics. The MATH is an easy to use tool supporting various numerical methods calculations with graphical user interface and integrated plotting tool for graphical representation written in Qt with extensive use of Qwt…

Analyzing Virtual Physics Simulations with Tracker

ERIC Educational Resources Information Center

Claessens, Tom

2017-01-01

In the physics teaching community, Tracker is well known as a user-friendly open source video analysis software, authored by Douglas Brown. With this tool, the user can trace markers indicated on a video or on stroboscopic photos and perform kinematic analyses. Tracker also includes a data modeling tool that allows one to fit some theoretical…

Data Standards for Flow Cytometry

PubMed Central

SPIDLEN, JOSEF; GENTLEMAN, ROBERT C.; HAALAND, PERRY D.; LANGILLE, MORGAN; MEUR, NOLWENN LE; OCHS, MICHAEL F.; SCHMITT, CHARLES; SMITH, CLAYTON A.; TREISTER, ADAM S.; BRINKMAN, RYAN R.

2009-01-01

Flow cytometry (FCM) is an analytical tool widely used for cancer and HIV/AIDS research, and treatment, stem cell manipulation and detecting microorganisms in environmental samples. Current data standards do not capture the full scope of FCM experiments and there is a demand for software tools that can assist in the exploration and analysis of large FCM datasets. We are implementing a standardized approach to capturing, analyzing, and disseminating FCM data that will facilitate both more complex analyses and analysis of datasets that could not previously be efficiently studied. Initial work has focused on developing a community-based guideline for recording and reporting the details of FCM experiments. Open source software tools that implement this standard are being created, with an emphasis on facilitating reproducible and extensible data analyses. As well, tools for electronic collaboration will assist the integrated access and comprehension of experiments to empower users to collaborate on FCM analyses. This coordinated, joint development of bioinformatics standards and software tools for FCM data analysis has the potential to greatly facilitate both basic and clinical research—impacting a notably diverse range of medical and environmental research areas. PMID:16901228

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

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

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

OASYS (OrAnge SYnchrotron Suite): an open-source graphical environment for x-ray virtual experiments

NASA Astrophysics Data System (ADS)

Rebuffi, Luca; Sanchez del Rio, Manuel

2017-08-01

The evolution of the hardware platforms, the modernization of the software tools, the access to the codes of a large number of young people and the popularization of the open source software for scientific applications drove us to design OASYS (ORange SYnchrotron Suite), a completely new graphical environment for modelling X-ray experiments. The implemented software architecture allows to obtain not only an intuitive and very-easy-to-use graphical interface, but also provides high flexibility and rapidity for interactive simulations, making configuration changes to quickly compare multiple beamline configurations. Its purpose is to integrate in a synergetic way the most powerful calculation engines available. OASYS integrates different simulation strategies via the implementation of adequate simulation tools for X-ray Optics (e.g. ray tracing and wave optics packages). It provides a language to make them to communicate by sending and receiving encapsulated data. Python has been chosen as main programming language, because of its universality and popularity in scientific computing. The software Orange, developed at the University of Ljubljana (SLO), is the high level workflow engine that provides the interaction with the user and communication mechanisms.

BioSig: The Free and Open Source Software Library for Biomedical Signal Processing

PubMed Central

Vidaurre, Carmen; Sander, Tilmann H.; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals. PMID:21437227

BioSig: the free and open source software library for biomedical signal processing.

PubMed

Vidaurre, Carmen; Sander, Tilmann H; Schlögl, Alois

2011-01-01

BioSig is an open source software library for biomedical signal processing. The aim of the BioSig project is to foster research in biomedical signal processing by providing free and open source software tools for many different application areas. Some of the areas where BioSig can be employed are neuroinformatics, brain-computer interfaces, neurophysiology, psychology, cardiovascular systems, and sleep research. Moreover, the analysis of biosignals such as the electroencephalogram (EEG), electrocorticogram (ECoG), electrocardiogram (ECG), electrooculogram (EOG), electromyogram (EMG), or respiration signals is a very relevant element of the BioSig project. Specifically, BioSig provides solutions for data acquisition, artifact processing, quality control, feature extraction, classification, modeling, and data visualization, to name a few. In this paper, we highlight several methods to help students and researchers to work more efficiently with biomedical signals.

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

NASA Astrophysics Data System (ADS)

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

1995-05-01

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

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

PubMed Central

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

2017-01-01

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

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level

PubMed Central

Rocca-Serra, Philippe; Brandizi, Marco; Maguire, Eamonn; Sklyar, Nataliya; Taylor, Chris; Begley, Kimberly; Field, Dawn; Harris, Stephen; Hide, Winston; Hofmann, Oliver; Neumann, Steffen; Sterk, Peter; Tong, Weida; Sansone, Susanna-Assunta

2010-01-01

Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies; (ii) empowers users to uptake community-defined checklists and ontologies; and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at http://www.isa-tools.org Contact: isatools@googlegroups.com PMID:20679334

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

PubMed

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

2013-01-01

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

Open source tools for management and archiving of digital microscopy data to allow integration with patient pathology and treatment information

PubMed Central

2013-01-01

Background Virtual microscopy includes digitisation of histology slides and the use of computer technologies for complex investigation of diseases such as cancer. However, automated image analysis, or website publishing of such digital images, is hampered by their large file sizes. Results We have developed two Java based open source tools: Snapshot Creator and NDPI-Splitter. Snapshot Creator converts a portion of a large digital slide into a desired quality JPEG image. The image is linked to the patient’s clinical and treatment information in a customised open source cancer data management software (Caisis) in use at the Australian Breast Cancer Tissue Bank (ABCTB) and then published on the ABCTB website (http://www.abctb.org.au) using Deep Zoom open source technology. Using the ABCTB online search engine, digital images can be searched by defining various criteria such as cancer type, or biomarkers expressed. NDPI-Splitter splits a large image file into smaller sections of TIFF images so that they can be easily analysed by image analysis software such as Metamorph or Matlab. NDPI-Splitter also has the capacity to filter out empty images. Conclusions Snapshot Creator and NDPI-Splitter are novel open source Java tools. They convert digital slides into files of smaller size for further processing. In conjunction with other open source tools such as Deep Zoom and Caisis, this suite of tools is used for the management and archiving of digital microscopy images, enabling digitised images to be explored and zoomed online. Our online image repository also has the capacity to be used as a teaching resource. These tools also enable large files to be sectioned for image analysis. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5330903258483934 PMID:23402499

Nestly--a framework for running software with nested parameter choices and aggregating results.

PubMed

McCoy, Connor O; Gallagher, Aaron; Hoffman, Noah G; Matsen, Frederick A

2013-02-01

The execution of a software application or pipeline using various combinations of parameters and inputs is a common task in bioinformatics. In the absence of a specialized tool to organize, streamline and formalize this process, scientists must write frequently complex scripts to perform these tasks. We present nestly, a Python package to facilitate running tools with nested combinations of parameters and inputs. nestly provides three components. First, a module to build nested directory structures corresponding to choices of parameters. Second, the nestrun script to run a given command using each set of parameter choices. Third, the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. We also include a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. Source, documentation and tutorial examples are available at http://github.com/fhcrc/nestly. nestly can be installed from the Python Package Index via pip; it is open source (MIT license).

Using Kepler for Tool Integration in Microarray Analysis Workflows.

PubMed

Gan, Zhuohui; Stowe, Jennifer C; Altintas, Ilkay; McCulloch, Andrew D; Zambon, Alexander C

Increasing numbers of genomic technologies are leading to massive amounts of genomic data, all of which requires complex analysis. More and more bioinformatics analysis tools are being developed by scientist to simplify these analyses. However, different pipelines have been developed using different software environments. This makes integrations of these diverse bioinformatics tools difficult. Kepler provides an open source environment to integrate these disparate packages. Using Kepler, we integrated several external tools including Bioconductor packages, AltAnalyze, a python-based open source tool, and R-based comparison tool to build an automated workflow to meta-analyze both online and local microarray data. The automated workflow connects the integrated tools seamlessly, delivers data flow between the tools smoothly, and hence improves efficiency and accuracy of complex data analyses. Our workflow exemplifies the usage of Kepler as a scientific workflow platform for bioinformatics pipelines.

The Western Aeronautical Test Range. Chapter 10 Tools

NASA Technical Reports Server (NTRS)

Knudtson, Kevin; Park, Alice; Downing, Robert; Sheldon, Jack; Harvey, Robert; Norcross, April

2011-01-01

The Western Aeronautical Test Range (WATR) staff at the NASA Dryden Flight Research Center is developing a translation software called Chapter 10 Tools in response to challenges posed by post-flight processing data files originating from various on-board digital recorders that follow the Range Commanders Council Inter-Range Instrumentation Group (IRIG) 106 Chapter 10 Digital Recording Standard but use differing interpretations of the Standard. The software will read the date files regardless of the vendor implementation of the source recorder, displaying data, identifying and correcting errors, and producing a data file that can be successfully processed post-flight

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

PubMed

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

2015-09-01

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

BioSPICE: access to the most current computational tools for biologists.

PubMed

Garvey, Thomas D; Lincoln, Patrick; Pedersen, Charles John; Martin, David; Johnson, Mark

2003-01-01

The goal of the BioSPICE program is to create a framework that provides biologists access to the most current computational tools. At the program midpoint, the BioSPICE member community has produced a software system that comprises contributions from approximately 20 participating laboratories integrated under the BioSPICE Dashboard and a methodology for continued software integration. These contributed software modules are the BioSPICE Dashboard, a graphical environment that combines Open Agent Architecture and NetBeans software technologies in a coherent, biologist-friendly user interface. The current Dashboard permits data sources, models, simulation engines, and output displays provided by different investigators and running on different machines to work together across a distributed, heterogeneous network. Among several other features, the Dashboard enables users to create graphical workflows by configuring and connecting available BioSPICE components. Anticipated future enhancements to BioSPICE include a notebook capability that will permit researchers to browse and compile data to support model building, a biological model repository, and tools to support the development, control, and data reduction of wet-lab experiments. In addition to the BioSPICE software products, a project website supports information exchange and community building.

Software Comparison for Renewable Energy Deployment in a Distribution Network

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

Gao, David Wenzhong; Muljadi, Eduard; Tian, Tian

The main objective of this report is to evaluate different software options for performing robust distributed generation (DG) power system modeling. The features and capabilities of four simulation tools, OpenDSS, GridLAB-D, CYMDIST, and PowerWorld Simulator, are compared to analyze their effectiveness in analyzing distribution networks with DG. OpenDSS and GridLAB-D, two open source software, have the capability to simulate networks with fluctuating data values. These packages allow the running of a simulation each time instant by iterating only the main script file. CYMDIST, a commercial software, allows for time-series simulation to study variations on network controls. PowerWorld Simulator, another commercialmore » tool, has a batch mode simulation function through the 'Time Step Simulation' tool, which obtains solutions for a list of specified time points. PowerWorld Simulator is intended for analysis of transmission-level systems, while the other three are designed for distribution systems. CYMDIST and PowerWorld Simulator feature easy-to-use graphical user interfaces (GUIs). OpenDSS and GridLAB-D, on the other hand, are based on command-line programs, which increase the time necessary to become familiar with the software packages.« less

Community Intercomparison Suite (CIS) v1.4.0: a tool for intercomparing models and observations

NASA Astrophysics Data System (ADS)

Watson-Parris, Duncan; Schutgens, Nick; Cook, Nicholas; Kipling, Zak; Kershaw, Philip; Gryspeerdt, Edward; Lawrence, Bryan; Stier, Philip

2016-09-01

The Community Intercomparison Suite (CIS) is an easy-to-use command-line tool which has been developed to allow the straightforward intercomparison of remote sensing, in situ and model data. While there are a number of tools available for working with climate model data, the large diversity of sources (and formats) of remote sensing and in situ measurements necessitated a novel software solution. Developed by a professional software company, CIS supports a large number of gridded and ungridded data sources "out-of-the-box", including climate model output in NetCDF or the UK Met Office pp file format, CloudSat, CALIOP (Cloud-Aerosol Lidar with Orthogonal Polarization), MODIS (MODerate resolution Imaging Spectroradiometer), Cloud and Aerosol CCI (Climate Change Initiative) level 2 satellite data and a number of in situ aircraft and ground station data sets. The open-source architecture also supports user-defined plugins to allow many other sources to be easily added. Many of the key operations required when comparing heterogenous data sets are provided by CIS, including subsetting, aggregating, collocating and plotting the data. Output data are written to CF-compliant NetCDF files to ensure interoperability with other tools and systems. The latest documentation, including a user manual and installation instructions, can be found on our website (http://cistools.net). Here, we describe the need which this tool fulfils, followed by descriptions of its main functionality (as at version 1.4.0) and plugin architecture which make it unique in the field.

NOTE: Development of modified voxel phantoms for the numerical dosimetric reconstruction of radiological accidents involving external sources: implementation in SESAME tool

NASA Astrophysics Data System (ADS)

Courageot, Estelle; Sayah, Rima; Huet, Christelle

2010-05-01

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. When the dose distribution is evaluated with a numerical anthropomorphic model, the posture and morphology of the victim have to be reproduced as realistically as possible. Several years ago, IRSN developed a specific software application, called the simulation of external source accident with medical images (SESAME), for the dosimetric reconstruction of radiological accidents by numerical simulation. This tool combines voxel geometry and the MCNP(X) Monte Carlo computer code for radiation-material interaction. This note presents a new functionality in this software that enables the modelling of a victim's posture and morphology based on non-uniform rational B-spline (NURBS) surfaces. The procedure for constructing the modified voxel phantoms is described, along with a numerical validation of this new functionality using a voxel phantom of the RANDO tissue-equivalent physical model.

Development of modified voxel phantoms for the numerical dosimetric reconstruction of radiological accidents involving external sources: implementation in SESAME tool.

PubMed

Courageot, Estelle; Sayah, Rima; Huet, Christelle

2010-05-07

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. When the dose distribution is evaluated with a numerical anthropomorphic model, the posture and morphology of the victim have to be reproduced as realistically as possible. Several years ago, IRSN developed a specific software application, called the simulation of external source accident with medical images (SESAME), for the dosimetric reconstruction of radiological accidents by numerical simulation. This tool combines voxel geometry and the MCNP(X) Monte Carlo computer code for radiation-material interaction. This note presents a new functionality in this software that enables the modelling of a victim's posture and morphology based on non-uniform rational B-spline (NURBS) surfaces. The procedure for constructing the modified voxel phantoms is described, along with a numerical validation of this new functionality using a voxel phantom of the RANDO tissue-equivalent physical model.

Data format standard for sharing light source measurements

NASA Astrophysics Data System (ADS)

Gregory, G. Groot; Ashdown, Ian; Brandenburg, Willi; Chabaud, Dominique; Dross, Oliver; Gangadhara, Sanjay; Garcia, Kevin; Gauvin, Michael; Hansen, Dirk; Haraguchi, Kei; Hasna, Günther; Jiao, Jianzhong; Kelley, Ryan; Koshel, John; Muschaweck, Julius

2013-09-01

Optical design requires accurate characterization of light sources for computer aided design (CAD) software. Various methods have been used to model sources, from accurate physical models to measurement of light output. It has become common practice for designers to include measured source data for design simulations. Typically, a measured source will contain rays which sample the output distribution of the source. The ray data must then be exported to various formats suitable for import into optical analysis or design software. Source manufacturers are also making measurements of their products and supplying CAD models along with ray data sets for designers. The increasing availability of data has been beneficial to the design community but has caused a large expansion in storage needs for the source manufacturers since each software program uses a unique format to describe the source distribution. In 2012, the Illuminating Engineering Society (IES) formed a working group to understand the data requirements for ray data and recommend a standard file format. The working group included representatives from software companies supplying the analysis and design tools, source measurement companies providing metrology, source manufacturers creating the data and users from the design community. Within one year the working group proposed a file format which was recently approved by the IES for publication as TM-25. This paper will discuss the process used to define the proposed format, highlight some of the significant decisions leading to the format and list the data to be included in the first version of the standard.

Generation of GHS Scores from TEST and online sources ...

EPA Pesticide Factsheets

Alternatives assessment frameworks such as DfE (Design for the Environment) evaluate chemical alternatives in terms of human health effects, ecotoxicity, and fate. T.E.S.T. (Toxicity Estimation Software Tool) can be utilized to evaluate human health in terms of acute oral rat toxicity, developmental toxicity, endocrine activity, and mutagenicity. It can be used to evaluate ecotoxicity (in terms of acute fathead minnow toxicity) and fate (in terms of bioconcentration factor). It also be used to estimate a variety of key physicochemical properties such as melting point, boiling point, vapor pressure, water solubility, and bioconcentration factor. A web-based version of T.E.S.T. is currently being developed to allow predictions to be made from other web tools. Online data sources such as from NCCT’s Chemistry Dashboard, REACH dossiers, or from ChemHat.org can also be utilized to obtain GHS (Global Harmonization System) scores for comparing alternatives. The purpose of this talk is to show how GHS (Global Harmonization Score) data can be obtained from literature sources and from T.E.S.T. (Toxicity Estimation Software Tool). This data will be used to compare chemical alternatives in the alternatives assessment dashboard (a 2018 CSS product).

The Role of Standards in Cloud-Computing Interoperability

DTIC Science & Technology

2012-10-01

services are not shared outside the organization. CloudStack, Eucalyptus, HP, Microsoft, OpenStack , Ubuntu, and VMWare provide tools for building...center requirements • Developing usage models for cloud ven- dors • Independent IT consortium OpenStack http://www.openstack.org • Open-source...software for running private clouds • Currently consists of three core software projects: OpenStack Compute (Nova), OpenStack Object Storage (Swift

Community-driven computational biology with Debian Linux

PubMed Central

2010-01-01

Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

SEURAT: Visual analytics for the integrated analysis of microarray data

PubMed Central

2010-01-01

Background In translational cancer research, gene expression data is collected together with clinical data and genomic data arising from other chip based high throughput technologies. Software tools for the joint analysis of such high dimensional data sets together with clinical data are required. Results We have developed an open source software tool which provides interactive visualization capability for the integrated analysis of high-dimensional gene expression data together with associated clinical data, array CGH data and SNP array data. The different data types are organized by a comprehensive data manager. Interactive tools are provided for all graphics: heatmaps, dendrograms, barcharts, histograms, eventcharts and a chromosome browser, which displays genetic variations along the genome. All graphics are dynamic and fully linked so that any object selected in a graphic will be highlighted in all other graphics. For exploratory data analysis the software provides unsupervised data analytics like clustering, seriation algorithms and biclustering algorithms. Conclusions The SEURAT software meets the growing needs of researchers to perform joint analysis of gene expression, genomical and clinical data. PMID:20525257

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

USDA-ARS?s Scientific Manuscript database

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

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

PubMed Central

Jurica, Peter; van Leeuwen, Cees

2008-01-01

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

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

NASA Technical Reports Server (NTRS)

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

2013-01-01

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

OpenCFU, a New Free and Open-Source Software to Count Cell Colonies and Other Circular Objects

PubMed Central

Geissmann, Quentin

2013-01-01

Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to provide a new tool to enumerate circular objects from digital pictures and video streams. Here, I demonstrate that the created program, OpenCFU, is very robust, accurate and fast. In addition, it provides control over the processing parameters and is implemented in an intuitive and modern interface. OpenCFU is a cross-platform and open-source software freely available at http://opencfu.sourceforge.net. PMID:23457446

Boiler: lossy compression of RNA-seq alignments using coverage vectors

PubMed Central

Pritt, Jacob; Langmead, Ben

2016-01-01

We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler. PMID:27298258

PRISM Software: Processing and Review Interface for Strong‐Motion Data

USGS Publications Warehouse

Jones, Jeanne M.; Kalkan, Erol; Stephens, Christopher D.; Ng, Peter

2017-01-01

A continually increasing number of high‐quality digital strong‐motion records from stations of the National Strong Motion Project (NSMP) of the U.S. Geological Survey, as well as data from regional seismic networks within the United States, calls for automated processing of strong‐motion records with human review limited to selected significant or flagged records. The NSMP has developed the Processing and Review Interface for Strong Motion data (PRISM) software to meet this need. In combination with the Advanced National Seismic System Quake Monitoring System (AQMS), PRISM automates the processing of strong‐motion records. When used without AQMS, PRISM provides batch‐processing capabilities. The PRISM software is platform independent (coded in Java), open source, and does not depend on any closed‐source or proprietary software. The software consists of two major components: a record processing engine composed of modules for each processing step, and a review tool, which is a graphical user interface for manual review, edit, and processing. To facilitate use by non‐NSMP earthquake engineers and scientists, PRISM (both its processing engine and review tool) is easy to install and run as a stand‐alone system on common operating systems such as Linux, OS X, and Windows. PRISM was designed to be flexible and extensible to accommodate implementation of new processing techniques. All the computing features have been thoroughly tested.

Image-Based Single Cell Profiling: High-Throughput Processing of Mother Machine Experiments

PubMed Central

Sachs, Christian Carsten; Grünberger, Alexander; Helfrich, Stefan; Probst, Christopher; Wiechert, Wolfgang; Kohlheyer, Dietrich; Nöh, Katharina

2016-01-01

Background Microfluidic lab-on-chip technology combined with live-cell imaging has enabled the observation of single cells in their spatio-temporal context. The mother machine (MM) cultivation system is particularly attractive for the long-term investigation of rod-shaped bacteria since it facilitates continuous cultivation and observation of individual cells over many generations in a highly parallelized manner. To date, the lack of fully automated image analysis software limits the practical applicability of the MM as a phenotypic screening tool. Results We present an image analysis pipeline for the automated processing of MM time lapse image stacks. The pipeline supports all analysis steps, i.e., image registration, orientation correction, channel/cell detection, cell tracking, and result visualization. Tailored algorithms account for the specialized MM layout to enable a robust automated analysis. Image data generated in a two-day growth study (≈ 90 GB) is analyzed in ≈ 30 min with negligible differences in growth rate between automated and manual evaluation quality. The proposed methods are implemented in the software molyso (MOther machine AnaLYsis SOftware) that provides a new profiling tool to analyze unbiasedly hitherto inaccessible large-scale MM image stacks. Conclusion Presented is the software molyso, a ready-to-use open source software (BSD-licensed) for the unsupervised analysis of MM time-lapse image stacks. molyso source code and user manual are available at https://github.com/modsim/molyso. PMID:27661996

Managing a Real-Time Embedded Linux Platform with Buildroot

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

Diamond, J.; Martin, K.

2015-01-01

Developers of real-time embedded software often need to build the operating system, kernel, tools and supporting applications from source to work with the differences in their hardware configuration. The first attempts to introduce Linux-based real-time embedded systems into the Fermilab accelerator controls system used this approach but it was found to be time-consuming, difficult to maintain and difficult to adapt to different hardware configurations. Buildroot is an open source build system with a menu-driven configuration tool (similar to the Linux kernel build system) that automates this process. A customized Buildroot [1] system has been developed for use in the Fermilabmore » accelerator controls system that includes several hardware configuration profiles (including Intel, ARM and PowerPC) and packages for Fermilab support software. A bootable image file is produced containing the Linux kernel, shell and supporting software suite that varies from 3 to 20 megabytes large – ideal for network booting. The result is a platform that is easier to maintain and deploy in diverse hardware configurations« less

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

PubMed

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

2017-01-01

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

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

PubMed Central

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

2017-01-01

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

Advantages and Disadvantages in Image Processing with Free Software in Radiology.

PubMed

Mujika, Katrin Muradas; Méndez, Juan Antonio Juanes; de Miguel, Andrés Framiñan

2018-01-15

Currently, there are sophisticated applications that make it possible to visualize medical images and even to manipulate them. These software applications are of great interest, both from a teaching and a radiological perspective. In addition, some of these applications are known as Free Open Source Software because they are free and the source code is freely available, and therefore it can be easily obtained even on personal computers. Two examples of free open source software are Osirix Lite® and 3D Slicer®. However, this last group of free applications have limitations in its use. For the radiological field, manipulating and post-processing images is increasingly important. Consequently, sophisticated computing tools that combine software and hardware to process medical images are needed. In radiology, graphic workstations allow their users to process, review, analyse, communicate and exchange multidimensional digital images acquired with different image-capturing radiological devices. These radiological devices are basically CT (Computerised Tomography), MRI (Magnetic Resonance Imaging), PET (Positron Emission Tomography), etc. Nevertheless, the programs included in these workstations have a high cost which always depends on the software provider and is always subject to its norms and requirements. With this study, we aim to present the advantages and disadvantages of these radiological image visualization systems in the advanced management of radiological studies. We will compare the features of the VITREA2® and AW VolumeShare 5® radiology workstation with free open source software applications like OsiriX® and 3D Slicer®, with examples from specific studies.

HydroDesktop as a Community Designed and Developed Resource for Hydrologic Data Discovery and Analysis

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

As has been seen in other informatics fields, well-documented and appropriately licensed open source software tools have the potential to significantly increase both opportunities and motivation for inter-institutional science and technology collaboration. The CUAHSI HIS (and related HydroShare) projects have aimed to foster such activities in hydrology resulting in the development of many useful community software components including the HydroDesktop software application. HydroDesktop is an open source, GIS-based, scriptable software application for discovering data on the CUAHSI Hydrologic Information System and related resources. It includes a well-defined plugin architecture and interface to allow 3rd party developers to create extensions and add new functionality without requiring recompiling of the full source code. HydroDesktop is built in the C# programming language and uses the open source DotSpatial GIS engine for spatial data management. Capabilities include data search, discovery, download, visualization, and export. An extension that integrates the R programming language with HydroDesktop provides scripting and data automation capabilities and an OpenMI plugin provides the ability to link models. Current revision and updates to HydroDesktop include migration of core business logic to cross platform, scriptable Python code modules that can be executed in any operating system or linked into other software front-end applications.

Use of the 3D surgical modelling technique with open-source software for mandibular fibula free flap reconstruction and its surgical guides.

PubMed

Ganry, L; Hersant, B; Quilichini, J; Leyder, P; Meningaud, J P

2017-06-01

Tridimensional (3D) surgical modelling is a necessary step to create 3D-printed surgical tools, and expensive professional software is generally needed. Open-source software are functional, reliable, updated, may be downloaded for free and used to produce 3D models. Few surgical teams have used free solutions for mastering 3D surgical modelling for reconstructive surgery with osseous free flaps. We described an Open-source software 3D surgical modelling protocol to perform a fast and nearly free mandibular reconstruction with microvascular fibula free flap and its surgical guides, with no need for engineering support. Four successive specialised Open-source software were used to perform our 3D modelling: OsiriX ® , Meshlab ® , Netfabb ® and Blender ® . Digital Imaging and Communications in Medicine (DICOM) data on patient skull and fibula, obtained with a computerised tomography (CT) scan, were needed. The 3D modelling of the reconstructed mandible and its surgical guides were created. This new strategy may improve surgical management in Oral and Craniomaxillofacial surgery. Further clinical studies are needed to demonstrate the feasibility, reproducibility, transfer of know how and benefits of this technique. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

Niu, Nan; Jin, Xiaoyu; Niu, Zhendong; Cheng, Jing-Ru C; Li, Ling; Kataev, Mikhail Yu

2016-09-01

Developers often spend valuable time navigating and seeking relevant code in software maintenance. Currently, there is a lack of theoretical foundations to guide tool design and evaluation to best shape the code base to developers. This paper contributes a unified code navigation theory in light of the optimal food-foraging principles. We further develop a novel framework for automatically assessing the foraging mechanisms in the context of program investigation. We use the framework to examine to what extent the clustering of software entities affects code foraging. Our quantitative analysis of long-lived open-source projects suggests that clustering enriches the software environment and improves foraging efficiency. Our qualitative inquiry reveals concrete insights into real developer's behavior. Our research opens the avenue toward building a new set of ecologically valid code navigation tools.

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

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

Segre, Daniel

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.

DraGnET: Software for storing, managing and analyzing annotated draft genome sequence data

PubMed Central

2010-01-01

Background New "next generation" DNA sequencing technologies offer individual researchers the ability to rapidly generate large amounts of genome sequence data at dramatically reduced costs. As a result, a need has arisen for new software tools for storage, management and analysis of genome sequence data. Although bioinformatic tools are available for the analysis and management of genome sequences, limitations still remain. For example, restrictions on the submission of data and use of these tools may be imposed, thereby making them unsuitable for sequencing projects that need to remain in-house or proprietary during their initial stages. Furthermore, the availability and use of next generation sequencing in industrial, governmental and academic environments requires biologist to have access to computational support for the curation and analysis of the data generated; however, this type of support is not always immediately available. Results To address these limitations, we have developed DraGnET (Draft Genome Evaluation Tool). DraGnET is an open source web application which allows researchers, with no experience in programming and database management, to setup their own in-house projects for storing, retrieving, organizing and managing annotated draft and complete genome sequence data. The software provides a web interface for the use of BLAST, allowing users to perform preliminary comparative analysis among multiple genomes. We demonstrate the utility of DraGnET for performing comparative genomics on closely related bacterial strains. Furthermore, DraGnET can be further developed to incorporate additional tools for more sophisticated analyses. Conclusions DraGnET is designed for use either by individual researchers or as a collaborative tool available through Internet (or Intranet) deployment. For genome projects that require genome sequencing data to initially remain proprietary, DraGnET provides the means for researchers to keep their data in-house for analysis using local programs or until it is made publicly available, at which point it may be uploaded to additional analysis software applications. The DraGnET home page is available at http://www.dragnet.cvm.iastate.edu and includes example files for examining the functionalities, a link for downloading the DraGnET setup package and a link to the DraGnET source code hosted with full documentation on SourceForge. PMID:20175920

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

PubMed Central

Bajorath, Jurgen

2012-01-01

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

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

Current distributions of open source forensic software provide digital investigators with a large set of heterogeneous tools. Their use is not always focused on the target and requires high technical expertise. We present a new GNU/Linux live distribution, named CAINE (Computer Aided INvestigative Environment) that contains a collection of tools wrapped up into a user friendly environment. The CAINE forensic framework introduces novel important features, aimed at filling the interoperability gap across different forensic tools. Moreover, it provides a homogeneous graphical interface that drives digital investigators during the acquisition and analysis of electronic evidence, and it offers a semi-automatic mechanism for the creation of the final report.

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

PubMed

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

2015-10-24

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

More flexibility in representing geometric distortion in astronomical images

NASA Astrophysics Data System (ADS)

Shupe, David L.; Laher, Russ R.; Storrie-Lombardi, Lisa; Surace, Jason; Grillmair, Carl; Levitan, David; Sesar, Branimir

2012-09-01

A number of popular software tools in the public domain are used by astronomers, professional and amateur alike, but some of the tools that have similar purposes cannot be easily interchanged, owing to the lack of a common standard. For the case of image distortion, SCAMP and SExtractor, available from Astromatic.net, perform astrometric calibration and source-object extraction on image data, and image-data geometric distortion is computed in celestial coordinates with polynomial coefficients stored in the FITS header with the PV i_j keywords. Another widely-used astrometric-calibration service, Astrometry.net, solves for distortion in pixel coordinates using the SIP convention that was introduced by the Spitzer Science Center. Up until now, due to the complexity of these distortion representations, it was very difficult to use the output of one of these packages as input to the other. New Python software, along with faster-computing C-language translations, have been developed at the Infrared Processing and Analysis Center (IPAC) to convert FITS-image headers from PV to SIP and vice versa. It is now possible to straightforwardly use Astrometry.net for astrometric calibration and then SExtractor for source-object extraction. The new software also enables astrometric calibration by SCAMP followed by image visualization with tools that support SIP distortion, but not PV . The software has been incorporated into the image-processing pipelines of the Palomar Transient Factory (PTF), which generate FITS images with headers containing both distortion representations. The software permits the conversion of archived images, such as from the Spitzer Heritage Archive and NASA/IPAC Infrared Science Archive, from SIP to PV or vice versa. This new capability renders unnecessary any new representation, such as the proposed TPV distortion convention.

Science and Software

NASA Astrophysics Data System (ADS)

Zelt, C. A.

2017-12-01

Earth science attempts to understand how the earth works. This research often depends on software for modeling, processing, inverting or imaging. Freely sharing open-source software is essential to prevent reinventing the wheel and allows software to be improved and applied in ways the original author may never have envisioned. For young scientists, releasing software can increase their name ID when applying for jobs and funding, and create opportunities for collaborations when scientists who collect data want the software's creator to be involved in their project. However, we frequently hear scientists say software is a tool, it's not science. Creating software that implements a new or better way of earth modeling or geophysical processing, inverting or imaging should be viewed as earth science. Creating software for things like data visualization, format conversion, storage, or transmission, or programming to enhance computational performance, may be viewed as computer science. The former, ideally with an application to real data, can be published in earth science journals, the latter possibly in computer science journals. Citations in either case should accurately reflect the impact of the software on the community. Funding agencies need to support more software development and open-source releasing, and the community should give more high-profile awards for developing impactful open-source software. Funding support and community recognition for software development can have far reaching benefits when the software is used in foreseen and unforeseen ways, potentially for years after the original investment in the software development. For funding, an open-source release that is well documented should be required, with example input and output files. Appropriate funding will provide the incentive and time to release user-friendly software, and minimize the need for others to duplicate the effort. All funded software should be available through a single web site, ideally maintained by someone in a funded position. Perhaps the biggest challenge is the reality that researches who use software, as opposed to develop software, are more attractive university hires because they are more likely to be "big picture" scientists that publish in the highest profile journals, although sometimes the two go together.

Design and validation of Segment--freely available software for cardiovascular image analysis.

PubMed

Heiberg, Einar; Sjögren, Jane; Ugander, Martin; Carlsson, Marcus; Engblom, Henrik; Arheden, Håkan

2010-01-11

Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format. Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page http://segment.heiberg.se. Segment is a well-validated comprehensive software package for cardiovascular image analysis. It is freely available for research purposes provided that relevant original research publications related to the software are cited.

Open-Source Tools for Enhancing Full-Text Searching of OPACs: Use of Koha, Greenstone and Fedora

ERIC Educational Resources Information Center

Anuradha, K. T.; Sivakaminathan, R.; Kumar, P. Arun

2011-01-01

Purpose: There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text…

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

NASA Astrophysics Data System (ADS)

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

2013-10-01

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

The Role of Free/Libre and Open Source Software in Learning Health Systems.

PubMed

Paton, C; Karopka, T

2017-08-01

Objective: To give an overview of the role of Free/Libre and Open Source Software (FLOSS) in the context of secondary use of patient data to enable Learning Health Systems (LHSs). Methods: We conducted an environmental scan of the academic and grey literature utilising the MedFLOSS database of open source systems in healthcare to inform a discussion of the role of open source in developing LHSs that reuse patient data for research and quality improvement. Results: A wide range of FLOSS is identified that contributes to the information technology (IT) infrastructure of LHSs including operating systems, databases, frameworks, interoperability software, and mobile and web apps. The recent literature around the development and use of key clinical data management tools is also reviewed. Conclusions: FLOSS already plays a critical role in modern health IT infrastructure for the collection, storage, and analysis of patient data. The nature of FLOSS systems to be collaborative, modular, and modifiable may make open source approaches appropriate for building the digital infrastructure for a LHS. Georg Thieme Verlag KG Stuttgart.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

PubMed

Perez-Riverol, Yasset; Ternent, Tobias; Koch, Maximilian; Barsnes, Harald; Vrousgou, Olga; Jupp, Simon; Vizcaíno, Juan Antonio

2017-10-01

The availability of user-friendly software to annotate biological datasets and experimental details is becoming essential in data management practices, both in local storage systems and in public databases. The Ontology Lookup Service (OLS, http://www.ebi.ac.uk/ols) is a popular centralized service to query, browse and navigate biomedical ontologies and controlled vocabularies. Recently, the OLS framework has been completely redeveloped (version 3.0), including enhancements in the data model, like the added support for Web Ontology Language based ontologies, among many other improvements. However, the new OLS is not backwards compatible and new software tools are needed to enable access to this widely used framework now that the previous version is no longer available. We here present the OLS Client as a free, open-source Java library to retrieve information from the new version of the OLS. It enables rapid tool creation by providing a robust, pluggable programming interface and common data model to programmatically access the OLS. The library has already been integrated and is routinely used by several bioinformatics resources and related data annotation tools. Secondly, we also introduce an updated version of the OLS Dialog (version 2.0), a Java graphical user interface that can be easily plugged into Java desktop applications to access the OLS. The software and related documentation are freely available at https://github.com/PRIDE-Utilities/ols-client and https://github.com/PRIDE-Toolsuite/ols-dialog. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

AdaNET phase 0 support for the AdaNET Dynamic Software Inventory (DSI) management system prototype. Catalog of available reusable software components

NASA Technical Reports Server (NTRS)

Hanley, Lionel

1989-01-01

The Ada Software Repository is a public-domain collection of Ada software and information. The Ada Software Repository is one of several repositories located on the SIMTEL20 Defense Data Network host computer at White Sands Missile Range, and available to any host computer on the network since 26 November 1984. This repository provides a free source for Ada programs and information. The Ada Software Repository is divided into several subdirectories. These directories are organized by topic, and their names and a brief overview of their topics are contained. The Ada Software Repository on SIMTEL20 serves two basic roles: to promote the exchange and use (reusability) of Ada programs and tools (including components) and to promote Ada education.

Collected Software Engineering Papers, Volume 10

NASA Technical Reports Server (NTRS)

1992-01-01

This document is a collection of selected technical papers produced by participants in the Software Engineering Laboratory (SEL) from Oct. 1991 - Nov. 1992. The purpose of the document is to make available, in one reference, some results of SEL research that originally appeared in a number of different forums. Although these papers cover several topics related to software engineering, they do not encompass the entire scope of SEL activities and interests. Additional information about the SEL and its research efforts may be obtained from the sources listed in the bibliography at the end of this document. For the convenience of this presentation, the 11 papers contained here are grouped into 5 major sections: (1) the Software Engineering Laboratory; (2) software tools studies; (3) software models studies; (4) software measurement studies; and (5) Ada technology studies.

Global Precipitation Mission Visualization Tool

NASA Technical Reports Server (NTRS)

Schwaller, Mathew

2011-01-01

The Global Precipitation Mission (GPM) software provides graphic visualization tools that enable easy comparison of ground- and space-based radar observations. It was initially designed to compare ground radar reflectivity from operational, ground-based, S- and C-band meteorological radars with comparable measurements from the Tropical Rainfall Measuring Mission (TRMM) satellite's precipitation radar instrument. This design is also applicable to other groundbased and space-based radars, and allows both ground- and space-based radar data to be compared for validation purposes. The tool creates an operational system that routinely performs several steps. It ingests satellite radar data (precipitation radar data from TRMM) and groundbased meteorological radar data from a number of sources. Principally, the ground radar data comes from national networks of weather radars (see figure). The data ingested by the visualization tool must conform to the data formats used in GPM Validation Network Geometry-matched data product generation. The software also performs match-ups of the radar volume data for the ground- and space-based data, as well as statistical and graphical analysis (including two-dimensional graphical displays) on the match-up data. The visualization tool software is written in IDL, and can be operated either in the IDL development environment or as a stand-alone executable function.

Software Hardware Asset Reuse Enterprise (SHARE) Repository Framework: Related Work and Development Plan

DTIC Science & Technology

2009-08-19

designed to collect the data and assist the analyst in drawing relationships between the data. Palantir Technologies has created one such software...application to support the DoD intelligence community by providing robust capabilities for managing data from various sources10. The Palantir tool...www.palantirtech.com/ - 38 - Figure 17. Palantir Graphical Interface (Gordon-Schlosberg, 2008) Similar examples of the use of ontologies to support data

Tailoring a software production environment for a large project

NASA Technical Reports Server (NTRS)

Levine, D. R.

1984-01-01

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

An expert system based software sizing tool, phase 2

NASA Technical Reports Server (NTRS)

Friedlander, David

1990-01-01

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

iGlobe Interactive Visualization and Analysis of Spatial Data

NASA Technical Reports Server (NTRS)

Hogan, Patrick

2012-01-01

iGlobe is open-source software built on NASA World Wind virtual globe technology. iGlobe provides a growing set of tools for weather science, climate research, and agricultural analysis. Up until now, these types of sophisticated tools have been developed in isolation by national agencies, academic institutions, and research organizations. By providing an open-source solution to analyze and visualize weather, climate, and agricultural data, the scientific and research communities can more readily advance solutions needed to understand better the dynamics of our home planet, Earth

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...

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).

CellTracker (not only) for dummies.

PubMed

Piccinini, Filippo; Kiss, Alexa; Horvath, Peter

2016-03-15

Time-lapse experiments play a key role in studying the dynamic behavior of cells. Single-cell tracking is one of the fundamental tools for such analyses. The vast majority of the recently introduced cell tracking methods are limited to fluorescently labeled cells. An equally important limitation is that most software cannot be effectively used by biologists without reasonable expertise in image processing. Here we present CellTracker, a user-friendly open-source software tool for tracking cells imaged with various imaging modalities, including fluorescent, phase contrast and differential interference contrast (DIC) techniques. CellTracker is written in MATLAB (The MathWorks, Inc., USA). It works with Windows, Macintosh and UNIX-based systems. Source code and graphical user interface (GUI) are freely available at: http://celltracker.website/ horvath.peter@brc.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

ProphTools: general prioritization tools for heterogeneous biological networks.

PubMed

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

2017-12-01

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

Post-processing open-source software for the CBCT monitoring of periapical lesions healing following endodontic treatment: technical report of two cases.

PubMed

Villoria, Eduardo M; Lenzi, Antônio R; Soares, Rodrigo V; Souki, Bernardo Q; Sigurdsson, Asgeir; Marques, Alexandre P; Fidel, Sandra R

2017-01-01

To describe the use of open-source software for the post-processing of CBCT imaging for the assessment of periapical lesions development after endodontic treatment. CBCT scans were retrieved from endodontic records of two patients. Three-dimensional virtual models, voxel counting, volumetric measurement (mm 3 ) and mean intensity of the periapical lesion were performed with ITK-SNAP v. 3.0 software. Three-dimensional models of the lesions were aligned and overlapped through the MeshLab software, which performed an automatic recording of the anatomical structures, based on the best fit. Qualitative and quantitative analyses of the changes in lesions size after treatment were performed with the 3DMeshMetric software. The ITK-SNAP v. 3.0 showed the smaller value corresponding to the voxel count and the volume of the lesion segmented in yellow, indicating reduction in volume of the lesion after the treatment. A higher value of the mean intensity of the segmented image in yellow was also observed, which suggested new bone formation. Colour mapping and "point value" tool allowed the visualization of the reduction of periapical lesions in several regions. Researchers and clinicians in the monitoring of endodontic periapical lesions have the opportunity to use open-source software.

Multimodal visualization interface for data management, self-learning and data presentation.

PubMed

Van Sint Jan, S; Demondion, X; Clapworthy, G; Louryan, S; Rooze, M; Cotten, A; Viceconti, M

2006-10-01

A multimodal visualization software, called the Data Manager (DM), has been developed to increase interdisciplinary communication around the topic of visualization and modeling of various aspects of the human anatomy. Numerous tools used in Radiology are integrated in the interface that runs on standard personal computers. The available tools, combined to hierarchical data management and custom layouts, allow analyzing of medical imaging data using advanced features outside radiological premises (for example, for patient review, conference presentation or tutorial preparation). The system is free, and based on an open-source software development architecture, and therefore updates of the system for custom applications are possible.

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

Computational System For Rapid CFD Analysis In Engineering

NASA Technical Reports Server (NTRS)

Barson, Steven L.; Ascoli, Edward P.; Decroix, Michelle E.; Sindir, Munir M.

1995-01-01

Computational system comprising modular hardware and software sub-systems developed to accelerate and facilitate use of techniques of computational fluid dynamics (CFD) in engineering environment. Addresses integration of all aspects of CFD analysis process, including definition of hardware surfaces, generation of computational grids, CFD flow solution, and postprocessing. Incorporates interfaces for integration of all hardware and software tools needed to perform complete CFD analysis. Includes tools for efficient definition of flow geometry, generation of computational grids, computation of flows on grids, and postprocessing of flow data. System accepts geometric input from any of three basic sources: computer-aided design (CAD), computer-aided engineering (CAE), or definition by user.

BeadArray Expression Analysis Using Bioconductor

PubMed Central

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

2011-01-01

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

Implementation of GenePattern within the Stanford Microarray Database.

PubMed

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

2009-01-01

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

Sonification Prototype for Space Physics

NASA Astrophysics Data System (ADS)

Candey, R. M.; Schertenleib, A. M.; Diaz Merced, W. L.

2005-12-01

As an alternative and adjunct to visual displays, auditory exploration of data via sonification (data controlled sound) and audification (audible playback of data samples) is promising for complex or rapidly/temporally changing visualizations, for data exploration of large datasets (particularly multi-dimensional datasets), and for exploring datasets in frequency rather than spatial dimensions (see also International Conferences on Auditory Display ). Besides improving data exploration and analysis for most researchers, the use of sound is especially valuable as an assistive technology for visually-impaired people and can make science and math more exciting for high school and college students. Only recently have the hardware and software come together to make a cross-platform open-source sonification tool feasible. We have developed a prototype sonification data analysis tool using the JavaSound API and NASA GSFC's ViSBARD software . Wanda Diaz Merced, a blind astrophysicist from Puerto Rico, is instrumental in advising on and testing the tool.

NeuroPG: open source software for optical pattern generation and data acquisition

PubMed Central

Avants, Benjamin W.; Murphy, Daniel B.; Dapello, Joel A.; Robinson, Jacob T.

2015-01-01

Patterned illumination using a digital micromirror device (DMD) is a powerful tool for optogenetics. Compared to a scanning laser, DMDs are inexpensive and can easily create complex illumination patterns. Combining these complex spatiotemporal illumination patterns with optogenetics allows DMD-equipped microscopes to probe neural circuits by selectively manipulating the activity of many individual cells or many subcellular regions at the same time. To use DMDs to study neural activity, scientists must develop specialized software to coordinate optical stimulation patterns with the acquisition of electrophysiological and fluorescence data. To meet this growing need we have developed an open source optical pattern generation software for neuroscience—NeuroPG—that combines, DMD control, sample visualization, and data acquisition in one application. Built on a MATLAB platform, NeuroPG can also process, analyze, and visualize data. The software is designed specifically for the Mightex Polygon400; however, as an open source package, NeuroPG can be modified to incorporate any data acquisition, imaging, or illumination equipment that is compatible with MATLAB’s Data Acquisition and Image Acquisition toolboxes. PMID:25784873

The FORTRAN static source code analyzer program (SAP) user's guide, revision 1

NASA Technical Reports Server (NTRS)

Decker, W.; Taylor, W.; Eslinger, S.

1982-01-01

The FORTRAN Static Source Code Analyzer Program (SAP) User's Guide (Revision 1) is presented. SAP is a software tool designed to assist Software Engineering Laboratory (SEL) personnel in conducting studies of FORTRAN programs. SAP scans FORTRAN source code and produces reports that present statistics and measures of statements and structures that make up a module. This document is a revision of the previous SAP user's guide, Computer Sciences Corporation document CSC/TM-78/6045. SAP Revision 1 is the result of program modifications to provide several new reports, additional complexity analysis, and recognition of all statements described in the FORTRAN 77 standard. This document provides instructions for operating SAP and contains information useful in interpreting SAP output.

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Conversion and Validation of Distribution System Model from a QSTS-Based Tool to a Real-Time Dynamic Phasor Simulator: Preprint

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Virtual GEOINT Center: C2ISR through an avatar's eyes

NASA Astrophysics Data System (ADS)

Seibert, Mark; Tidbal, Travis; Basil, Maureen; Muryn, Tyler; Scupski, Joseph; Williams, Robert

2013-05-01

As the number of devices collecting and sending data in the world are increasing, finding ways to visualize and understand that data is becoming more and more of a problem. This has often been coined as the problem of "Big Data." The Virtual Geoint Center (VGC) aims to aid in solving that problem by providing a way to combine the use of the virtual world with outside tools. Using open-source software such as OpenSim and Blender, the VGC uses a visually stunning 3D environment to display the data sent to it. The VGC is broken up into two major components: The Kinect Minimap, and the Geoint Map. The Kinect Minimap uses the Microsoft Kinect and its open-source software to make a miniature display of people the Kinect detects in front of it. The Geoint Map collect smartphone sensor information from online databases and displays them in real time onto a map generated by Google Maps. By combining outside tools and the virtual world, the VGC can help a user "visualize" data, and provide additional tools to "understand" the data.

Modern software approaches applied to a Hydrological model: the GEOtop Open-Source Software Project

NASA Astrophysics Data System (ADS)

Cozzini, Stefano; Endrizzi, Stefano; Cordano, Emanuele; Bertoldi, Giacomo; Dall'Amico, Matteo

2017-04-01

The GEOtop hydrological scientific package is an integrated hydrological model that simulates the heat and water budgets at and below the soil surface. It describes the three-dimensional water flow in the soil and the energy exchange with the atmosphere, considering the radiative and turbulent fluxes. Furthermore, it reproduces the highly non-linear interactions between the water and energy balance during soil freezing and thawing, and simulates the temporal evolution of snow cover, soil temperature and moisture. The core components of the package were presented in the 2.0 version (Endrizzi et al, 2014), which was released as Free Software Open-source project. However, despite the high scientific quality of the project, a modern software engineering approach was still missing. Such weakness hindered its scientific potential and its use both as a standalone package and, more importantly, in an integrate way with other hydrological software tools. In this contribution we present our recent software re-engineering efforts to create a robust and stable scientific software package open to the hydrological community, easily usable by researchers and experts, and interoperable with other packages. The activity takes as a starting point the 2.0 version, scientifically tested and published. This version, together with several test cases based on recent published or available GEOtop applications (Cordano and Rigon, 2013, WRR, Kollet et al, 2016, WRR) provides the baseline code and a certain number of referenced results as benchmark. Comparison and scientific validation can then be performed for each software re-engineering activity performed on the package. To keep track of any single change the package is published on its own github repository geotopmodel.github.io/geotop/ under GPL v3.0 license. A Continuous Integration mechanism by means of Travis-CI has been enabled on the github repository on master and main development branches. The usage of CMake configuration tool and the suite of tests (easily manageable by means of ctest tools) greatly reduces the burden of the installation and allows us to enhance portability on different compilers and Operating system platforms. The package was also complemented by several software tools which provide web-based visualization of results based on R plugins, in particular "shiny" (Chang at al, 2016), "geotopbricks" and "geotopOptim2" (Cordano et al, 2016) packages, which allow rapid and efficient scientific validation of new examples and tests. The software re-engineering activities are still under development. However, our first results are promising enough to eventually reach a robust and stable software project that manages in a flexible way a complex state-of-the-art hydrological model like GEOtop and integrates it into wider workflows.

COMPOSE-HPC: A Transformational Approach to Exascale

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

Bernholdt, David E; Allan, Benjamin A.; Armstrong, Robert C.

2012-04-01

The goal of the COMPOSE-HPC project is to 'democratize' tools for automatic transformation of program source code so that it becomes tractable for the developers of scientific applications to create and use their own transformations reliably and safely. This paper describes our approach to this challenge, the creation of the KNOT tool chain, which includes tools for the creation of annotation languages to control the transformations (PAUL), to perform the transformations (ROTE), and optimization and code generation (BRAID), which can be used individually and in combination. We also provide examples of current and future uses of the KNOT tools, whichmore » include transforming code to use different programming models and environments, providing tests that can be used to detect errors in software or its execution, as well as composition of software written in different programming languages, or with different threading patterns.« less

The center for causal discovery of biomedical knowledge from big data

PubMed Central

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

2015-01-01

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

A Modular GIS-Based Software Architecture for Model Parameter Estimation using the Method of Anchored Distributions (MAD)

NASA Astrophysics Data System (ADS)

Ames, D. P.; Osorio-Murillo, C.; Over, M. W.; Rubin, Y.

2012-12-01

The Method of Anchored Distributions (MAD) is an inverse modeling technique that is well-suited for estimation of spatially varying parameter fields using limited observations and Bayesian methods. This presentation will discuss the design, development, and testing of a free software implementation of the MAD technique using the open source DotSpatial geographic information system (GIS) framework, R statistical software, and the MODFLOW groundwater model. This new tool, dubbed MAD-GIS, is built using a modular architecture that supports the integration of external analytical tools and models for key computational processes including a forward model (e.g. MODFLOW, HYDRUS) and geostatistical analysis (e.g. R, GSLIB). The GIS-based graphical user interface provides a relatively simple way for new users of the technique to prepare the spatial domain, to identify observation and anchor points, to perform the MAD analysis using a selected forward model, and to view results. MAD-GIS uses the Managed Extensibility Framework (MEF) provided by the Microsoft .NET programming platform to support integration of different modeling and analytical tools at run-time through a custom "driver." Each driver establishes a connection with external programs through a programming interface, which provides the elements for communicating with core MAD software. This presentation gives an example of adapting the MODFLOW to serve as the external forward model in MAD-GIS for inferring the distribution functions of key MODFLOW parameters. Additional drivers for other models are being developed and it is expected that the open source nature of the project will engender the development of additional model drivers by 3rd party scientists.

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

PubMed

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

2018-06-01

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

STARS 2.0: 2nd-generation open-source archiving and query software

NASA Astrophysics Data System (ADS)

Winegar, Tom

2008-07-01

The Subaru Telescope is in process of developing an open-source alternative to the 1st-generation software and databases (STARS 1) used for archiving and query. For STARS 2, we have chosen PHP and Python for scripting and MySQL as the database software. We have collected feedback from staff and observers, and used this feedback to significantly improve the design and functionality of our future archiving and query software. Archiving - We identified two weaknesses in 1st-generation STARS archiving software: a complex and inflexible table structure and uncoordinated system administration for our business model: taking pictures from the summit and archiving them in both Hawaii and Japan. We adopted a simplified and normalized table structure with passive keyword collection, and we are designing an archive-to-archive file transfer system that automatically reports real-time status and error conditions and permits error recovery. Query - We identified several weaknesses in 1st-generation STARS query software: inflexible query tools, poor sharing of calibration data, and no automatic file transfer mechanisms to observers. We are developing improved query tools and sharing of calibration data, and multi-protocol unassisted file transfer mechanisms for observers. In the process, we have redefined a 'query': from an invisible search result that can only transfer once in-house right now, with little status and error reporting and no error recovery - to a stored search result that can be monitored, transferred to different locations with multiple protocols, reporting status and error conditions and permitting recovery from errors.

GeolOkit 1.0: a new Open Source, Cross-Platform software for geological data visualization in Google Earth environment

NASA Astrophysics Data System (ADS)

Triantafyllou, Antoine; Bastin, Christophe; Watlet, Arnaud

2016-04-01

GIS software suites are today's essential tools to gather and visualise geological data, to apply spatial and temporal analysis and in fine, to create and share interactive maps for further geosciences' investigations. For these purposes, we developed GeolOkit: an open-source, freeware and lightweight software, written in Python, a high-level, cross-platform programming language. GeolOkit software is accessible through a graphical user interface, designed to run in parallel with Google Earth. It is a super user-friendly toolbox that allows 'geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to plot these one into Google Earth environment using KML code. This workflow requires no need of any third party software, except Google Earth itself. GeolOkit comes with large number of geosciences' labels, symbols, colours and placemarks and may process : (i) multi-points data, (ii) contours via several interpolations methods, (iii) discrete planar and linear structural data in 2D or 3D supporting large range of structures input format, (iv) clustered stereonets and rose diagram, (v) drawn cross-sections as vertical sections, (vi) georeferenced maps and vectors, (vii) field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS. We are looking for you to discover all the functionalities of GeolOkit software. As this project is under development, we are definitely looking to discussions regarding your proper needs, your ideas and contributions to GeolOkit project.

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

NASA Astrophysics Data System (ADS)

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

2012-04-01

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

Putting tools in the toolbox: Development of a free, open-source toolbox for quantitative image analysis of porous media.

NASA Astrophysics Data System (ADS)

Iltis, G.; Caswell, T. A.; Dill, E.; Wilkins, S.; Lee, W. K.

2014-12-01

X-ray tomographic imaging of porous media has proven to be a valuable tool for investigating and characterizing the physical structure and state of both natural and synthetic porous materials, including glass bead packs, ceramics, soil and rock. Given that most synchrotron facilities have user programs which grant academic researchers access to facilities and x-ray imaging equipment free of charge, a key limitation or hindrance for small research groups interested in conducting x-ray imaging experiments is the financial cost associated with post-experiment data analysis. While the cost of high performance computing hardware continues to decrease, expenses associated with licensing commercial software packages for quantitative image analysis continue to increase, with current prices being as high as $24,000 USD, for a single user license. As construction of the Nation's newest synchrotron accelerator nears completion, a significant effort is being made here at the National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory (BNL), to provide an open-source, experiment-to-publication toolbox that reduces the financial and technical 'activation energy' required for performing sophisticated quantitative analysis of multidimensional porous media data sets, collected using cutting-edge x-ray imaging techniques. Implementation focuses on leveraging existing open-source projects and developing additional tools for quantitative analysis. We will present an overview of the software suite that is in development here at BNL including major design decisions, a demonstration of several test cases illustrating currently available quantitative tools for analysis and characterization of multidimensional porous media image data sets and plans for their future development.

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

PubMed

Jurica, Peter; van Leeuwen, Cees

2009-01-01

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

Aperture Photometry Tool

NASA Astrophysics Data System (ADS)

Laher, Russ R.; Gorjian, Varoujan; Rebull, Luisa M.; Masci, Frank J.; Fowler, John W.; Helou, George; Kulkarni, Shrinivas R.; Law, Nicholas M.

2012-07-01

Aperture Photometry Tool (APT) is software for astronomers and students interested in manually exploring the photometric qualities of astronomical images. It is a graphical user interface (GUI) designed to allow the image data associated with aperture photometry calculations for point and extended sources to be visualized and, therefore, more effectively analyzed. The finely tuned layout of the GUI, along with judicious use of color-coding and alerting, is intended to give maximal user utility and convenience. Simply mouse-clicking on a source in the displayed image will instantly draw a circular or elliptical aperture and sky annulus around the source and will compute the source intensity and its uncertainty, along with several commonly used measures of the local sky background and its variability. The results are displayed and can be optionally saved to an aperture-photometry-table file and plotted on graphs in various ways using functions available in the software. APT is geared toward processing sources in a small number of images and is not suitable for bulk processing a large number of images, unlike other aperture photometry packages (e.g., SExtractor). However, APT does have a convenient source-list tool that enables calculations for a large number of detections in a given image. The source-list tool can be run either in automatic mode to generate an aperture photometry table quickly or in manual mode to permit inspection and adjustment of the calculation for each individual detection. APT displays a variety of useful graphs with just the push of a button, including image histogram, x and y aperture slices, source scatter plot, sky scatter plot, sky histogram, radial profile, curve of growth, and aperture-photometry-table scatter plots and histograms. APT has many functions for customizing the calculations, including outlier rejection, pixel “picking” and “zapping,” and a selection of source and sky models. The radial-profile-interpolation source model, which is accessed via the radial-profile-plot panel, allows recovery of source intensity from pixels with missing data and can be especially beneficial in crowded fields.

The Simple Concurrent Online Processing System (SCOPS) - An open-source interface for remotely sensed data processing

NASA Astrophysics Data System (ADS)

Warren, M. A.; Goult, S.; Clewley, D.

2018-06-01

Advances in technology allow remotely sensed data to be acquired with increasingly higher spatial and spectral resolutions. These data may then be used to influence government decision making and solve a number of research and application driven questions. However, such large volumes of data can be difficult to handle on a single personal computer or on older machines with slower components. Often the software required to process data is varied and can be highly technical and too advanced for the novice user to fully understand. This paper describes an open-source tool, the Simple Concurrent Online Processing System (SCOPS), which forms part of an airborne hyperspectral data processing chain that allows users accessing the tool over a web interface to submit jobs and process data remotely. It is demonstrated using Natural Environment Research Council Airborne Research Facility (NERC-ARF) instruments together with other free- and open-source tools to take radiometrically corrected data from sensor geometry into geocorrected form and to generate simple or complex band ratio products. The final processed data products are acquired via an HTTP download. SCOPS can cut data processing times and introduce complex processing software to novice users by distributing jobs across a network using a simple to use web interface.

NDEx - the Network Data Exchange, A Network Commons for Biologists | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Network models of biology, whether curated or derived from large-scale data analysis, are critical tools in the understanding of cancer mechanisms and in the design and personalization of therapies. The NDEx Project (Network Data Exchange) will create, deploy, and maintain an open-source, web-based software platform and public website to enable scientists, organizations, and software applications to share, store, manipulate, and publish biological networks.

Scaling Agile Infrastructure to People

NASA Astrophysics Data System (ADS)

Jones, B.; McCance, G.; Traylen, S.; Barrientos Arias, N.

2015-12-01

When CERN migrated its infrastructure away from homegrown fabric management tools to emerging industry-standard open-source solutions, the immediate technical challenges and motivation were clear. The move to a multi-site Cloud Computing model meant that the tool chains that were growing around this ecosystem would be a good choice, the challenge was to leverage them. The use of open-source tools brings challenges other than merely how to deploy them. Homegrown software, for all the deficiencies identified at the outset of the project, has the benefit of growing with the organization. This paper will examine what challenges there were in adapting open-source tools to the needs of the organization, particularly in the areas of multi-group development and security. Additionally, the increase in scale of the plant required changes to how Change Management was organized and managed. Continuous Integration techniques are used in order to manage the rate of change across multiple groups, and the tools and workflow for this will be examined.

Collected software engineering papers, volume 8

NASA Technical Reports Server (NTRS)

1990-01-01

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

Technology transfer in software engineering

NASA Technical Reports Server (NTRS)

Bishop, Peter C.

1989-01-01

The University of Houston-Clear Lake is the prime contractor for the AdaNET Research Project under the direction of NASA Johnson Space Center. AdaNET was established to promote the principles of software engineering to the software development industry. AdaNET will contain not only environments and tools, but also concepts, principles, models, standards, guidelines and practices. Initially, AdaNET will serve clients from the U.S. government and private industry who are working in software development. It will seek new clients from those who have not yet adopted the principles and practices of software engineering. Some of the goals of AdaNET are to become known as an objective, authoritative source of new software engineering information and parts, to provide easy access to information and parts, and to keep abreast of innovations in the field.

The SCEC/UseIT Intern Program: Creating Open-Source Visualization Software Using Diverse Resources

NASA Astrophysics Data System (ADS)

Francoeur, H.; Callaghan, S.; Perry, S.; Jordan, T.

2004-12-01

The Southern California Earthquake Center undergraduate IT intern program (SCEC UseIT) conducts IT research to benefit collaborative earth science research. Through this program, interns have developed real-time, interactive, 3D visualization software using open-source tools. Dubbed LA3D, a distribution of this software is now in use by the seismic community. LA3D enables the user to interactively view Southern California datasets and models of importance to earthquake scientists, such as faults, earthquakes, fault blocks, digital elevation models, and seismic hazard maps. LA3D is now being extended to support visualizations anywhere on the planet. The new software, called SCEC-VIDEO (Virtual Interactive Display of Earth Objects), makes use of a modular, plugin-based software architecture which supports easy development and integration of new data sets. Currently SCEC-VIDEO is in beta testing, with a full open-source release slated for the future. Both LA3D and SCEC-VIDEO were developed using a wide variety of software technologies. These, which included relational databases, web services, software management technologies, and 3-D graphics in Java, were necessary to integrate the heterogeneous array of data sources which comprise our software. Currently the interns are working to integrate new technologies and larger data sets to increase software functionality and value. In addition, both LA3D and SCEC-VIDEO allow the user to script and create movies. Thus program interns with computer science backgrounds have been writing software while interns with other interests, such as cinema, geology, and education, have been making movies that have proved of great use in scientific talks, media interviews, and education. Thus, SCEC UseIT incorporates a wide variety of scientific and human resources to create products of value to the scientific and outreach communities. The program plans to continue with its interdisciplinary approach, increasing the relevance of the software and expanding its use in the scientific community.

AOFlagger: RFI Software

NASA Astrophysics Data System (ADS)

Offringa, A. R.

2010-10-01

The RFI software presented here can automatically flag data and can be used to analyze the data in a measurement. The purpose of flagging is to mark samples that are affected by interfering sources such as radio stations, airplanes, electrical fences or other transmitting interferers. The tools in the package are meant for offline use. The software package contains a graphical interface ("rfigui") that can be used to visualize a measurement set and analyze mitigation techniques. It also contains a console flagger ("rficonsole") that can execute a script of mitigation functions without the overhead of a graphical environment. All tools were written in C++. The software has been tested extensively on low radio frequencies (150 MHz or lower) produced by the WSRT and LOFAR telescopes. LOFAR is the Low Frequency Array that is built in and around the Netherlands. Higher frequencies should work as well. Some of the methods implemented are the SumThreshold, the VarThreshold and the singular value decomposition (SVD) method. Included also are several surface fitting algorithms. The software is published under the GNU General Public License version 3.

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses.

PubMed

Bokhart, Mark T; Nazari, Milad; Garrard, Kenneth P; Muddiman, David C

2018-01-01

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

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

PubMed

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

2017-03-22

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

Software Tools for In-Situ Documentation of Built Heritage

NASA Astrophysics Data System (ADS)

Smars, P.

2013-07-01

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

An integrated, open-source set of tools for urban vulnerability monitoring from Earth observation data

NASA Astrophysics Data System (ADS)

De Vecchi, Daniele; Harb, Mostapha; Dell'Acqua, Fabio; Aurelio Galeazzo, Daniel

2015-04-01

Aim: The paper introduces an integrated set of open-source tools designed to process medium and high-resolution imagery with the aim to extract vulnerability indicators [1]. Problem: In the context of risk monitoring [2], a series of vulnerability proxies can be defined, such as the extension of a built-up area or buildings regularity [3]. Different open-source C and Python libraries are already available for image processing and geospatial information (e.g. OrfeoToolbox, OpenCV and GDAL). They include basic processing tools but not vulnerability-oriented workflows. Therefore, it is of significant importance to provide end-users with a set of tools capable to return information at a higher level. Solution: The proposed set of python algorithms is a combination of low-level image processing and geospatial information handling tools along with high-level workflows. In particular, two main products are released under the GPL license: source code, developers-oriented, and a QGIS plugin. These tools were produced within the SENSUM project framework (ended December 2014) where the main focus was on earthquake and landslide risk. Further development and maintenance is guaranteed by the decision to include them in the platform designed within the FP 7 RASOR project . Conclusion: With the lack of a unified software suite for vulnerability indicators extraction, the proposed solution can provide inputs for already available models like the Global Earthquake Model. The inclusion of the proposed set of algorithms within the RASOR platforms can guarantee support and enlarge the community of end-users. Keywords: Vulnerability monitoring, remote sensing, optical imagery, open-source software tools References [1] M. Harb, D. De Vecchi, F. Dell'Acqua, "Remote sensing-based vulnerability proxies in the EU FP7 project SENSUM", Symposium on earthquake and landslide risk in Central Asia and Caucasus: exploiting remote sensing and geo-spatial information management, 29-30th January 2014, Bishkek, Kyrgyz Republic. [2] UNISDR, "Living with Risk", Geneva, Switzerland, 2004. [3] P. Bisch, E. Carvalho, H. Degree, P. Fajfar, M. Fardis, P. Franchin, M. Kreslin, A. Pecker, "Eurocode 8: Seismic Design of Buildings", Lisbon, 2011. (SENSUM: www.sensum-project.eu, grant number: 312972 ) (RASOR: www.rasor-project.eu, grant number: 606888 )

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar.

PubMed

Taylor, Philip D; Brzustowski, John M; Matkovich, Carolyn; Peckford, Michael L; Wilson, Dave

2010-10-26

Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets.

radR: an open-source platform for acquiring and analysing data on biological targets observed by surveillance radar

PubMed Central

2010-01-01

Background Radar has been used for decades to study movement of insects, birds and bats. In spite of this, there are few readily available software tools for the acquisition, storage and processing of such data. Program radR was developed to solve this problem. Results Program radR is an open source software tool for the acquisition, storage and analysis of data from marine radars operating in surveillance mode. radR takes time series data with a two-dimensional spatial component as input from some source (typically a radar digitizing card) and extracts and retains information of biological relevance (i.e. moving targets). Low-level data processing is implemented in "C" code, but user-defined functions written in the "R" statistical programming language can be called at pre-defined steps in the calculations. Output data formats are designed to allow for future inclusion of additional data items without requiring change to C code. Two brands of radar digitizing card are currently supported as data sources. We also provide an overview of the basic considerations of setting up and running a biological radar study. Conclusions Program radR provides a convenient, open source platform for the acquisition and analysis of radar data of biological targets. PMID:20977735

Navigation and Elctro-Optic Sensor Integration Technology for Fusion of Imagery and Digital Mapping Products

DTIC Science & Technology

1999-08-01

Electro - Optic Sensor Integration Technology (NEOSIT) software application. The design is highly modular and based on COTS tools to facilitate integration with sensors, navigation and digital data sources already installed on different host

Mining the Geophysical Research Abstracts Corpus: Mapping the impact of Free and Open Source Software on the EGU Divisions

NASA Astrophysics Data System (ADS)

Löwe, Peter; Klump, Jens; Robertson, Jesse

2015-04-01

Text mining is commonly employed as a tool in data science to investigate and chart emergent information from corpora of research abstracts, such as the Geophysical Research Abstracts (GRA) published by Copernicus. In this context current standards, such as persistent identifiers like DOI and ORCID, allow us to trace, cite and map links between journal publications, the underlying research data and scientific software. This network can be expressed as a directed graph which enables us to chart networks of cooperation and innovation, thematic foci and the locations of research communities in time and space. However, this approach of data science, focusing on the research process in a self-referential manner, rather than the topical work, is still in a developing stage. Scientific work presented at the EGU General Assembly is often the first step towards new approaches and innovative ideas to the geospatial community. It represents a rich, deep and heterogeneous source of geoscientific thought. This corpus is a significant data source for data science, which has not been analysed on this scale previously. In this work, the corpus of the Geophysical Research Abstracts is used for the first time as a data base for analyses of topical text mining. For this, we used a sturdy and customizable software framework, based on the work of Schmitt et al. [1]. For the analysis we used the High Performance Computing infrastructure of the German Research Centre for Geosciences GFZ in Potsdam, Germany. Here, we report on the first results from the analysis of the continuous spreading the of use of Free and Open Source Software Tools (FOSS) within the EGU communities, mapping the general increase of FOSS-themed GRA articles in the last decade and the developing spatial patterns of involved parties and FOSS topics. References: [1] Schmitt, L. M., Christianson, K.T, Gupta R..: Linguistic Computing with UNIX Tools, in Kao, A., Poteet S.R. (Eds.): Natural Language processing and Text Mining, Springer, 2007. doi:10.1007/978-1-84628-754-1_12.

OOSTethys - Open Source Software for the Global Earth Observing Systems of Systems

NASA Astrophysics Data System (ADS)

Bridger, E.; Bermudez, L. E.; Maskey, M.; Rueda, C.; Babin, B. L.; Blair, R.

2009-12-01

An open source software project is much more than just picking the right license, hosting modular code and providing effective documentation. Success in advancing in an open collaborative way requires that the process match the expected code functionality to the developer's personal expertise and organizational needs as well as having an enthusiastic and responsive core lead group. We will present the lessons learned fromOOSTethys , which is a community of software developers and marine scientists who develop open source tools, in multiple languages, to integrate ocean observing systems into an Integrated Ocean Observing System (IOOS). OOSTethys' goal is to dramatically reduce the time it takes to install, adopt and update standards-compliant web services. OOSTethys has developed servers, clients and a registry. Open source PERL, PYTHON, JAVA and ASP tool kits and reference implementations are helping the marine community publish near real-time observation data in interoperable standard formats. In some cases publishing an OpenGeospatial Consortium (OGC), Sensor Observation Service (SOS) from NetCDF files or a database or even CSV text files could take only minutes depending on the skills of the developer. OOSTethys is also developing an OGC standard registry, Catalog Service for Web (CSW). This open source CSW registry was implemented to easily register and discover SOSs using ISO 19139 service metadata. A web interface layer over the CSW registry simplifies the registration process by harvesting metadata describing the observations and sensors from the “GetCapabilities” response of SOS. OPENIOOS is the web client, developed in PERL to visualize the sensors in the SOS services. While the number of OOSTethys software developers is small, currently about 10 around the world, the number of OOSTethys toolkit implementers is larger and growing and the ease of use has played a large role in spreading the use of interoperable standards compliant web services widely in the marine community.

Software Management for the NOνAExperiment

NASA Astrophysics Data System (ADS)

Davies, G. S.; Davies, J. P.; C Group; Rebel, B.; Sachdev, K.; Zirnstein, J.

2015-12-01

The NOvAsoftware (NOνASoft) is written in C++, and built on the Fermilab Computing Division's art framework that uses ROOT analysis software. NOνASoftmakes use of more than 50 external software packages, is developed by more than 50 developers and is used by more than 100 physicists from over 30 universities and laboratories in 3 continents. The software builds are handled by Fermilab's custom version of Software Release Tools (SRT), a UNIX based software management system for large, collaborative projects that is used by several experiments at Fermilab. The system provides software version control with SVN configured in a client-server mode and is based on the code originally developed by the BaBar collaboration. In this paper, we present efforts towards distributing the NOvA software via the CernVM File System distributed file system. We will also describe our recent work to use a CMake build system and Jenkins, the open source continuous integration system, for NOνASoft.

C++ software quality in the ATLAS experiment: tools and experience

NASA Astrophysics Data System (ADS)

Martin-Haugh, S.; Kluth, S.; Seuster, R.; Snyder, S.; Obreshkov, E.; Roe, S.; Sherwood, P.; Stewart, G. A.

2017-10-01

In this paper we explain how the C++ code quality is managed in ATLAS using a range of tools from compile-time through to run time testing and reflect on the substantial progress made in the last two years largely through the use of static analysis tools such as Coverity®, an industry-standard tool which enables quality comparison with general open source C++ code. Other available code analysis tools are also discussed, as is the role of unit testing with an example of how the GoogleTest framework can be applied to our codebase.

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

Verification Tools Secure Online Shopping, Banking

NASA Technical Reports Server (NTRS)

2010-01-01

Just like rover or rocket technology sent into space, the software that controls these technologies must be extensively tested to ensure reliability and effectiveness. Ames Research Center invented the open-source Java Pathfinder (JPF) toolset for the deep testing of Java-based programs. Fujitsu Labs of America Inc., based in Sunnyvale, California, improved the capabilities of the JPF Symbolic Pathfinder tool, establishing the tool as a means of thoroughly testing the functionality and security of Web-based Java applications such as those used for Internet shopping and banking.

FDTD simulation tools for UWB antenna analysis.

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

Brocato, Robert Wesley

2004-12-01

This paper describes the development of a set of software tools useful for analyzing ultra-wideband (UWB) antennas and structures. These tools are used to perform finite difference time domain (FDTD) simulation of a conical antenna with continuous wave (CW) and UWB pulsed excitations. The antenna is analyzed using spherical coordinate-based FDTD equations that are derived from first principles. The simulation results for CW excitation are compared to simulation and measured results from published sources; the results for UWB excitation are new.

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

PubMed

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

2018-02-01

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

SESAME: a software tool for the numerical dosimetric reconstruction of radiological accidents involving external sources and its application to the accident in Chile in December 2005.

PubMed

Huet, C; Lemosquet, A; Clairand, I; Rioual, J B; Franck, D; de Carlan, L; Aubineau-Lanièce, I; Bottollier-Depois, J F

2009-01-01

Estimating the dose distribution in a victim's body is a relevant indicator in assessing biological damage from exposure in the event of a radiological accident caused by an external source. This dose distribution can be assessed by physical dosimetric reconstruction methods. Physical dosimetric reconstruction can be achieved using experimental or numerical techniques. This article presents the laboratory-developed SESAME--Simulation of External Source Accident with MEdical images--tool specific to dosimetric reconstruction of radiological accidents through numerical simulations which combine voxel geometry and the radiation-material interaction MCNP(X) Monte Carlo computer code. The experimental validation of the tool using a photon field and its application to a radiological accident in Chile in December 2005 are also described.

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

PubMed

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

2006-10-01

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

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

Chamana, Manohar; Prabakar, Kumaraguru; Palmintier, Bryan

A software process is developed to convert distribution network models from a quasi-static time-series tool (OpenDSS) to a real-time dynamic phasor simulator (ePHASORSIM). The description of this process in this paper would be helpful for researchers who intend to perform similar conversions. The converter could be utilized directly by users of real-time simulators who intend to perform software-in-the-loop or hardware-in-the-loop tests on large distribution test feeders for a range of use cases, including testing functions of advanced distribution management systems against a simulated distribution system. In the future, the developers intend to release the conversion tool as open source tomore » enable use by others.« less

Quantitative fluorescence angiography for neurosurgical interventions.

PubMed

Weichelt, Claudia; Duscha, Philipp; Steinmeier, Ralf; Meyer, Tobias; Kuß, Julia; Cimalla, Peter; Kirsch, Matthias; Sobottka, Stephan B; Koch, Edmund; Schackert, Gabriele; Morgenstern, Ute

2013-06-01

Present methods for quantitative measurement of cerebral perfusion during neurosurgical operations require additional technology for measurement, data acquisition, and processing. This study used conventional fluorescence video angiography--as an established method to visualize blood flow in brain vessels--enhanced by a quantifying perfusion software tool. For these purposes, the fluorescence dye indocyanine green is given intravenously, and after activation by a near-infrared light source the fluorescence signal is recorded. Video data are analyzed by software algorithms to allow quantification of the blood flow. Additionally, perfusion is measured intraoperatively by a reference system. Furthermore, comparing reference measurements using a flow phantom were performed to verify the quantitative blood flow results of the software and to validate the software algorithm. Analysis of intraoperative video data provides characteristic biological parameters. These parameters were implemented in the special flow phantom for experimental validation of the developed software algorithms. Furthermore, various factors that influence the determination of perfusion parameters were analyzed by means of mathematical simulation. Comparing patient measurement, phantom experiment, and computer simulation under certain conditions (variable frame rate, vessel diameter, etc.), the results of the software algorithms are within the range of parameter accuracy of the reference methods. Therefore, the software algorithm for calculating cortical perfusion parameters from video data presents a helpful intraoperative tool without complex additional measurement technology.

Air Data Report Improves Flight Safety

NASA Technical Reports Server (NTRS)

2007-01-01

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

Open source software in a practical approach for post processing of radiologic images.

PubMed

Valeri, Gianluca; Mazza, Francesco Antonino; Maggi, Stefania; Aramini, Daniele; La Riccia, Luigi; Mazzoni, Giovanni; Giovagnoni, Andrea

2015-03-01

The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images. We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points. Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10. OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

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

PubMed

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

2016-09-02

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

NREL's Water Power Software Makes a Splash; NREL Highlights, Research & Development, NREL (National Renewable Energy Laboratory)

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

None

2015-06-01

WEC-Sim is a DOE-funded software tool being jointly developed by NREL and SNL. WEC-Sim computationally models wave energy converters (WEC), devices that generate electricity using movement of water systems such as oceans, rivers, etc. There is great potential for WECs to generate electricity, but as of yet, the industry has yet to establish a commercially viable concept. Modeling, design, and simulations tools are essential to the successful development of WECs. Commercial WEC modeling software tools can't be modified by the user. In contrast, WEC-Sim is a free, open-source, and flexible enough to be modified to meet the rapidly evolving needsmore » of the WEC industry. By modeling the power generation performance and dynamic loads of WEC designs, WEC-Sim can help support the development of new WEC devices by optimizing designs for cost of energy and competitiveness. By being easily accessible, WEC-Sim promises to help level the playing field in the WEC industry. Importantly, WEC-Sim is also excellent at its job! In 2014, WEC-Sim was used in conjunction with NREL’s FAST modeling software to win a hydrodynamic modeling competition. WEC-Sim and FAST performed very well at predicting the motion of a test device in comparison to other modeling tools. The most recent version of WEC-Sim (v1.1) was released in April 2015.« less

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

Boiler: lossy compression of RNA-seq alignments using coverage vectors.

PubMed

Pritt, Jacob; Langmead, Ben

2016-09-19

We describe Boiler, a new software tool for compressing and querying large collections of RNA-seq alignments. Boiler discards most per-read data, keeping only a genomic coverage vector plus a few empirical distributions summarizing the alignments. Since most per-read data is discarded, storage footprint is often much smaller than that achieved by other compression tools. Despite this, the most relevant per-read data can be recovered; we show that Boiler compression has only a slight negative impact on results given by downstream tools for isoform assembly and quantification. Boiler also allows the user to pose fast and useful queries without decompressing the entire file. Boiler is free open source software available from github.com/jpritt/boiler. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

PubMed

Pegg, Elise C; Gill, Harinderjit S

2016-09-06

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

Methods, Knowledge Support, and Experimental Tools for Modeling

DTIC Science & Technology

2006-10-01

open source software entities: the PostgreSQL relational database management system (http://www.postgres.org), the Apache web server (http...past. The revision control system allows the program to capture disagreements, and allows users to explore the history of such disagreements by

OpenMebius: an open source software for isotopically nonstationary 13C-based metabolic flux analysis.

PubMed

Kajihata, Shuichi; Furusawa, Chikara; Matsuda, Fumio; Shimizu, Hiroshi

2014-01-01

The in vivo measurement of metabolic flux by (13)C-based metabolic flux analysis ((13)C-MFA) provides valuable information regarding cell physiology. Bioinformatics tools have been developed to estimate metabolic flux distributions from the results of tracer isotopic labeling experiments using a (13)C-labeled carbon source. Metabolic flux is determined by nonlinear fitting of a metabolic model to the isotopic labeling enrichment of intracellular metabolites measured by mass spectrometry. Whereas (13)C-MFA is conventionally performed under isotopically constant conditions, isotopically nonstationary (13)C metabolic flux analysis (INST-(13)C-MFA) has recently been developed for flux analysis of cells with photosynthetic activity and cells at a quasi-steady metabolic state (e.g., primary cells or microorganisms under stationary phase). Here, the development of a novel open source software for INST-(13)C-MFA on the Windows platform is reported. OpenMebius (Open source software for Metabolic flux analysis) provides the function of autogenerating metabolic models for simulating isotopic labeling enrichment from a user-defined configuration worksheet. Analysis using simulated data demonstrated the applicability of OpenMebius for INST-(13)C-MFA. Confidence intervals determined by INST-(13)C-MFA were less than those determined by conventional methods, indicating the potential of INST-(13)C-MFA for precise metabolic flux analysis. OpenMebius is the open source software for the general application of INST-(13)C-MFA.

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.

Voxel Datacubes for 3D Visualization in Blender

NASA Astrophysics Data System (ADS)

Gárate, Matías

2017-05-01

The growth of computational astrophysics and the complexity of multi-dimensional data sets evidences the need for new versatile visualization tools for both the analysis and presentation of the data. In this work, we show how to use the open-source software Blender as a three-dimensional (3D) visualization tool to study and visualize numerical simulation results, focusing on astrophysical hydrodynamic experiments. With a datacube as input, the software can generate a volume rendering of the 3D data, show the evolution of a simulation in time, and do a fly-around camera animation to highlight the points of interest. We explain the process to import simulation outputs into Blender using the voxel data format, and how to set up a visualization scene in the software interface. This method allows scientists to perform a complementary visual analysis of their data and display their results in an appealing way, both for outreach and science presentations.

Thoth: Software for data visualization & statistics

NASA Astrophysics Data System (ADS)

Laher, R. R.

2016-10-01

Thoth is a standalone software application with a graphical user interface for making it easy to query, display, visualize, and analyze tabular data stored in relational databases and data files. From imported data tables, it can create pie charts, bar charts, scatter plots, and many other kinds of data graphs with simple menus and mouse clicks (no programming required), by leveraging the open-source JFreeChart library. It also computes useful table-column data statistics. A mature tool, having underwent development and testing over several years, it is written in the Java computer language, and hence can be run on any computing platform that has a Java Virtual Machine and graphical-display capability. It can be downloaded and used by anyone free of charge, and has general applicability in science, engineering, medical, business, and other fields. Special tools and features for common tasks in astronomy and astrophysical research are included in the software.

PD5: a general purpose library for primer design software.

PubMed

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

2013-01-01

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

Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose volume outcome relationships

NASA Astrophysics Data System (ADS)

El Naqa, I.; Suneja, G.; Lindsay, P. E.; Hope, A. J.; Alaly, J. R.; Vicic, M.; Bradley, J. D.; Apte, A.; Deasy, J. O.

2006-11-01

Radiotherapy treatment outcome models are a complicated function of treatment, clinical and biological factors. Our objective is to provide clinicians and scientists with an accurate, flexible and user-friendly software tool to explore radiotherapy outcomes data and build statistical tumour control or normal tissue complications models. The software tool, called the dose response explorer system (DREES), is based on Matlab, and uses a named-field structure array data type. DREES/Matlab in combination with another open-source tool (CERR) provides an environment for analysing treatment outcomes. DREES provides many radiotherapy outcome modelling features, including (1) fitting of analytical normal tissue complication probability (NTCP) and tumour control probability (TCP) models, (2) combined modelling of multiple dose-volume variables (e.g., mean dose, max dose, etc) and clinical factors (age, gender, stage, etc) using multi-term regression modelling, (3) manual or automated selection of logistic or actuarial model variables using bootstrap statistical resampling, (4) estimation of uncertainty in model parameters, (5) performance assessment of univariate and multivariate analyses using Spearman's rank correlation and chi-square statistics, boxplots, nomograms, Kaplan-Meier survival plots, and receiver operating characteristics curves, and (6) graphical capabilities to visualize NTCP or TCP prediction versus selected variable models using various plots. DREES provides clinical researchers with a tool customized for radiotherapy outcome modelling. DREES is freely distributed. We expect to continue developing DREES based on user feedback.

SIMA: Python software for analysis of dynamic fluorescence imaging data.

PubMed

Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

2014-01-01

Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

Performance of Compiler-Assisted Memory Safety Checking

DTIC Science & Technology

2014-08-01

software developer has in mind a particular object to which the pointer should point, the intended referent. A memory access error occurs when an ac...Performance of Compiler-Assisted Memory Safety Checking David Keaton Robert C. Seacord August 2014 TECHNICAL NOTE CMU/SEI-2014-TN...based memory safety checking tool and the performance that can be achieved with two such tools whose source code is freely available. The note then

A Problem-Solving Environment for Biological Network Informatics: Bio-Spice

DTIC Science & Technology

2007-06-01

user an environment to access software tools. The Dashboard is built upon the NetBeans Integrated Development Environment (IDE), an open source Java...based integration platform was demonstrated. During the subsequent six month development cycle, the first version of the NetBeans based Bio-SPICE...frameworks (OAA, NetBeans , and Systems Biology Workbench (SBW)[15]), it becomes possible for Bio-SPICE tools to truly interoperate. This interoperation

MicMac GIS application: free open source

NASA Astrophysics Data System (ADS)

Duarte, L.; Moutinho, O.; Teodoro, A.

2016-10-01

The use of Remotely Piloted Aerial System (RPAS) for remote sensing applications is becoming more frequent as the technologies on on-board cameras and the platform itself are becoming a serious contender to satellite and airplane imagery. MicMac is a photogrammetric tool for image matching that can be used in different contexts. It is an open source software and it can be used as a command line or with a graphic interface (for each command). The main objective of this work was the integration of MicMac with QGIS, which is also an open source software, in order to create a new open source tool applied to photogrammetry/remote sensing. Python language was used to develop the application. This tool would be very useful in the manipulation and 3D modelling of a set of images. The main objective was to create a toolbar in QGIS with the basic functionalities with intuitive graphic interfaces. The toolbar is composed by three buttons: produce the points cloud, create the Digital Elevation Model (DEM) and produce the orthophoto of the study area. The application was tested considering 35 photos, a subset of images acquired by a RPAS in the Aguda beach area, Porto, Portugal. They were used in order to create a 3D terrain model and from this model obtain an orthophoto and the corresponding DEM. The code is open and can be modified according to the user requirements. This integration would be very useful in photogrammetry and remote sensing community combined with GIS capabilities.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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.

WE-D-204-06: An Open Source ImageJ CatPhan Analysis Tool

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

Nelson, G

2015-06-15

Purpose: The CatPhan is a popular QA device for assessing CT image quality. There are a number of software options which perform analysis of the CatPhan. However, there is often little ability for the user to adjust the analysis if it isn’t running properly, and these are all expensive options. An open source tool is an effective solution. Methods: To use the software, the user imports the CT as an image sequence in ImageJ. The user then scrolls to the slice with the lateral dots. The user then runs the plugin. If tolerance constraints are not already created, the usermore » is prompted to enter them or to use generic tolerances. Upon completion of the analysis, the plugin calls pdfLaTex to compile the pdf report. There is a csv version of the report as well. A log of the results from all CatPhan scans is kept as a csv file. The user can use this to baseline the machine. Results: The tool is capable of detecting the orientation of the phantom. If the CatPhan was scanned backwards, one can simply flip the stack of images horizontally and proceed with the analysis. The analysis includes Sensitometry (estimating the effective beam energy), HU values and linearity, Low Contrast Visibility (using LDPE & Polystyrene), Contrast Scale, Geometric Accuracy, Slice Thickness Accuracy, Spatial resolution (giving the MTF using the line pairs as well as the point spread function), CNR, Low Contrast Detectability (including the raw data), Uniformity (including the Cupping Effect). Conclusion: This is a robust tool that analyzes more components of the CatPhan than other software options (with the exception of ImageOwl). It produces an elegant pdf and keeps a log of analyses for long-term tracking of the system. Because it is open source, users are able to customize any component of it.« less

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

PubMed

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

2015-06-16

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

Development of a software package for solid-angle calculations using the Monte Carlo method

NASA Astrophysics Data System (ADS)

Zhang, Jie; Chen, Xiulian; Zhang, Changsheng; Li, Gang; Xu, Jiayun; Sun, Guangai

2014-02-01

Solid-angle calculations play an important role in the absolute calibration of radioactivity measurement systems and in the determination of the activity of radioactive sources, which are often complicated. In the present paper, a software package is developed to provide a convenient tool for solid-angle calculations in nuclear physics. The proposed software calculates solid angles using the Monte Carlo method, in which a new type of variance reduction technique was integrated. The package, developed under the environment of Microsoft Foundation Classes (MFC) in Microsoft Visual C++, has a graphical user interface, in which, the visualization function is integrated in conjunction with OpenGL. One advantage of the proposed software package is that it can calculate the solid angle subtended by a detector with different geometric shapes (e.g., cylinder, square prism, regular triangular prism or regular hexagonal prism) to a point, circular or cylindrical source without any difficulty. The results obtained from the proposed software package were compared with those obtained from previous studies and calculated using Geant4. It shows that the proposed software package can produce accurate solid-angle values with a greater computation speed than Geant4.

Continuous integration and quality control for scientific software

NASA Astrophysics Data System (ADS)

Neidhardt, A.; Ettl, M.; Brisken, W.; Dassing, R.

2013-08-01

Modern software has to be stable, portable, fast and reliable. This is going to be also more and more important for scientific software. But this requires a sophisticated way to inspect, check and evaluate the quality of source code with a suitable, automated infrastructure. A centralized server with a software repository and a version control system is one essential part, to manage the code basis and to control the different development versions. While each project can be compiled separately, the whole code basis can also be compiled with one central “Makefile”. This is used to create automated, nightly builds. Additionally all sources are inspected automatically with static code analysis and inspection tools, which check well-none error situations, memory and resource leaks, performance issues, or style issues. In combination with an automatic documentation generator it is possible to create the developer documentation directly from the code and the inline comments. All reports and generated information are presented as HTML page on a Web server. Because this environment increased the stability and quality of the software of the Geodetic Observatory Wettzell tremendously, it is now also available for scientific communities. One regular customer is already the developer group of the DiFX software correlator project.

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.

AWIPS II in the University Community: Unidata's efforts and capabilities of the software

NASA Astrophysics Data System (ADS)

Ramamurthy, Mohan; James, Michael

2015-04-01

The Advanced Weather Interactive Processing System, version II (AWIPS II) is a weather forecasting, display and analysis tool that is used by the National Oceanic and Atmospheric Administration/National Weather Service (NOAA/NWS) and the National Centers for Environmental Prediction (NCEP) to ingest analyze and disseminate operational weather data. The AWIPS II software is built on a Service Oriented Architecture, takes advantage of open source software, and its design affords expandability, flexibility, and portability. Since many university meteorology programs are eager to use the same tools used by NWS forecasters, Unidata community interest in AWIPS II is high. The Unidata Program Center (UPC) has worked closely with NCEP staff during AWIPS II development in order to devise a way to make it available to the university. The Unidata AWIPS II software was released in beta form in 2014, and it incorporates a number of key changes to the baseline U. S. National Weather Service release to process and display additional data formats and run all components in a single-server standalone configuration. In addition to making available open-source instances of the software libraries that can be downloaded and run at any university, Unidata has also deployed the data-server side of AWIPS II, known as EDEX, in the Amazon Web Service and Microsoft Azure cloud environments. In this set up, universities receive all of the data from remote cloud instances, while they only have to run the AWIPS II client, known as CAVE, to analyze and visualize the data. In this presentation, we will describe Unidata's AWIPS II efforts, including the capabilities of the software in visualizing many different types of real-time meteorological data and its myriad uses in university and other settings.

The Chandra Source Catalog 2.0: Building The Catalog

NASA Astrophysics Data System (ADS)

Grier, John D.; Plummer, David A.; Allen, Christopher E.; Anderson, Craig S.; Budynkiewicz, Jamie A.; Burke, Douglas; Chen, Judy C.; Civano, Francesca Maria; D'Abrusco, Raffaele; Doe, Stephen M.; Evans, Ian N.; Evans, Janet D.; Fabbiano, Giuseppina; Gibbs, Danny G., II; Glotfelty, Kenny J.; Graessle, Dale E.; Hain, Roger; Hall, Diane M.; Harbo, Peter N.; Houck, John C.; Lauer, Jennifer L.; Laurino, Omar; Lee, Nicholas P.; Martínez-Galarza, Juan Rafael; McCollough, Michael L.; McDowell, Jonathan C.; Miller, Joseph; McLaughlin, Warren; Morgan, Douglas L.; Mossman, Amy E.; Nguyen, Dan T.; Nichols, Joy S.; Nowak, Michael A.; Paxson, Charles; Primini, Francis Anthony; Rots, Arnold H.; Siemiginowska, Aneta; Sundheim, Beth A.; Tibbetts, Michael; Van Stone, David W.; Zografou, Panagoula

2018-01-01

To build release 2.0 of the Chandra Source Catalog (CSC2), we require scientific software tools and processing pipelines to evaluate and analyze the data. Additionally, software and hardware infrastructure is needed to coordinate and distribute pipeline execution, manage data i/o, and handle data for Quality Assurance (QA) intervention. We also provide data product staging for archive ingestion.Release 2 utilizes a database driven system used for integration and production. Included are four distinct instances of the Automatic Processing (AP) system (Source Detection, Master Match, Source Properties and Convex Hulls) and a high performance computing (HPC) cluster that is managed to provide efficient catalog processing. In this poster we highlight the internal systems developed to meet the CSC2 challenge.This work has been supported by NASA under contract NAS 8-03060 to the Smithsonian Astrophysical Observatory for operation of the Chandra X-ray Center.

Open Source Clinical NLP - More than Any Single System.

PubMed

Masanz, James; Pakhomov, Serguei V; Xu, Hua; Wu, Stephen T; Chute, Christopher G; Liu, Hongfang

2014-01-01

The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP's mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice.

The BiSciCol Triplifier: bringing biodiversity data to the Semantic Web.

PubMed

Stucky, Brian J; Deck, John; Conlin, Tom; Ziemba, Lukasz; Cellinese, Nico; Guralnick, Robert

2014-07-29

Recent years have brought great progress in efforts to digitize the world's biodiversity data, but integrating data from many different providers, and across research domains, remains challenging. Semantic Web technologies have been widely recognized by biodiversity scientists for their potential to help solve this problem, yet these technologies have so far seen little use for biodiversity data. Such slow uptake has been due, in part, to the relative complexity of Semantic Web technologies along with a lack of domain-specific software tools to help non-experts publish their data to the Semantic Web. The BiSciCol Triplifier is new software that greatly simplifies the process of converting biodiversity data in standard, tabular formats, such as Darwin Core-Archives, into Semantic Web-ready Resource Description Framework (RDF) representations. The Triplifier uses a vocabulary based on the popular Darwin Core standard, includes both Web-based and command-line interfaces, and is fully open-source software. Unlike most other RDF conversion tools, the Triplifier does not require detailed familiarity with core Semantic Web technologies, and it is tailored to a widely popular biodiversity data format and vocabulary standard. As a result, the Triplifier can often fully automate the conversion of biodiversity data to RDF, thereby making the Semantic Web much more accessible to biodiversity scientists who might otherwise have relatively little knowledge of Semantic Web technologies. Easy availability of biodiversity data as RDF will allow researchers to combine data from disparate sources and analyze them with powerful linked data querying tools. However, before software like the Triplifier, and Semantic Web technologies in general, can reach their full potential for biodiversity science, the biodiversity informatics community must address several critical challenges, such as the widespread failure to use robust, globally unique identifiers for biodiversity data.

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.

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.

MS Data Miner: a web-based software tool to analyze, compare, and share mass spectrometry protein identifications.

PubMed

Dyrlund, Thomas F; Poulsen, Ebbe T; Scavenius, Carsten; Sanggaard, Kristian W; Enghild, Jan J

2012-09-01

Data processing and analysis of proteomics data are challenging and time consuming. In this paper, we present MS Data Miner (MDM) (http://sourceforge.net/p/msdataminer), a freely available web-based software solution aimed at minimizing the time required for the analysis, validation, data comparison, and presentation of data files generated in MS software, including Mascot (Matrix Science), Mascot Distiller (Matrix Science), and ProteinPilot (AB Sciex). The program was developed to significantly decrease the time required to process large proteomic data sets for publication. This open sourced system includes a spectra validation system and an automatic screenshot generation tool for Mascot-assigned spectra. In addition, a Gene Ontology term analysis function and a tool for generating comparative Excel data reports are included. We illustrate the benefits of MDM during a proteomics study comprised of more than 200 LC-MS/MS analyses recorded on an AB Sciex TripleTOF 5600, identifying more than 3000 unique proteins and 3.5 million peptides. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Integrating data from the Investigational Medicinal Product Dossier/investigator's brochure. A new tool for translational integration of preclinical effects.

PubMed

van Gerven, Joop; Cohen, Adam

2018-01-30

The first administration of a new compound in humans is an important milestone. A major source of information for the researcher is the investigator's brochure (IB). Such a document, has a size of several hundred pages. The IB should enable investigators or regulators to independently assess the risk-benefit of the proposed trial but the size and complexity makes this difficult. This article offers a practical tool for the integration and subsequent communication of the complex information from the IB or other relevant data sources. This paper is accompanied by an accessible software tool to construct a single page colour-coded overview of preclinical and clinical data. © 2018 The British Pharmacological Society.

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.

75 FR 35457 - Draft of the 2010 Causal Analysis/Diagnosis Decision Information System (CADDIS)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-22

... Causal Analysis/Diagnosis Decision Information System (CADDIS) AGENCY: Environmental Protection Agency... site, ``2010 release of the Causal Analysis/Diagnosis Decision Information System (CADDIS).'' The... analyses, downloadable software tools, and links to outside information sources. II. How to Submit Comments...

PYTHON for Variable Star Astronomy (Abstract)

NASA Astrophysics Data System (ADS)

Craig, M.

2018-06-01

(Abstract only) Open source PYTHON packages that are useful for data reduction, photometry, and other tasks relevant to variable star astronomy have been developed over the last three to four years as part of the Astropy project. Using this software, it is relatively straightforward to reduce images, automatically detect sources, and match them to catalogs. Over the last year browser-based tools for performing some of those tasks have been developed that minimize or eliminate the need to write any of your own code. After providing an overview of the current state of the software, an application that calculates transformation coefficients on a frame-by-frame basis by matching stars in an image to the APASS catalog will be described.

PYCHEM: a multivariate analysis package for python.

PubMed

Jarvis, Roger M; Broadhurst, David; Johnson, Helen; O'Boyle, Noel M; Goodacre, Royston

2006-10-15

We have implemented a multivariate statistical analysis toolbox, with an optional standalone graphical user interface (GUI), using the Python scripting language. This is a free and open source project that addresses the need for a multivariate analysis toolbox in Python. Although the functionality provided does not cover the full range of multivariate tools that are available, it has a broad complement of methods that are widely used in the biological sciences. In contrast to tools like MATLAB, PyChem 2.0.0 is easily accessible and free, allows for rapid extension using a range of Python modules and is part of the growing amount of complementary and interoperable scientific software in Python based upon SciPy. One of the attractions of PyChem is that it is an open source project and so there is an opportunity, through collaboration, to increase the scope of the software and to continually evolve a user-friendly platform that has applicability across a wide range of analytical and post-genomic disciplines. http://sourceforge.net/projects/pychem

AstroBlend: An astrophysical visualization package for Blender

NASA Astrophysics Data System (ADS)

Naiman, J. P.

2016-04-01

The rapid growth in scale and complexity of both computational and observational astrophysics over the past decade necessitates efficient and intuitive methods for examining and visualizing large datasets. Here, I present AstroBlend, an open-source Python library for use within the three dimensional modeling software, Blender. While Blender has been a popular open-source software among animators and visual effects artists, in recent years it has also become a tool for visualizing astrophysical datasets. AstroBlend combines the three dimensional capabilities of Blender with the analysis tools of the widely used astrophysical toolset, yt, to afford both computational and observational astrophysicists the ability to simultaneously analyze their data and create informative and appealing visualizations. The introduction of this package includes a description of features, work flow, and various example visualizations. A website - www.astroblend.com - has been developed which includes tutorials, and a gallery of example images and movies, along with links to downloadable data, three dimensional artistic models, and various other resources.

Electronic Engineering Notebook: A software environment for research execution, documentation and dissemination

NASA Technical Reports Server (NTRS)

Moerder, Dan

1994-01-01

The electronic engineering notebook (EEN) consists of a free form research notebook, implemented in a commercial package for distributed hypermedia, which includes utilities for graphics capture, formatting and display of LaTex constructs, and interfaces to the host operating system. The latter capability consists of an information computer-aided software engineering (CASE) tool and a means to associate executable scripts with source objects. The EEN runs on Sun and HP workstations. The EEN, in day-to-day use can be used in much the same manner as the sort of research notes most researchers keep during development of projects. Graphics can be pasted in, equations can be entered via LaTex, etc. In addition, the fact that the EEN is hypermedia permits easy management of 'context', e.g., derivations and data can contain easily formed links to other supporting derivations and data. The CASE tool also permits development and maintenance of source code directly in the notebook, with access to its derivations and data.

Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools.

PubMed

Dutta, Priyanka; Lehmann, Christina; Odedra, Devang; Singh, Deepika; Pohl, Christian

2015-12-16

Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.

Globes from global data: Charting international research networks with the GRASS GIS r.out.polycones add-on module.

NASA Astrophysics Data System (ADS)

Löwe, Peter

2015-04-01

Many Free and Open Source Software (FOSS) tools have been created for the various application fields within geoscience. While FOSS allows re-implementation of functionalities in new environments by access to the original codebase, the easiest approach to build new software solutions for new problems is the combination or merging of existing software tools. Such mash-ups are implemented by embedding and encapsulating FOSS tools within each another, effectively focusing the use of the embedded software to the specific role it needs to perform in the given scenario, while ignoring all its other capabilities. GRASS GIS is a powerful and established FOSS GIS for raster, vector and volume data processing while the Generic Mapping Tools (GMT) are a suite of powerful Open Source mapping tools, which exceed the mapping capabilities of GRASS GIS. This poster reports on the new GRASS GIS add-on module r.out.polycones. It enables users to utilize non-continuous projections for map production within the GRASS production environment. This is implemented on the software level by encapsulating a subset of GMT mapping capabilities into a GRASS GIS (Version 6.x) add-on module. The module was developed at the German National Library of Science and Technology (TIB) to provide custom global maps of scientific collaboration networks, such as the DataCite consortium, the registration agency for Digital Object Identifiers (DOI) for research data. The GRASS GIS add-on module can be used for global mapping of raster data into a variety of non continuous sinosoidal projections, allowing the creation of printable biangles (gores) to be used for globe making. Due to the well structured modular nature of GRASS modules, technical follow-up work will focus on API-level Python-based integration in GRASS 7 [1]. Based on this, GMT based mapping capabilities in GRASS will be extended beyond non-continuous sinosoidal maps and advanced from raster-layers to content GRASS display monitors. References: [1] Petras, V., Petrasova, A., Chemin, Y., Zambelli, P., Landa, M., Gebbert, S., Neteler, N., Löwe, P.: Analyzing rasters, vectors and time series using new Python interfaces in GRASS GIS 7, Geophysical Research Abstracts Vol. 17, EGU2015-8142, 2015 (in preparation)

UNESCO's HOPE Initiative—Providing Free and Open-Source Hydrologic Software for Effective and Sustainable Management of Africa's Water Resources Temporary Title

NASA Astrophysics Data System (ADS)

Barlow, P. M.; Filali-Meknassi, Y.; Sanford, W. E.; Winston, R. B.; Kuniansky, E.; Dawson, C.

2015-12-01

UNESCO's HOPE Initiative—the Hydro Free and (or) Open-source Platform of Experts—was launched in June 2013 as part of UNESCO's International Hydrological Programme. The Initiative arose in response to a recognized need to make free and (or) open-source water-resources software more widely accessible to Africa's water sector. A kit of software is being developed to provide African water authorities, teachers, university lecturers, and researchers with a set of programs that can be enhanced and (or) applied to the development of efficient and sustainable management strategies for Africa's water resources. The Initiative brings together experts from the many fields of water resources to identify software that might be included in the kit, to oversee an objective process for selecting software for the kit, and to engage in training and other modes of capacity building to enhance dissemination of the software. To date, teams of experts from the fields of wastewater treatment, groundwater hydrology, surface-water hydrology, and data management have been formed to identify relevant software from their respective fields. An initial version of the HOPE Software Kit was released in late August 2014 and consists of the STOAT model for wastewater treatment developed by the Water Research Center (United Kingdom) and the MODFLOW-2005 model for groundwater-flow simulation developed by the U.S. Geological Survey. The Kit is available on the UNESCO HOPE website (http://www.hope-initiative.net/).Training in the theory and use of MODFLOW-2005 is planned in southern Africa in conjunction with UNESCO's study of the Kalahari-Karoo/Stampriet Transboundary Aquifer, which extends over an area that includes parts of Botswana, Namibia, and South Africa, and in support of the European Commission's Horizon 2020 FREEWAT project (FREE and open source software tools for WATer resource management; see the UNESCO HOPE website).

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.

DATA-MEAns: an open source tool for the classification and management of neural ensemble recordings.

PubMed

Bonomini, María P; Ferrandez, José M; Bolea, Jose Angel; Fernandez, Eduardo

2005-10-30

The number of laboratories using techniques that allow to acquire simultaneous recordings of as many units as possible is considerably increasing. However, the development of tools used to analyse this multi-neuronal activity is generally lagging behind the development of the tools used to acquire these data. Moreover, the data exchange between research groups using different multielectrode acquisition systems is hindered by commercial constraints such as exclusive file structures, high priced licenses and hard policies on intellectual rights. This paper presents a free open-source software for the classification and management of neural ensemble data. The main goal is to provide a graphical user interface that links the experimental data to a basic set of routines for analysis, visualization and classification in a consistent framework. To facilitate the adaptation and extension as well as the addition of new routines, tools and algorithms for data analysis, the source code and documentation are freely available.

MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses

NASA Astrophysics Data System (ADS)

Bokhart, Mark T.; Nazari, Milad; Garrard, Kenneth P.; Muddiman, David C.

2018-01-01

A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. [Figure not available: see fulltext.

ELAS: A powerful, general purpose image processing package

NASA Technical Reports Server (NTRS)

Walters, David; Rickman, Douglas

1991-01-01

ELAS is a software package which has been utilized as an image processing tool for more than a decade. It has been the source of several commercial packages. Now available on UNIX workstations it is a very powerful, flexible set of software. Applications at Stennis Space Center have included a very wide range of areas including medicine, forestry, geology, ecological modeling, and sonar imagery. It remains one of the most powerful image processing packages available, either commercially or in the public domain.

Optics simulations: a Python workshop

NASA Astrophysics Data System (ADS)

Ghalila, H.; Ammar, A.; Varadharajan, S.; Majdi, Y.; Zghal, M.; Lahmar, S.; Lakshminarayanan, V.

2017-08-01

Numerical simulations allow teachers and students to indirectly perform sophisticated experiments that cannot be realizable otherwise due to cost and other constraints. During the past few decades there has been an explosion in the development of numerical tools concurrently with open source environments such as Python software. This availability of open source software offers an incredible opportunity for advancing teaching methodologies as well as in research. More specifically it is possible to correlate theoretical knowledge with experimental measurements using "virtual" experiments. We have been working on the development of numerical simulation tools using the Python program package and we have concentrated on geometric and physical optics simulations. The advantage of doing hands-on numerical experiments is that it allows the student learner to be an active participant in the pedagogical/learning process rather than playing a passive role as in the traditional lecture format. Even in laboratory classes because of constraints of space, lack of equipment and often-large numbers of students, many students play a passive role since they work in groups of 3 or more students. Furthermore these new tools help students get a handle on numerical methods as well simulations and impart a "feel" for the physics under investigation.

Tracing catchment fine sediment sources using the new SIFT (SedIment Fingerprinting Tool) open source software.

PubMed

Pulley, S; Collins, A L

2018-09-01

The mitigation of diffuse sediment pollution requires reliable provenance information so that measures can be targeted. Sediment source fingerprinting represents one approach for supporting these needs, but recent methodological developments have resulted in an increasing complexity of data processing methods rendering the approach less accessible to non-specialists. A comprehensive new software programme (SIFT; SedIment Fingerprinting Tool) has therefore been developed which guides the user through critical data analysis decisions and automates all calculations. Multiple source group configurations and composite fingerprints are identified and tested using multiple methods of uncertainty analysis. This aims to explore the sediment provenance information provided by the tracers more comprehensively than a single model, and allows for model configurations with high uncertainties to be rejected. This paper provides an overview of its application to an agricultural catchment in the UK to determine if the approach used can provide a reduction in uncertainty and increase in precision. Five source group classifications were used; three formed using a k-means cluster analysis containing 2, 3 and 4 clusters, and two a-priori groups based upon catchment geology. Three different composite fingerprints were used for each classification and bi-plots, range tests, tracer variability ratios and virtual mixtures tested the reliability of each model configuration. Some model configurations performed poorly when apportioning the composition of virtual mixtures, and different model configurations could produce different sediment provenance results despite using composite fingerprints able to discriminate robustly between the source groups. Despite this uncertainty, dominant sediment sources were identified, and those in close proximity to each sediment sampling location were found to be of greatest importance. This new software, by integrating recent methodological developments in tracer data processing, guides users through key steps. Critically, by applying multiple model configurations and uncertainty assessment, it delivers more robust solutions for informing catchment management of the sediment problem than many previously used approaches. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

EEG and MEG data analysis in SPM8.

PubMed

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools.

EEG and MEG Data Analysis in SPM8

PubMed Central

Litvak, Vladimir; Mattout, Jérémie; Kiebel, Stefan; Phillips, Christophe; Henson, Richard; Kilner, James; Barnes, Gareth; Oostenveld, Robert; Daunizeau, Jean; Flandin, Guillaume; Penny, Will; Friston, Karl

2011-01-01

SPM is a free and open source software written in MATLAB (The MathWorks, Inc.). In addition to standard M/EEG preprocessing, we presently offer three main analysis tools: (i) statistical analysis of scalp-maps, time-frequency images, and volumetric 3D source reconstruction images based on the general linear model, with correction for multiple comparisons using random field theory; (ii) Bayesian M/EEG source reconstruction, including support for group studies, simultaneous EEG and MEG, and fMRI priors; (iii) dynamic causal modelling (DCM), an approach combining neural modelling with data analysis for which there are several variants dealing with evoked responses, steady state responses (power spectra and cross-spectra), induced responses, and phase coupling. SPM8 is integrated with the FieldTrip toolbox , making it possible for users to combine a variety of standard analysis methods with new schemes implemented in SPM and build custom analysis tools using powerful graphical user interface (GUI) and batching tools. PMID:21437221

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The General Mission Analysis Tool (GMAT) is a space trajectory optimization and mission analysis system developed by NASA and private industry in the spirit of the NASA Mission. GMAT contains new technology and is a testbed for future technology development. The goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities, businesses, and other government organizations, and to share that technology in an open and unhindered way. GMAT is a free and open source software system licensed under the NASA Open Source Agreement: free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or further technology development.

Unclassified Information Sharing and Coordination in Security, Stabilization, Transition and Reconstruction Efforts

DTIC Science & Technology

2008-03-01

is implemented using the Drupal (2007) content management system (CMS) and many of the baseline information sharing and collaboration tools have...been contributed through the Dru- pal open source community. Drupal is a very modular open source software written in PHP hypertext processor...needed to suit the particular problem domain. While other frameworks have the potential to provide similar advantages (“Ruby,” 2007), Drupal was

Runtime Detection of C-Style Errors in UPC Code

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

Pirkelbauer, P; Liao, C; Panas, T

2011-09-29

Unified Parallel C (UPC) extends the C programming language (ISO C 99) with explicit parallel programming support for the partitioned global address space (PGAS), which provides a global memory space with localized partitions to each thread. Like its ancestor C, UPC is a low-level language that emphasizes code efficiency over safety. The absence of dynamic (and static) safety checks allows programmer oversights and software flaws that can be hard to spot. In this paper, we present an extension of a dynamic analysis tool, ROSE-Code Instrumentation and Runtime Monitor (ROSECIRM), for UPC to help programmers find C-style errors involving the globalmore » address space. Built on top of the ROSE source-to-source compiler infrastructure, the tool instruments source files with code that monitors operations and keeps track of changes to the system state. The resulting code is linked to a runtime monitor that observes the program execution and finds software defects. We describe the extensions to ROSE-CIRM that were necessary to support UPC. We discuss complications that arise from parallel code and our solutions. We test ROSE-CIRM against a runtime error detection test suite, and present performance results obtained from running error-free codes. ROSE-CIRM is released as part of the ROSE compiler under a BSD-style open source license.« less

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

PubMed

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

2017-10-01

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

The Azimuth Project: an Open-Access Educational Resource

NASA Astrophysics Data System (ADS)

Baez, J. C.

2012-12-01

The Azimuth Project is an online collaboration of scientists, engineers and programmers who are volunteering their time to do something about a wide range of environmental problems. The project has several aspects: 1) a wiki designed to make reliable, sourced information easy to find and accessible to a technically literate nonexperts, 2) a blog featuring expository articles and news items, 3) a project to write programs that explain basic concepts of climate physics and illustrate principles of good open-source software design, and 4) a project to develop mathematical tools for studying complex networked systems. We discuss the progress so far and some preliminary lessons. For example, enlisting the help of experts outside academia highlights the problems with pay-walled journals and the benefits of open access, as well as differences between how software development is done commercially, in the free software community, and in academe.

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.

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

Building Geospatial Web Services for Ecological Monitoring and Forecasting

NASA Astrophysics Data System (ADS)

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

2008-12-01

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

Open source software and low cost sensors for teaching UAV science

NASA Astrophysics Data System (ADS)

Kefauver, S. C.; Sanchez-Bragado, R.; El-Haddad, G.; Araus, J. L.

2016-12-01

Drones, also known as UASs (unmanned aerial systems), UAVs (Unmanned Aerial Vehicles) or RPAS (Remotely piloted aircraft systems), are both useful advanced scientific platforms and recreational toys that are appealing to younger generations. As such, they can make for excellent education tools as well as low-cost scientific research project alternatives. However, the process of taking pretty pictures to remote sensing science can be daunting if one is presented with only expensive software and sensor options. There are a number of open-source tools and low cost platform and sensor options available that can provide excellent scientific research results, and, by often requiring more user-involvement than commercial software and sensors, provide even greater educational benefits. Scale-invariant feature transform (SIFT) algorithm implementations, such as the Microsoft Image Composite Editor (ICE), which can create quality 2D image mosaics with some motion and terrain adjustments and VisualSFM (Structure from Motion), which can provide full image mosaicking with movement and orthorectification capacities. RGB image quantification using alternate color space transforms, such as the BreedPix indices, can be calculated via plugins in the open-source software Fiji (http://fiji.sc/Fiji; http://github.com/george-haddad/CIMMYT). Recent analyses of aerial images from UAVs over different vegetation types and environments have shown RGB metrics can outperform more costly commercial sensors. Specifically, Hue-based pixel counts, the Triangle Greenness Index (TGI), and the Normalized Green Red Difference Index (NGRDI) consistently outperformed NDVI in estimating abiotic and biotic stress impacts on crop health. Also, simple kits are available for NDVI camera conversions. Furthermore, suggestions for multivariate analyses of the different RGB indices in the "R program for statistical computing", such as classification and regression trees can allow for a more approachable interpretation of results in the classroom.

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Christe, S.; Mueller, D.

2012-12-01

We discuss two ongoing software projects in solar physics that have adopted best practices of the open source software community. The first, the Helioviewer Project, is a powerful data visualization tool which includes online and Java interfaces inspired by Google Maps (tm). This effort allows users to find solar features and events of interest, and download the corresponding data. Having found data of interest, the user now has to analyze it. The dominant solar data analysis platform is an open-source library called SolarSoft (SSW). Although SSW itself is open-source, the programming language used is IDL, a proprietary language with licensing costs that are prohibative for many institutions and individuals. SSW is composed of a collection of related scripts written by missions and individuals for solar data processing and analysis, without any consistent data structures or common interfaces. Further, at the time when SSW was initially developed, many of the best software development processes of today (mirrored and distributed version control, unit testing, continuous integration, etc.) were not standard, and have not since been adopted. The challenges inherent in developing SolarSoft led to a second software project known as SunPy. SunPy is an open-source Python-based library which seeks to create a unified solar data analysis environment including a number of core datatypes such as Maps, Lightcurves, and Spectra which have consistent interfaces and behaviors. By taking advantage of the large and sophisticated body of scientific software already available in Python (e.g. SciPy, NumPy, Matplotlib), and by adopting many of the best practices refined in open-source software development, SunPy has been able to develop at a very rapid pace while still ensuring a high level of reliability. The Helioviewer Project and SunPy represent two pioneering technologies in solar physics - simple yet flexible data visualization and a powerful, new data analysis environment. We discuss the development of both these efforts and how they are beginning to influence the solar physics community.

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

White, Amanda M.; Daly, Don S.; Willse, Alan R.

The Automated Microarray Image Analysis (AMIA) Toolbox for MATLAB is a flexible, open-source microarray image analysis tool that allows the user to customize analysis of sets of microarray images. This tool provides several methods of identifying and quantify spot statistics, as well as extensive diagnostic statistics and images to identify poor data quality or processing. The open nature of this software allows researchers to understand the algorithms used to provide intensity estimates and to modify them easily if desired.

An Integrated Suite of Text and Data Mining Tools - Phase II

DTIC Science & Technology

2005-08-30

Riverside, CA, USA Mazda Motor Corp, Jpn Univ of Darmstadt, Darmstadt, Ger Navy Center for Applied Research in Artificial Intelligence Univ of...with Georgia Tech Research Corporation developed a desktop text-mining software tool named TechOASIS (known commercially as VantagePoint). By the...of this dataset and groups the Corporate Source items that co-occur with the found items. He decides he is only interested in the institutions

ARX - A Comprehensive Tool for Anonymizing Biomedical Data

PubMed Central

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

2014-01-01

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

The Human Exposure Model (HEM): A Tool to Support Rapid ...

EPA Pesticide Factsheets

The US EPA is developing an open and publically available software program called the Human Exposure Model (HEM) to provide near-field exposure information for Life Cycle Impact Assessments (LCIAs). Historically, LCIAs have often omitted impacts from near-field sources of exposure. The use of consumer products often results in near-field exposures (exposures that occur directly from the use of a product) that are larger than environmentally mediated exposures (i.e. far-field sources)1,2. Failure to consider near-field exposures could result in biases in LCIA-based determinations of the relative sustainability of consumer products. HEM is designed to provide this information.Characterizing near-field sources of chemical exposures present a challenge to LCIA practitioners. Unlike far-field sources, where multimedia mass balance models have been used to determine human exposure, near-field sources require product-specific models of human exposure and considerable information on product use and product composition. Such information is difficult and time-consuming to gather and curate. The HEM software will characterize the distribution of doses and product intake fractions2 across populations of product users and bystanders, allowing for differentiation by various demographic characteristics. The tool incorporates a newly developed database of the composition of more than 17,000 products, data on physical and chemical properties for more than 2,000 chemicals, and mo

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.

Final Report. Center for Scalable Application Development Software

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

Mellor-Crummey, John

2014-10-26

The Center for Scalable Application Development Software (CScADS) was established as a part- nership between Rice University, Argonne National Laboratory, University of California Berkeley, University of Tennessee – Knoxville, and University of Wisconsin – Madison. CScADS pursued an integrated set of activities with the aim of increasing the productivity of DOE computational scientists by catalyzing the development of systems software, libraries, compilers, and tools for leadership computing platforms. Principal Center activities were workshops to engage the research community in the challenges of leadership computing, research and development of open-source software, and work with computational scientists to help them develop codesmore » for leadership computing platforms. This final report summarizes CScADS activities at Rice University in these areas.« less

Towards Efficient Scientific Data Management Using Cloud Storage

NASA Technical Reports Server (NTRS)

He, Qiming

2013-01-01

A software prototype allows users to backup and restore data to/from both public and private cloud storage such as Amazon's S3 and NASA's Nebula. Unlike other off-the-shelf tools, this software ensures user data security in the cloud (through encryption), and minimizes users operating costs by using space- and bandwidth-efficient compression and incremental backup. Parallel data processing utilities have also been developed by using massively scalable cloud computing in conjunction with cloud storage. One of the innovations in this software is using modified open source components to work with a private cloud like NASA Nebula. Another innovation is porting the complex backup to- cloud software to embedded Linux, running on the home networking devices, in order to benefit more users.

Neural network technologies

NASA Technical Reports Server (NTRS)

Villarreal, James A.

1991-01-01

A whole new arena of computer technologies is now beginning to form. Still in its infancy, neural network technology is a biologically inspired methodology which draws on nature's own cognitive processes. The Software Technology Branch has provided a software tool, Neural Execution and Training System (NETS), to industry, government, and academia to facilitate and expedite the use of this technology. NETS is written in the C programming language and can be executed on a variety of machines. Once a network has been debugged, NETS can produce a C source code which implements the network. This code can then be incorporated into other software systems. Described here are various software projects currently under development with NETS and the anticipated future enhancements to NETS and the technology.

An Investigation of Software Scaffolds Supporting Modeling Practices

NASA Astrophysics Data System (ADS)

Fretz, Eric B.; Wu, Hsin-Kai; Zhang, Baohui; Davis, Elizabeth A.; Krajcik, Joseph S.; Soloway, Elliot

2002-08-01

Modeling of complex systems and phenomena is of value in science learning and is increasingly emphasised as an important component of science teaching and learning. Modeling engages learners in desired pedagogical activities. These activities include practices such as planning, building, testing, analysing, and critiquing. Designing realistic models is a difficult task. Computer environments allow the creation of dynamic and even more complex models. One way of bringing the design of models within reach is through the use of scaffolds. Scaffolds are intentional assistance provided to learners from a variety of sources, allowing them to complete tasks that would otherwise be out of reach. Currently, our understanding of how scaffolds in software tools assist learners is incomplete. In this paper the scaffolds designed into a dynamic modeling software tool called Model-It are assessed in terms of their ability to support learners' use of modeling practices. Four pairs of middle school students were video-taped as they used the modeling software for three hours, spread over a two week time frame. Detailed analysis of coded videotape transcripts provided evidence of the importance of scaffolds in supporting the use of modeling practices. Learners used a variety of modeling practices, the majority of which occurred in conjunction with scaffolds. The use of three tool scaffolds was assessed as directly as possible, and these scaffolds were seen to support a variety of modeling practices. An argument is made for the continued empirical validation of types and instances of tool scaffolds, and further investigation of the important role of teacher and peer scaffolding in the use of scaffolded tools.

Generation of GHS Scores from TEST and online sources

EPA Science Inventory

Alternatives assessment frameworks such as DfE (Design for the Environment) evaluate chemical alternatives in terms of human health effects, ecotoxicity, and fate. T.E.S.T. (Toxicity Estimation Software Tool) can be utilized to evaluate human health in terms of acute oral rat tox...

Lakes, landscapes, and R: A framework for open science on freshwater cyanobacteria

EPA Science Inventory

In the last several years scientific reproducibility has been a hot topic with several fields openly struggling with reproducing and replicating research results. One of the key tools to address reproducibility is the use of open source software. Increasingly in ecology, the R ...

An open-source Java-based Toolbox for environmental model evaluation: The MOUSE Software Application

USDA-ARS?s Scientific Manuscript database

A consequence of environmental model complexity is that the task of understanding how environmental models work and identifying their sensitivities/uncertainties, etc. becomes progressively more difficult. Comprehensive numerical and visual evaluation tools have been developed such as the Monte Carl...

Analysis of High-Throughput ELISA Microarray Data

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

White, Amanda M.; Daly, Don S.; Zangar, Richard C.

Our research group develops analytical methods and software for the high-throughput analysis of quantitative enzyme-linked immunosorbent assay (ELISA) microarrays. ELISA microarrays differ from DNA microarrays in several fundamental aspects and most algorithms for analysis of DNA microarray data are not applicable to ELISA microarrays. In this review, we provide an overview of the steps involved in ELISA microarray data analysis and how the statistically sound algorithms we have developed provide an integrated software suite to address the needs of each data-processing step. The algorithms discussed are available in a set of open-source software tools (http://www.pnl.gov/statistics/ProMAT).

g-PRIME: A Free, Windows Based Data Acquisition and Event Analysis Software Package for Physiology in Classrooms and Research Labs.

PubMed

Lott, Gus K; Johnson, Bruce R; Bonow, Robert H; Land, Bruce R; Hoy, Ronald R

2009-01-01

We present g-PRIME, a software based tool for physiology data acquisition, analysis, and stimulus generation in education and research. This software was developed in an undergraduate neurophysiology course and strongly influenced by instructor and student feedback. g-PRIME is a free, stand-alone, windows application coded and "compiled" in Matlab (does not require a Matlab license). g-PRIME supports many data acquisition interfaces from the PC sound card to expensive high throughput calibrated equipment. The program is designed as a software oscilloscope with standard trigger modes, multi-channel visualization controls, and data logging features. Extensive analysis options allow real time and offline filtering of signals, multi-parameter threshold-and-window based event detection, and two-dimensional display of a variety of parameters including event time, energy density, maximum FFT frequency component, max/min amplitudes, and inter-event rate and intervals. The software also correlates detected events with another simultaneously acquired source (event triggered average) in real time or offline. g-PRIME supports parameter histogram production and a variety of elegant publication quality graphics outputs. A major goal of this software is to merge powerful engineering acquisition and analysis tools with a biological approach to studies of nervous system function.

PROVAT: a tool for Voronoi tessellation analysis of protein structures and complexes.

PubMed

Gore, Swanand P; Burke, David F; Blundell, Tom L

2005-08-01

Voronoi tessellation has proved to be a useful tool in protein structure analysis. We have developed PROVAT, a versatile public domain software that enables computation and visualization of Voronoi tessellations of proteins and protein complexes. It is a set of Python scripts that integrate freely available specialized software (Qhull, Pymol etc.) into a pipeline. The calculation component of the tool computes Voronoi tessellation of a given protein system in a way described by a user-supplied XML recipe and stores resulting neighbourhood information as text files with various styles. The Python pickle file generated in the process is used by the visualization component, a Pymol plug-in, that offers a GUI to explore the tessellation visually. PROVAT source code can be downloaded from http://raven.bioc.cam.ac.uk/~swanand/Provat1, which also provides a webserver for its calculation component, documentation and examples.

A Flexible Method for Producing F.E.M. Analysis of Bone Using Open-Source Software

NASA Technical Reports Server (NTRS)

Boppana, Abhishektha; Sefcik, Ryan; Meyers, Jerry G.; Lewandowski, Beth E.

2016-01-01

This project, performed in support of the NASA GRC Space Academy summer program, sought to develop an open-source workflow methodology that segmented medical image data, created a 3D model from the segmented data, and prepared the model for finite-element analysis. In an initial step, a technological survey evaluated the performance of various existing open-source software that claim to perform these tasks. However, the survey concluded that no single software exhibited the wide array of functionality required for the potential NASA application in the area of bone, muscle and bio fluidic studies. As a result, development of a series of Python scripts provided the bridging mechanism to address the shortcomings of the available open source tools. The implementation of the VTK library provided the most quick and effective means of segmenting regions of interest from the medical images; it allowed for the export of a 3D model by using the marching cubes algorithm to build a surface mesh. To facilitate the development of the model domain from this extracted information required a surface mesh to be processed in the open-source software packages Blender and Gmsh. The Preview program of the FEBio suite proved to be sufficient for volume filling the model with an unstructured mesh and preparing boundaries specifications for finite element analysis. To fully allow FEM modeling, an in house developed Python script allowed assignment of material properties on an element by element basis by performing a weighted interpolation of voxel intensity of the parent medical image correlated to published information of image intensity to material properties, such as ash density. A graphical user interface combined the Python scripts and other software into a user friendly interface. The work using Python scripts provides a potential alternative to expensive commercial software and inadequate, limited open-source freeware programs for the creation of 3D computational models. More work will be needed to validate this approach in creating finite-element models.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

Application for internal dosimetry using biokinetic distribution of photons based on nuclear medicine images.

PubMed

Leal Neto, Viriato; Vieira, José Wilson; Lima, Fernando Roberto de Andrade

2014-01-01

This article presents a way to obtain estimates of dose in patients submitted to radiotherapy with basis on the analysis of regions of interest on nuclear medicine images. A software called DoRadIo (Dosimetria das Radiações Ionizantes [Ionizing Radiation Dosimetry]) was developed to receive information about source organs and target organs, generating graphical and numerical results. The nuclear medicine images utilized in the present study were obtained from catalogs provided by medical physicists. The simulations were performed with computational exposure models consisting of voxel phantoms coupled with the Monte Carlo EGSnrc code. The software was developed with the Microsoft Visual Studio 2010 Service Pack and the project template Windows Presentation Foundation for C# programming language. With the mentioned tools, the authors obtained the file for optimization of Monte Carlo simulations using the EGSnrc; organization and compaction of dosimetry results with all radioactive sources; selection of regions of interest; evaluation of grayscale intensity in regions of interest; the file of weighted sources; and, finally, all the charts and numerical results. The user interface may be adapted for use in clinical nuclear medicine as a computer-aided tool to estimate the administered activity.

A component-based software environment for visualizing large macromolecular assemblies.

PubMed

Sanner, Michel F

2005-03-01

The interactive visualization of large biological assemblies poses a number of challenging problems, including the development of multiresolution representations and new interaction methods for navigating and analyzing these complex systems. An additional challenge is the development of flexible software environments that will facilitate the integration and interoperation of computational models and techniques from a wide variety of scientific disciplines. In this paper, we present a component-based software development strategy centered on the high-level, object-oriented, interpretive programming language: Python. We present several software components, discuss their integration, and describe some of their features that are relevant to the visualization of large molecular assemblies. Several examples are given to illustrate the interoperation of these software components and the integration of structural data from a variety of experimental sources. These examples illustrate how combining visual programming with component-based software development facilitates the rapid prototyping of novel visualization tools.

Increasing the impact of medical image computing using community-based open-access hackathons: The NA-MIC and 3D Slicer experience.

PubMed

Kapur, Tina; Pieper, Steve; Fedorov, Andriy; Fillion-Robin, J-C; Halle, Michael; O'Donnell, Lauren; Lasso, Andras; Ungi, Tamas; Pinter, Csaba; Finet, Julien; Pujol, Sonia; Jagadeesan, Jayender; Tokuda, Junichi; Norton, Isaiah; Estepar, Raul San Jose; Gering, David; Aerts, Hugo J W L; Jakab, Marianna; Hata, Nobuhiko; Ibanez, Luiz; Blezek, Daniel; Miller, Jim; Aylward, Stephen; Grimson, W Eric L; Fichtinger, Gabor; Wells, William M; Lorensen, William E; Schroeder, Will; Kikinis, Ron

2016-10-01

The National Alliance for Medical Image Computing (NA-MIC) was launched in 2004 with the goal of investigating and developing an open source software infrastructure for the extraction of information and knowledge from medical images using computational methods. Several leading research and engineering groups participated in this effort that was funded by the US National Institutes of Health through a variety of infrastructure grants. This effort transformed 3D Slicer from an internal, Boston-based, academic research software application into a professionally maintained, robust, open source platform with an international leadership and developer and user communities. Critical improvements to the widely used underlying open source libraries and tools-VTK, ITK, CMake, CDash, DCMTK-were an additional consequence of this effort. This project has contributed to close to a thousand peer-reviewed publications and a growing portfolio of US and international funded efforts expanding the use of these tools in new medical computing applications every year. In this editorial, we discuss what we believe are gaps in the way medical image computing is pursued today; how a well-executed research platform can enable discovery, innovation and reproducible science ("Open Science"); and how our quest to build such a software platform has evolved into a productive and rewarding social engineering exercise in building an open-access community with a shared vision. Copyright © 2016 Elsevier B.V. All rights reserved.

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

New developments in the McStas neutron instrument simulation package

NASA Astrophysics Data System (ADS)

Willendrup, P. K.; Knudsen, E. B.; Klinkby, E.; Nielsen, T.; Farhi, E.; Filges, U.; Lefmann, K.

2014-07-01

The McStas neutron ray-tracing software package is a versatile tool for building accurate simulators of neutron scattering instruments at reactors, short- and long-pulsed spallation sources such as the European Spallation Source. McStas is extensively used for design and optimization of instruments, virtual experiments, data analysis and user training. McStas was founded as a scientific, open-source collaborative code in 1997. This contribution presents the project at its current state and gives an overview of the main new developments in McStas 2.0 (December 2012) and McStas 2.1 (expected fall 2013), including many new components, component parameter uniformisation, partial loss of backward compatibility, updated source brilliance descriptions, developments toward new tools and user interfaces, web interfaces and a new method for estimating beam losses and background from neutron optics.

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

PubMed

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

2010-05-01

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

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

PubMed

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

2017-07-07

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

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

PubMed

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

2018-03-01

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

sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping.

PubMed

Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

2015-01-01

A major challenge in the diagnosis and treatment of brain tumors is tissue heterogeneity leading to mixed treatment response. Additionally, they are often difficult or at very high risk for biopsy, further hindering the clinical management process. To overcome this, novel advanced imaging methods are increasingly being adapted clinically to identify useful noninvasive biomarkers capable of disease stage characterization and treatment response prediction. One promising technique is called functional diffusion mapping (fDM), which uses diffusion-weighted imaging (DWI) to generate parametric maps between two imaging time points in order to identify significant voxel-wise changes in water diffusion within the tumor tissue. Here we introduce serial functional diffusion mapping (sfDM), an extension of existing fDM methods, to analyze the entire tumor diffusion profile along the temporal course of the disease. sfDM provides the tools necessary to analyze a tumor data set in the context of spatiotemporal parametric mapping: the image registration pipeline, biomarker extraction, and visualization tools. We present the general workflow of the pipeline, along with a typical use case for the software. sfDM is written in Python and is freely available as an open-source package under the Berkley Software Distribution (BSD) license to promote transparency and reproducibility.

OptFlux: an open-source software platform for in silico metabolic engineering.

PubMed

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

2010-04-19

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.

OptFlux: an open-source software platform for in silico metabolic engineering

PubMed Central

2010-01-01

Background Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. Conclusions The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models. PMID:20403172

Using open source computational tools for predicting human metabolic stability and additional absorption, distribution, metabolism, excretion, and toxicity properties.

PubMed

Gupta, Rishi R; Gifford, Eric M; Liston, Ted; Waller, Chris L; Hohman, Moses; Bunin, Barry A; Ekins, Sean

2010-11-01

Ligand-based computational models could be more readily shared between researchers and organizations if they were generated with open source molecular descriptors [e.g., chemistry development kit (CDK)] and modeling algorithms, because this would negate the requirement for proprietary commercial software. We initially evaluated open source descriptors and model building algorithms using a training set of approximately 50,000 molecules and a test set of approximately 25,000 molecules with human liver microsomal metabolic stability data. A C5.0 decision tree model demonstrated that CDK descriptors together with a set of Smiles Arbitrary Target Specification (SMARTS) keys had good statistics [κ = 0.43, sensitivity = 0.57, specificity = 0.91, and positive predicted value (PPV) = 0.64], equivalent to those of models built with commercial Molecular Operating Environment 2D (MOE2D) and the same set of SMARTS keys (κ = 0.43, sensitivity = 0.58, specificity = 0.91, and PPV = 0.63). Extending the dataset to ∼193,000 molecules and generating a continuous model using Cubist with a combination of CDK and SMARTS keys or MOE2D and SMARTS keys confirmed this observation. When the continuous predictions and actual values were binned to get a categorical score we observed a similar κ statistic (0.42). The same combination of descriptor set and modeling method was applied to passive permeability and P-glycoprotein efflux data with similar model testing statistics. In summary, open source tools demonstrated predictive results comparable to those of commercial software with attendant cost savings. We discuss the advantages and disadvantages of open source descriptors and the opportunity for their use as a tool for organizations to share data precompetitively, avoiding repetition and assisting drug discovery.

Conjunctive programming: An interactive approach to software system synthesis

NASA Technical Reports Server (NTRS)

Tausworthe, Robert C.

1992-01-01

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

FROMS3D: New Software for 3-D Visualization of Fracture Network System in Fractured Rock Masses

NASA Astrophysics Data System (ADS)

Noh, Y. H.; Um, J. G.; Choi, Y.

2014-12-01

A new software (FROMS3D) is presented to visualize fracture network system in 3-D. The software consists of several modules that play roles in management of borehole and field fracture data, fracture network modelling, visualization of fracture geometry in 3-D and calculation and visualization of intersections and equivalent pipes between fractures. Intel Parallel Studio XE 2013, Visual Studio.NET 2010 and the open source VTK library were utilized as development tools to efficiently implement the modules and the graphical user interface of the software. The results have suggested that the developed software is effective in visualizing 3-D fracture network system, and can provide useful information to tackle the engineering geological problems related to strength, deformability and hydraulic behaviors of the fractured rock masses.

Simplified Deployment of Health Informatics Applications by Providing Docker Images.

PubMed

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

2016-01-01

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

Processing and review interface for strong motion data (PRISM) software, version 1.0.0—Methodology and automated processing

USGS Publications Warehouse

Jones, Jeanne; Kalkan, Erol; Stephens, Christopher

2017-02-23

A continually increasing number of high-quality digital strong-motion records from stations of the National Strong-Motion Project (NSMP) of the U.S. Geological Survey (USGS), as well as data from regional seismic networks within the United States, call for automated processing of strong-motion records with human review limited to selected significant or flagged records. The NSMP has developed the Processing and Review Interface for Strong Motion data (PRISM) software to meet this need. In combination with the Advanced National Seismic System Quake Monitoring System (AQMS), PRISM automates the processing of strong-motion records. When used without AQMS, PRISM provides batch-processing capabilities. The PRISM version 1.0.0 is platform independent (coded in Java), open source, and does not depend on any closed-source or proprietary software. The software consists of two major components: a record processing engine and a review tool that has a graphical user interface (GUI) to manually review, edit, and process records. To facilitate use by non-NSMP earthquake engineers and scientists, PRISM (both its processing engine and review tool) is easy to install and run as a stand-alone system on common operating systems such as Linux, OS X, and Windows. PRISM was designed to be flexible and extensible in order to accommodate new processing techniques. This report provides a thorough description and examples of the record processing features supported by PRISM. All the computing features of PRISM have been thoroughly tested.

Open-source image registration for MRI-TRUS fusion-guided prostate interventions.

PubMed

Fedorov, Andriy; Khallaghi, Siavash; Sánchez, C Antonio; Lasso, Andras; Fels, Sidney; Tuncali, Kemal; Sugar, Emily Neubauer; Kapur, Tina; Zhang, Chenxi; Wells, William; Nguyen, Paul L; Abolmaesumi, Purang; Tempany, Clare

2015-06-01

We propose two software tools for non-rigid registration of MRI and transrectal ultrasound (TRUS) images of the prostate. Our ultimate goal is to develop an open-source solution to support MRI-TRUS fusion image guidance of prostate interventions, such as targeted biopsy for prostate cancer detection and focal therapy. It is widely hypothesized that image registration is an essential component in such systems. The two non-rigid registration methods are: (1) a deformable registration of the prostate segmentation distance maps with B-spline regularization and (2) a finite element-based deformable registration of the segmentation surfaces in the presence of partial data. We evaluate the methods retrospectively using clinical patient image data collected during standard clinical procedures. Computation time and Target Registration Error (TRE) calculated at the expert-identified anatomical landmarks were used as quantitative measures for the evaluation. The presented image registration tools were capable of completing deformable registration computation within 5 min. Average TRE was approximately 3 mm for both methods, which is comparable with the slice thickness in our MRI data. Both tools are available under nonrestrictive open-source license. We release open-source tools that may be used for registration during MRI-TRUS-guided prostate interventions. Our tools implement novel registration approaches and produce acceptable registration results. We believe these tools will lower the barriers in development and deployment of interventional research solutions and facilitate comparison with similar tools.

The Argument for Open

ERIC Educational Resources Information Center

Byrd, Rob

2008-01-01

Is open source business intelligence (OS BI) software ready for prime time? The author thoroughly investigated each of three OS BI toolsets--Pentaho BI Suite, Jaspersoft BI Suite, and Talend Open Studio--by installing the OS BI tools himself, by interviewing technologists at academic institutions who had implemented these OS BI solutions, and by…

Generation of Alternative Assessment Scores using TEST and online data sources

EPA Science Inventory

Alternatives assessment frameworks such as DfE (Design for the Environment) evaluate chemical alternatives in terms of human health effects, ecotoxicity, and fate. T.E.S.T. (Toxicity Estimation Software Tool) can be utilized to evaluate human health in terms of acute oral rat tox...

Homology Modeling and Molecular Docking for the Science Curriculum

ERIC Educational Resources Information Center

McDougal, Owen M.; Cornia, Nic; Sambasivarao, S. V.; Remm, Andrew; Mallory, Chris; Oxford, Julia Thom; Maupin, C. Mark; Andersen, Tim

2014-01-01

DockoMatic 2.0 is a powerful open source software program (downloadable from sourceforge.net) that allows users to utilize a readily accessible computational tool to explore biomolecules and their interactions. This manuscript describes a practical tutorial for use in the undergraduate curriculum that introduces students to macromolecular…

No Strings Attached: Open Source Solutions

ERIC Educational Resources Information Center

Fredricks, Kathy

2009-01-01

Imagine downloading a new software application and not having to worry about licensing, finding dollars in the budget, or incurring additional maintenance costs. Imagine finding a Web design tool in the public domain--free for use. Imagine major universities that provide online courses with no strings attached. Imagine online textbooks without a…

Data for Environmental Modeling (D4EM): Background and Applications of Data Automation

EPA Science Inventory

The Data for Environmental Modeling (D4EM) project demonstrates the development of a comprehensive set of open source software tools that overcome obstacles to accessing data needed by automating the process of populating model input data sets with environmental data available fr...

A New Key to Scholarly Collaboration?

ERIC Educational Resources Information Center

Fitzmier, Jack

2012-01-01

The American Academy of Religion, in concert with the Sakai Foundation, has envisioned a scholarly use of the new Sakai Open Academic Environment open-source software. Currently working under the title "Biosphere," the program would put a rich collection of collaborative tools in the hands of AAR members, their colleagues in related scholarly…

Validation of the PCN Concept: Mobility, Traffic Flow Confidentiality and Protection Against Directed Attacks

DTIC Science & Technology

2010-11-01

peer, racoon (IKE-daemon) will start authenticating using certificates. After a successful authentication, IPSec security associations will be set up...colour had credentials from one CA. Racoon and ipsec-tools are open-source software, implementing IKE and IPSec. Validation of the PCN Concept; Mobility

Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.

PubMed

Ham, Timothy S; Dmytriv, Zinovii; Plahar, Hector; Chen, Joanna; Hillson, Nathan J; Keasling, Jay D

2012-10-01

The Joint BioEnergy Institute Inventory of Composable Elements (JBEI-ICEs) is an open source registry platform for managing information about biological parts. It is capable of recording information about 'legacy' parts, such as plasmids, microbial host strains and Arabidopsis seeds, as well as DNA parts in various assembly standards. ICE is built on the idea of a web of registries and thus provides strong support for distributed interconnected use. The information deposited in an ICE installation instance is accessible both via a web browser and through the web application programming interfaces, which allows automated access to parts via third-party programs. JBEI-ICE includes several useful web browser-based graphical applications for sequence annotation, manipulation and analysis that are also open source. As with open source software, users are encouraged to install, use and customize JBEI-ICE and its components for their particular purposes. As a web application programming interface, ICE provides well-developed parts storage functionality for other synthetic biology software projects. A public instance is available at public-registry.jbei.org, where users can try out features, upload parts or simply use it for their projects. The ICE software suite is available via Google Code, a hosting site for community-driven open source projects.

CROPPER: a metagene creator resource for cross-platform and cross-species compendium studies.

PubMed

Paananen, Jussi; Storvik, Markus; Wong, Garry

2006-09-22

Current genomic research methods provide researchers with enormous amounts of data. Combining data from different high-throughput research technologies commonly available in biological databases can lead to novel findings and increase research efficiency. However, combining data from different heterogeneous sources is often a very arduous task. These sources can be different microarray technology platforms, genomic databases, or experiments performed on various species. Our aim was to develop a software program that could facilitate the combining of data from heterogeneous sources, and thus allow researchers to perform genomic cross-platform/cross-species studies and to use existing experimental data for compendium studies. We have developed a web-based software resource, called CROPPER that uses the latest genomic information concerning different data identifiers and orthologous genes from the Ensembl database. CROPPER can be used to combine genomic data from different heterogeneous sources, allowing researchers to perform cross-platform/cross-species compendium studies without the need for complex computational tools or the requirement of setting up one's own in-house database. We also present an example of a simple cross-platform/cross-species compendium study based on publicly available Parkinson's disease data derived from different sources. CROPPER is a user-friendly and freely available web-based software resource that can be successfully used for cross-species/cross-platform compendium studies.

Analysis of Ten Reverse Engineering Tools

NASA Astrophysics Data System (ADS)

Koskinen, Jussi; Lehmonen, Tero

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

Development of AN Open-Source Automatic Deformation Monitoring System for Geodetical and Geotechnical Measurements

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

The deformation monitoring of structures and buildings is an important task field of modern engineering surveying, ensuring the standing and reliability of supervised objects over a long period. Several commercial hardware and software solutions for the realization of such monitoring measurements are available on the market. In addition to them, a research team at the Neubrandenburg University of Applied Sciences (NUAS) is actively developing a software package for monitoring purposes in geodesy and geotechnics, which is distributed under an open source licence and free of charge. The task of managing an open source project is well-known in computer science, but it is fairly new in a geodetic context. This paper contributes to that issue by detailing applications, frameworks, and interfaces for the design and implementation of open hardware and software solutions for sensor control, sensor networks, and data management in automatic deformation monitoring. It will be discussed how the development effort of networked applications can be reduced by using free programming tools, cloud computing technologies, and rapid prototyping methods.

Clinical records anonymisation and text extraction (CRATE): an open-source software system.

PubMed

Cardinal, Rudolf N

2017-04-26

Electronic medical records contain information of value for research, but contain identifiable and often highly sensitive confidential information. Patient-identifiable information cannot in general be shared outside clinical care teams without explicit consent, but anonymisation/de-identification allows research uses of clinical data without explicit consent. This article presents CRATE (Clinical Records Anonymisation and Text Extraction), an open-source software system with separable functions: (1) it anonymises or de-identifies arbitrary relational databases, with sensitivity and precision similar to previous comparable systems; (2) it uses public secure cryptographic methods to map patient identifiers to research identifiers (pseudonyms); (3) it connects relational databases to external tools for natural language processing; (4) it provides a web front end for research and administrative functions; and (5) it supports a specific model through which patients may consent to be contacted about research. Creation and management of a research database from sensitive clinical records with secure pseudonym generation, full-text indexing, and a consent-to-contact process is possible and practical using entirely free and open-source software.

Quantitative computed tomography (QCT) as a radiology reporting tool by using optical character recognition (OCR) and macro program.

PubMed

Lee, Young Han; Song, Ho-Taek; Suh, Jin-Suck

2012-12-01

The objectives are (1) to introduce a new concept of making a quantitative computed tomography (QCT) reporting system by using optical character recognition (OCR) and macro program and (2) to illustrate the practical usages of the QCT reporting system in radiology reading environment. This reporting system was created as a development tool by using an open-source OCR software and an open-source macro program. The main module was designed for OCR to report QCT images in radiology reading process. The principal processes are as follows: (1) to save a QCT report as a graphic file, (2) to recognize the characters from an image as a text, (3) to extract the T scores from the text, (4) to perform error correction, (5) to reformat the values into QCT radiology reporting template, and (6) to paste the reports into the electronic medical record (EMR) or picture archiving and communicating system (PACS). The accuracy test of OCR was performed on randomly selected QCTs. QCT as a radiology reporting tool successfully acted as OCR of QCT. The diagnosis of normal, osteopenia, or osteoporosis is also determined. Error correction of OCR is done with AutoHotkey-coded module. The results of T scores of femoral neck and lumbar vertebrae had an accuracy of 100 and 95.4 %, respectively. A convenient QCT reporting system could be established by utilizing open-source OCR software and open-source macro program. This method can be easily adapted for other QCT applications and PACS/EMR.

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

NASA Astrophysics Data System (ADS)

Achtor, T. H.; Rink, T.

2010-12-01

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

FoodChain-Lab: A Trace-Back and Trace-Forward Tool Developed and Applied during Food-Borne Disease Outbreak Investigations in Germany and Europe.

PubMed

Weiser, Armin A; Thöns, Christian; Filter, Matthias; Falenski, Alexander; Appel, Bernd; Käsbohrer, Annemarie

2016-01-01

FoodChain-Lab is modular open-source software for trace-back and trace-forward analysis in food-borne disease outbreak investigations. Development of FoodChain-Lab has been driven by a need for appropriate software in several food-related outbreaks in Germany since 2011. The software allows integrated data management, data linkage, enrichment and visualization as well as interactive supply chain analyses. Identification of possible outbreak sources or vehicles is facilitated by calculation of tracing scores for food-handling stations (companies or persons) and food products under investigation. The software also supports consideration of station-specific cross-contamination, analysis of geographical relationships, and topological clustering of the tracing network structure. FoodChain-Lab has been applied successfully in previous outbreak investigations, for example during the 2011 EHEC outbreak and the 2013/14 European hepatitis A outbreak. The software is most useful in complex, multi-area outbreak investigations where epidemiological evidence may be insufficient to discriminate between multiple implicated food products. The automated analysis and visualization components would be of greater value if trading information on food ingredients and compound products was more easily available.

FoodChain-Lab: A Trace-Back and Trace-Forward Tool Developed and Applied during Food-Borne Disease Outbreak Investigations in Germany and Europe

PubMed Central

Filter, Matthias; Falenski, Alexander; Appel, Bernd; Käsbohrer, Annemarie

2016-01-01

FoodChain-Lab is modular open-source software for trace-back and trace-forward analysis in food-borne disease outbreak investigations. Development of FoodChain-Lab has been driven by a need for appropriate software in several food-related outbreaks in Germany since 2011. The software allows integrated data management, data linkage, enrichment and visualization as well as interactive supply chain analyses. Identification of possible outbreak sources or vehicles is facilitated by calculation of tracing scores for food-handling stations (companies or persons) and food products under investigation. The software also supports consideration of station-specific cross-contamination, analysis of geographical relationships, and topological clustering of the tracing network structure. FoodChain-Lab has been applied successfully in previous outbreak investigations, for example during the 2011 EHEC outbreak and the 2013/14 European hepatitis A outbreak. The software is most useful in complex, multi-area outbreak investigations where epidemiological evidence may be insufficient to discriminate between multiple implicated food products. The automated analysis and visualization components would be of greater value if trading information on food ingredients and compound products was more easily available. PMID:26985673

Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

NASA Astrophysics Data System (ADS)

Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

2012-12-01

Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

CrossTalk: The Journal of Defense Software Engineering. Volume 24, Number 4, July/August 2011

DTIC Science & Technology

2011-07-01

Project Management Tool (SSPMT), JASMINE , and ALADDIN, respectively [11, 12]. SSPMT is a web-based Six Sigma project management sup- porting tool...PSP/TSP data gathered from JASMINE and ALADDIN, SSPMT performs each step of DMAIC and provides analytic results. JASMINE and ALADDIN are web-based...done by using JASMINE . JASMINE collects an individual developer’s work product information such as Source Lines of Code (SLOC), fault counts, and

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

DTIC Science & Technology

2010-12-01

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

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

PubMed

Curtis, Darren S; Phillips, Aaron R; Callister, Stephen J; Conlan, Sean; McCue, Lee Ann

2013-10-15

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

PNNL Future Power Grid Initiative-developed GridOPTICS Software System (GOSS)

ScienceCinema

None

2018-01-16

The power grid is changing and evolving. One aspect of this change is the growing use of smart meters and other devices, which are producing large volumes of useful data. However, in many cases, the data can’t be translated quickly into actionable guidance to improve grid performance. There's a need for innovative tools. The GridOPTICS(TM) Software System, or GOSS, developed through PNNL's Future Power Grid Initiative, is open source and became publicly available in spring 2014. The value of this middleware is that it easily integrates grid applications with sources of data and facilitates communication between them. Such a capability provides a foundation for developing a range of applications to improve grid management.

Spinoff 2013

NASA Technical Reports Server (NTRS)

2014-01-01

Topics covered include: Innovative Software Tools Measure Behavioral Alertness; Miniaturized, Portable Sensors Monitor Metabolic Health; Patient Simulators Train Emergency Caregivers; Solar Refrigerators Store Life-Saving Vaccines; Monitors Enable Medication Management in Patients' Homes; Handheld Diagnostic Device Delivers Quick Medical Readings; Experiments Result in Safer, Spin-Resistant Aircraft; Interfaces Visualize Data for Airline Safety, Efficiency; Data Mining Tools Make Flights Safer, More Efficient; NASA Standards Inform Comfortable Car Seats; Heat Shield Paves the Way for Commercial Space; Air Systems Provide Life Support to Miners; Coatings Preserve Metal, Stone, Tile, and Concrete; Robots Spur Software That Lends a Hand; Cloud-Based Data Sharing Connects Emergency Managers; Catalytic Converters Maintain Air Quality in Mines; NASA-Enhanced Water Bottles Filter Water on the Go; Brainwave Monitoring Software Improves Distracted Minds; Thermal Materials Protect Priceless, Personal Keepsakes; Home Air Purifiers Eradicate Harmful Pathogens; Thermal Materials Drive Professional Apparel Line; Radiant Barriers Save Energy in Buildings; Open Source Initiative Powers Real-Time Data Streams; Shuttle Engine Designs Revolutionize Solar Power; Procedure-Authoring Tool Improves Safety on Oil Rigs; Satellite Data Aid Monitoring of Nation's Forests; Mars Technologies Spawn Durable Wind Turbines; Programs Visualize Earth and Space for Interactive Education; Processor Units Reduce Satellite Construction Costs; Software Accelerates Computing Time for Complex Math; Simulation Tools Prevent Signal Interference on Spacecraft; Software Simplifies the Sharing of Numerical Models; Virtual Machine Language Controls Remote Devices; Micro-Accelerometers Monitor Equipment Health; Reactors Save Energy, Costs for Hydrogen Production; Cameras Monitor Spacecraft Integrity to Prevent Failures; Testing Devices Garner Data on Insulation Performance; Smart Sensors Gather Information for Machine Diagnostics; Oxygen Sensors Monitor Bioreactors and Ensure Health and Safety; Vision Algorithms Catch Defects in Screen Displays; and Deformable Mirrors Capture Exoplanet Data, Reflect Lasers.

Digital Image Correlation from Commercial to FOS Software: a Mature Technique for Full-Field Displacement Measurements

NASA Astrophysics Data System (ADS)

Belloni, V.; Ravanelli, R.; Nascetti, A.; Di Rita, M.; Mattei, D.; Crespi, M.

2018-05-01

In the last few decades, there has been a growing interest in studying non-contact methods for full-field displacement and strain measurement. Among such techniques, Digital Image Correlation (DIC) has received particular attention, thanks to its ability to provide these information by comparing digital images of a sample surface before and after deformation. The method is now commonly adopted in the field of civil, mechanical and aerospace engineering and different companies and some research groups implemented 2D and 3D DIC software. In this work a review on DIC software status is given at first. Moreover, a free and open source 2D DIC software is presented, named py2DIC and developed in Python at the Geodesy and Geomatics Division of DICEA of the University of Rome "La Sapienza"; its potentialities were evaluated by processing the images captured during tensile tests performed in the Structural Engineering Lab of the University of Rome "La Sapienza" and comparing them to those obtained using the commercial software Vic-2D developed by Correlated Solutions Inc, USA. The agreement of these results at one hundredth of millimetre level demonstrate the possibility to use this open source software as a valuable 2D DIC tool to measure full-field displacements on the investigated sample surface.

Coastal On-line Assessment and Synthesis Tool 2.0

NASA Technical Reports Server (NTRS)

Brown, Richard; Navard, Andrew; Nguyen, Beth

2011-01-01

COAST (Coastal On-line Assessment and Synthesis Tool) is a 3D, open-source Earth data browser developed by leveraging and enhancing previous NASA open-source tools. These tools use satellite imagery and elevation data in a way that allows any user to zoom from orbit view down into any place on Earth, and enables the user to experience Earth terrain in a visually rich 3D view. The benefits associated with taking advantage of an open-source geo-browser are that it is free, extensible, and offers a worldwide developer community that is available to provide additional development and improvement potential. What makes COAST unique is that it simplifies the process of locating and accessing data sources, and allows a user to combine them into a multi-layered and/or multi-temporal visual analytical look into possible data interrelationships and coeffectors for coastal environment phenomenology. COAST provides users with new data visual analytic capabilities. COAST has been upgraded to maximize use of open-source data access, viewing, and data manipulation software tools. The COAST 2.0 toolset has been developed to increase access to a larger realm of the most commonly implemented data formats used by the coastal science community. New and enhanced functionalities that upgrade COAST to COAST 2.0 include the development of the Temporal Visualization Tool (TVT) plug-in, the Recursive Online Remote Data-Data Mapper (RECORD-DM) utility, the Import Data Tool (IDT), and the Add Points Tool (APT). With these improvements, users can integrate their own data with other data sources, and visualize the resulting layers of different data types (such as spatial and spectral, for simultaneous visual analysis), and visualize temporal changes in areas of interest.

Tools for Embedded Computing Systems Software

NASA Technical Reports Server (NTRS)

1978-01-01

A workshop was held to assess the state of tools for embedded systems software and to determine directions for tool development. A synopsis of the talk and the key figures of each workshop presentation, together with chairmen summaries, are presented. The presentations covered four major areas: (1) tools and the software environment (development and testing); (2) tools and software requirements, design, and specification; (3) tools and language processors; and (4) tools and verification and validation (analysis and testing). The utility and contribution of existing tools and research results for the development and testing of embedded computing systems software are described and assessed.

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.

Software Tool for Researching Annotations of Proteins (STRAP): Open-Source Protein Annotation Software with Data Visualization

PubMed Central

Bhatia, Vivek N.; Perlman, David H.; Costello, Catherine E.; McComb, Mark E.

2009-01-01

In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP) – a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP includes meta-information on the protein in addition to complimentary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger dataset. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie (biological process, cellular component and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large datasets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry data, and gene names corresponding to the proteins in the lists may be encoded in the Gaggle microformat for further characterization, including pathway analysis. STRAP, a tutorial, and the C# source code are freely available from http://cpctools.sourceforge.net. PMID:19839595

PH5: HDF5 Based Format for Integrating and Archiving Seismic Data

NASA Astrophysics Data System (ADS)

Hess, D.; Azevedo, S.; Falco, N.; Beaudoin, B. C.

2017-12-01

PH5 is a seismic data format created by IRIS PASSCAL using HDF5. Building PH5 on HDF5 allows for portability and extensibility on a scale that is unavailable in older seismic data formats. PH5 is designed to evolve to accept new data types as they become available in the future and to operate on a variety of platforms (i.e. Mac, Linux, Windows). Exemplifying PH5's flexibility is the evolution from just handling active source seismic data to now including passive source, onshore-offshore, OBS and mixed source seismic data sets. In PH5, metadata is separated from the time series data and stored in a size and performance efficient manner that also allows for easy user interaction and output of the metadata in a format appropriate for the data set. PH5's full-fledged "Kitchen Software Suite" comprises tools for data ingestion (e.g. RefTek, SEG-Y, SEG-D, SEG-2, MSEED), meta-data management, QC, waveform viewing, and data output. This software suite not only includes command line and GUI tools for interacting with PH5, it is also a comprehensive Python package to support the creation of software tools by the community to further enhance PH5. The PH5 software suite is currently being used in multiple capacities, including in-field for creating archive ready data sets as well as by the IRIS Data Management Center (DMC) to offer an FDSN compliant set of web services for serving PH5 data to the community in a variety of standard data and meta-data formats (i.e. StationXML, QuakeML, EventXML, SAC + Poles and Zeroes, MiniSEED, and SEG-Y) as well as StationTXT and ShotText formats. These web services can be accessed via standard FDSN clients such as ObsPy, irisFetch.m, FetchData, and FetchMetadata. This presentation will highlight and demonstrate the benefits of PH5 as a next generation adaptable and extensible data format for use in both archiving and working with seismic data.

Simulation Modelling in Healthcare: An Umbrella Review of Systematic Literature Reviews.

PubMed

Salleh, Syed; Thokala, Praveen; Brennan, Alan; Hughes, Ruby; Booth, Andrew

2017-09-01

Numerous studies examine simulation modelling in healthcare. These studies present a bewildering array of simulation techniques and applications, making it challenging to characterise the literature. The aim of this paper is to provide an overview of the level of activity of simulation modelling in healthcare and the key themes. We performed an umbrella review of systematic literature reviews of simulation modelling in healthcare. Searches were conducted of academic databases (JSTOR, Scopus, PubMed, IEEE, SAGE, ACM, Wiley Online Library, ScienceDirect) and grey literature sources, enhanced by citation searches. The articles were included if they performed a systematic review of simulation modelling techniques in healthcare. After quality assessment of all included articles, data were extracted on numbers of studies included in each review, types of applications, techniques used for simulation modelling, data sources and simulation software. The search strategy yielded a total of 117 potential articles. Following sifting, 37 heterogeneous reviews were included. Most reviews achieved moderate quality rating on a modified AMSTAR (A Measurement Tool used to Assess systematic Reviews) checklist. All the review articles described the types of applications used for simulation modelling; 15 reviews described techniques used for simulation modelling; three reviews described data sources used for simulation modelling; and six reviews described software used for simulation modelling. The remaining reviews either did not report or did not provide enough detail for the data to be extracted. Simulation modelling techniques have been used for a wide range of applications in healthcare, with a variety of software tools and data sources. The number of reviews published in recent years suggest an increased interest in simulation modelling in healthcare.

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

Apte, A; Veeraraghavan, H; Oh, J

Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features andmore » (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.« less

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

PubMed

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

2009-08-25

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

Critical evaluation of reverse engineering tool Imagix 4D!

PubMed

Yadav, Rashmi; Patel, Ravindra; Kothari, Abhay

2016-01-01

The comprehension of legacy codes is difficult to understand. Various commercial reengineering tools are available that have unique working styles, and are equipped with their inherent capabilities and shortcomings. The focus of the available tools is in visualizing static behavior not the dynamic one. Therefore, it is difficult for people who work in software product maintenance, code understanding reengineering/reverse engineering. Consequently, the need for a comprehensive reengineering/reverse engineering tool arises. We found the usage of Imagix 4D to be good as it generates the maximum pictorial representations in the form of flow charts, flow graphs, class diagrams, metrics and, to a partial extent, dynamic visualizations. We evaluated Imagix 4D with the help of a case study involving a few samples of source code. The behavior of the tool was analyzed on multiple small codes and a large code gcc C parser. Large code evaluation was performed to uncover dead code, unstructured code, and the effect of not including required files at preprocessing level. The utility of Imagix 4D to prepare decision density and complexity metrics for a large code was found to be useful in getting to know how much reengineering is required. At the outset, Imagix 4D offered limitations in dynamic visualizations, flow chart separation (large code) and parsing loops. The outcome of evaluation will eventually help in upgrading Imagix 4D and posed a need of full featured tools in the area of software reengineering/reverse engineering. It will also help the research community, especially those who are interested in the realm of software reengineering tool building.

A Padawan Programmer's Guide to Developing Software Libraries.

PubMed

Yurkovich, James T; Yurkovich, Benjamin J; Dräger, Andreas; Palsson, Bernhard O; King, Zachary A

2017-11-22

With the rapid adoption of computational tools in the life sciences, scientists are taking on the challenge of developing their own software libraries and releasing them for public use. This trend is being accelerated by popular technologies and platforms, such as GitHub, Jupyter, R/Shiny, that make it easier to develop scientific software and by open-source licenses that make it easier to release software. But how do you build a software library that people will use? And what characteristics do the best libraries have that make them enduringly popular? Here, we provide a reference guide, based on our own experiences, for developing software libraries along with real-world examples to help provide context for scientists who are learning about these concepts for the first time. While we can only scratch the surface of these topics, we hope that this article will act as a guide for scientists who want to write great software that is built to last. Copyright © 2017 Elsevier Inc. All rights reserved.

Agile Acceptance Test–Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software

PubMed Central

Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-01-01

Background Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test–driven development and automated regression testing promotes reliability. Test–driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a “safety net” for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and “living” design documentation. Rapid-cycle development or “agile” methods are being successfully applied to CDS development. The agile practice of automated test–driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as “executable requirements.” Objective We aimed to establish feasibility of acceptance test–driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Methods Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory’s expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. Results We used test–driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the “executable requirements” are shown prior to building the CDS alert, during build, and after successful build. Conclusions Automated acceptance test–driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test–driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. PMID:29653922

Agile Acceptance Test-Driven Development of Clinical Decision Support Advisories: Feasibility of Using Open Source Software.

PubMed

Basit, Mujeeb A; Baldwin, Krystal L; Kannan, Vaishnavi; Flahaven, Emily L; Parks, Cassandra J; Ott, Jason M; Willett, Duwayne L

2018-04-13

Moving to electronic health records (EHRs) confers substantial benefits but risks unintended consequences. Modern EHRs consist of complex software code with extensive local configurability options, which can introduce defects. Defects in clinical decision support (CDS) tools are surprisingly common. Feasible approaches to prevent and detect defects in EHR configuration, including CDS tools, are needed. In complex software systems, use of test-driven development and automated regression testing promotes reliability. Test-driven development encourages modular, testable design and expanding regression test coverage. Automated regression test suites improve software quality, providing a "safety net" for future software modifications. Each automated acceptance test serves multiple purposes, as requirements (prior to build), acceptance testing (on completion of build), regression testing (once live), and "living" design documentation. Rapid-cycle development or "agile" methods are being successfully applied to CDS development. The agile practice of automated test-driven development is not widely adopted, perhaps because most EHR software code is vendor-developed. However, key CDS advisory configuration design decisions and rules stored in the EHR may prove amenable to automated testing as "executable requirements." We aimed to establish feasibility of acceptance test-driven development of clinical decision support advisories in a commonly used EHR, using an open source automated acceptance testing framework (FitNesse). Acceptance tests were initially constructed as spreadsheet tables to facilitate clinical review. Each table specified one aspect of the CDS advisory's expected behavior. Table contents were then imported into a test suite in FitNesse, which queried the EHR database to automate testing. Tests and corresponding CDS configuration were migrated together from the development environment to production, with tests becoming part of the production regression test suite. We used test-driven development to construct a new CDS tool advising Emergency Department nurses to perform a swallowing assessment prior to administering oral medication to a patient with suspected stroke. Test tables specified desired behavior for (1) applicable clinical settings, (2) triggering action, (3) rule logic, (4) user interface, and (5) system actions in response to user input. Automated test suite results for the "executable requirements" are shown prior to building the CDS alert, during build, and after successful build. Automated acceptance test-driven development and continuous regression testing of CDS configuration in a commercial EHR proves feasible with open source software. Automated test-driven development offers one potential contribution to achieving high-reliability EHR configuration. Vetting acceptance tests with clinicians elicits their input on crucial configuration details early during initial CDS design and iteratively during rapid-cycle optimization. ©Mujeeb A Basit, Krystal L Baldwin, Vaishnavi Kannan, Emily L Flahaven, Cassandra J Parks, Jason M Ott, Duwayne L Willett. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.04.2018.

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

DOE PAGES

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

2017-03-27

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

ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments.

PubMed

Khan, Imtiaz A; Fraser, Adam; Bray, Mark-Anthony; Smith, Paul J; White, Nick S; Carpenter, Anne E; Errington, Rachel J

2014-12-01

Experimental reproducibility is fundamental to the progress of science. Irreproducible research decreases the efficiency of basic biological research and drug discovery and impedes experimental data reuse. A major contributing factor to irreproducibility is difficulty in interpreting complex experimental methodologies and designs from written text and in assessing variations among different experiments. Current bioinformatics initiatives either are focused on computational research reproducibility (i.e. data analysis) or laboratory information management systems. Here, we present a software tool, ProtocolNavigator, which addresses the largely overlooked challenges of interpretation and assessment. It provides a biologist-friendly open-source emulation-based tool for designing, documenting and reproducing biological experiments. ProtocolNavigator was implemented in Python 2.7, using the wx module to build the graphical user interface. It is a platform-independent software and freely available from http://protocolnavigator.org/index.html under the GPL v2 license. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

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

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

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

Embedded systems for supporting computer accessibility.

PubMed

Mulfari, Davide; Celesti, Antonio; Fazio, Maria; Villari, Massimo; Puliafito, Antonio

2015-01-01

Nowadays, customized AT software solutions allow their users to interact with various kinds of computer systems. Such tools are generally available on personal devices (e.g., smartphones, laptops and so on) commonly used by a person with a disability. In this paper, we investigate a way of using the aforementioned AT equipments in order to access many different devices without assistive preferences. The solution takes advantage of open source hardware and its core component consists of an affordable Linux embedded system: it grabs data coming from the assistive software, which runs on the user's personal device, then, after processing, it generates native keyboard and mouse HID commands for the target computing device controlled by the end user. This process supports any operating system available on the target machine and it requires no specialized software installation; therefore the user with a disability can rely on a single assistive tool to control a wide range of computing platforms, including conventional computers and many kinds of mobile devices, which receive input commands through the USB HID protocol.

Vulnerabilities in GSM technology and feasibility of selected attacks

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

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

PubMed

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

2017-06-28

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

Rapid development of medical imaging tools with open-source libraries.

PubMed

Caban, Jesus J; Joshi, Alark; Nagy, Paul

2007-11-01

Rapid prototyping is an important element in researching new imaging analysis techniques and developing custom medical applications. In the last ten years, the open source community and the number of open source libraries and freely available frameworks for biomedical research have grown significantly. What they offer are now considered standards in medical image analysis, computer-aided diagnosis, and medical visualization. A cursory review of the peer-reviewed literature in imaging informatics (indeed, in almost any information technology-dependent scientific discipline) indicates the current reliance on open source libraries to accelerate development and validation of processes and techniques. In this survey paper, we review and compare a few of the most successful open source libraries and frameworks for medical application development. Our dual intentions are to provide evidence that these approaches already constitute a vital and essential part of medical image analysis, diagnosis, and visualization and to motivate the reader to use open source libraries and software for rapid prototyping of medical applications and tools.

A multimedia perioperative record keeper for clinical research.

PubMed

Perrino, A C; Luther, M A; Phillips, D B; Levin, F L

1996-05-01

To develop a multimedia perioperative recordkeeper that provides: 1. synchronous, real-time acquisition of multimedia data, 2. on-line access to the patient's chart data, and 3. advanced data analysis capabilities through integrated, multimedia database and analysis applications. To minimize cost and development time, the system design utilized industry standard hardware components and graphical. software development tools. The system was configured to use a Pentium PC complemented with a variety of hardware interfaces to external data sources. These sources included physiologic monitors with data in digital, analog, video, and audio as well as paper-based formats. The development process was guided by trials in over 80 clinical cases and by the critiques from numerous users. As a result of this process, a suite of custom software applications were created to meet the design goals. The Perioperative Data Acquisition application manages data collection from a variety of physiological monitors. The Charter application provides for rapid creation of an electronic medical record from the patient's paper-based chart and investigator's notes. The Multimedia Medical Database application provides a relational database for the organization and management of multimedia data. The Triscreen application provides an integrated data analysis environment with simultaneous, full-motion data display. With recent technological advances in PC power, data acquisition hardware, and software development tools, the clinical researcher now has the ability to collect and examine a more complete perioperative record. It is hoped that the description of the MPR and its development process will assist and encourage others to advance these tools for perioperative research.

Software risk management through independent verification and validation

NASA Technical Reports Server (NTRS)

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

1995-01-01

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

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

PubMed Central

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

2018-01-01

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

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology.

PubMed

Mariano, Diego C B; Pereira, Felipe L; Aguiar, Edgar L; Oliveira, Letícia C; Benevides, Leandro; Guimarães, Luís C; Folador, Edson L; Sousa, Thiago J; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique C P; Silva, Artur; Ramos, Rommel T J; Azevedo, Vasco A C

2016-12-15

The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net .

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

PubMed

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

2018-01-31

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

PolNet: A Tool to Quantify Network-Level Cell Polarity and Blood Flow in Vascular Remodeling.

PubMed

Bernabeu, Miguel O; Jones, Martin L; Nash, Rupert W; Pezzarossa, Anna; Coveney, Peter V; Gerhardt, Holger; Franco, Claudio A

2018-05-08

In this article, we present PolNet, an open-source software tool for the study of blood flow and cell-level biological activity during vessel morphogenesis. We provide an image acquisition, segmentation, and analysis protocol to quantify endothelial cell polarity in entire in vivo vascular networks. In combination, we use computational fluid dynamics to characterize the hemodynamics of the vascular networks under study. The tool enables, to our knowledge for the first time, a network-level analysis of polarity and flow for individual endothelial cells. To date, PolNet has proven invaluable for the study of endothelial cell polarization and migration during vascular patterning, as demonstrated by two recent publications. Additionally, the tool can be easily extended to correlate blood flow with other experimental observations at the cellular/molecular level. We release the source code of our tool under the Lesser General Public License. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

NASA Technical Reports Server (NTRS)

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

1985-01-01

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

Debugging and Performance Analysis Software Tools for Peregrine System |

Science.gov Websites

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

Support for Systematic Code Reviews with the SCRUB Tool

NASA Technical Reports Server (NTRS)

Holzmann, Gerald J.

2010-01-01

SCRUB is a code review tool that supports both large, team-based software development efforts (e.g., for mission software) as well as individual tasks. The tool was developed at JPL to support a new, streamlined code review process that combines human-generated review reports with program-generated review reports from a customizable range of state-of-the-art source code analyzers. The leading commercial tools include Codesonar, Coverity, and Klocwork, each of which can achieve a reasonably low rate of false-positives in the warnings that they generate. The time required to analyze code with these tools can vary greatly. In each case, however, the tools produce results that would be difficult to realize with human code inspections alone. There is little overlap in the results produced by the different analyzers, and each analyzer used generally increases the effectiveness of the overall effort. The SCRUB tool allows all reports to be accessed through a single, uniform interface (see figure) that facilitates brows ing code and reports. Improvements over existing software include significant simplification, and leveraging of a range of commercial, static source code analyzers in a single, uniform framework. The tool runs as a small stand-alone application, avoiding the security problems related to tools based on Web browsers. A developer or reviewer, for instance, must have already obtained access rights to a code base before that code can be browsed and reviewed with the SCRUB tool. The tool cannot open any files or folders to which the user does not already have access. This means that the tool does not need to enforce or administer any additional security policies. The analysis results presented through the SCRUB tool s user interface are always computed off-line, given that, especially for larger projects, this computation can take longer than appropriate for interactive tool use. The recommended code review process that is supported by the SCRUB tool consists of three phases: Code Review, Developer Response, and Closeout Resolution. In the Code Review phase, all tool-based analysis reports are generated, and specific comments from expert code reviewers are entered into the SCRUB tool. In the second phase, Developer Response, the developer is asked to respond to each comment and tool-report that was produced, either agreeing or disagreeing to provide a fix that addresses the issue that was raised. In the third phase, Closeout Resolution, all disagreements are discussed in a meeting of all parties involved, and a resolution is made for all disagreements. The first two phases generally take one week each, and the third phase is concluded in a single closeout meeting.

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

PubMed

Davoodi, Rahman; Loeb, Gerald E

2012-03-01

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

Open Source Clinical NLP – More than Any Single System

PubMed Central

Masanz, James; Pakhomov, Serguei V.; Xu, Hua; Wu, Stephen T.; Chute, Christopher G.; Liu, Hongfang

2014-01-01

The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP’s mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice. PMID:25954581

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

PubMed

Maguire, Eamonn; González-Beltrán, Alejandra; Whetzel, Patricia L; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2013-02-15

Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.

pyam: Python Implementation of YaM

NASA Technical Reports Server (NTRS)

Myint, Steven; Jain, Abhinandan

2012-01-01

pyam is a software development framework with tools for facilitating the rapid development of software in a concurrent software development environment. pyam provides solutions for development challenges associated with software reuse, managing multiple software configurations, developing software product lines, and multiple platform development and build management. pyam uses release-early, release-often development cycles to allow developers to integrate their changes incrementally into the system on a continual basis. It facilitates the creation and merging of branches to support the isolated development of immature software to avoid impacting the stability of the development effort. It uses modules and packages to organize and share software across multiple software products, and uses the concepts of link and work modules to reduce sandbox setup times even when the code-base is large. One sidebenefit is the enforcement of a strong module-level encapsulation of a module s functionality and interface. This increases design transparency, system stability, and software reuse. pyam is written in Python and is organized as a set of utilities on top of the open source SVN software version control package. All development software is organized into a collection of modules. pyam packages are defined as sub-collections of the available modules. Developers can set up private sandboxes for module/package development. All module/package development takes place on private SVN branches. High-level pyam commands support the setup, update, and release of modules and packages. Released and pre-built versions of modules are available to developers. Developers can tailor the source/link module mix for their sandboxes so that new sandboxes (even large ones) can be built up easily and quickly by pointing to pre-existing module releases. All inter-module interfaces are publicly exported via links. A minimal, but uniform, convention is used for building modules.

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

General Mission Analysis Tool (GMAT): Mission, Vision, and Business Case

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

The Goal of the GMAT project is to develop new space trajectory optimization and mission design technology by working inclusively with ordinary people, universities businesses and other government organizations; and to share that technology in an open and unhindered way. GMAT's a free and open source software system; free for anyone to use in development of new mission concepts or to improve current missions, freely available in source code form for enhancement or future technology development.

Towards open-source, low-cost haptics for surgery simulation.

PubMed

Suwelack, Stefan; Sander, Christian; Schill, Julian; Serf, Manuel; Danz, Marcel; Asfour, Tamim; Burger, Wolfgang; Dillmann, Rüdiger; Speidel, Stefanie

2014-01-01

In minimally invasive surgery (MIS), virtual reality (VR) training systems have become a promising education tool. However, the adoption of these systems in research and clinical settings is still limited by the high costs of dedicated haptics hardware for MIS. In this paper, we present ongoing research towards an open-source, low-cost haptic interface for MIS simulation. We demonstrate the basic mechanical design of the device, the sensor setup as well as its software integration.

Friendly Extensible Transfer Tool Beta Version

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

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

2016-04-15

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

GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.

PubMed

Madec, Morgan; Pecheux, François; Gendrault, Yves; Rosati, Elise; Lallement, Christophe; Haiech, Jacques

2016-10-01

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.

Building Automatic Grading Tools for Basic of Programming Lab in an Academic Institution

NASA Astrophysics Data System (ADS)

Harimurti, Rina; Iwan Nurhidayat, Andi; Asmunin

2018-04-01

The skills of computer programming is a core competency that must be mastered by students majoring in computer sciences. The best way to improve this skill is through the practice of writing many programs to solve various problems from simple to complex. It takes hard work and a long time to check and evaluate the results of student labs one by one, especially if the number of students a lot. Based on these constrain, web proposes Automatic Grading Tools (AGT), the application that can evaluate and deeply check the source code in C, C++. The application architecture consists of students, web-based applications, compilers, and operating systems. Automatic Grading Tools (AGT) is implemented MVC Architecture and using open source software, such as laravel framework version 5.4, PostgreSQL 9.6, Bootstrap 3.3.7, and jquery library. Automatic Grading Tools has also been tested for real problems by submitting source code in C/C++ language and then compiling. The test results show that the AGT application has been running well.

Tool Support for Software Lookup Table Optimization

DOE PAGES

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

2011-01-01

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

Control and Information Systems for the National Ignition Facility

DOE PAGES

Brunton, Gordon; Casey, Allan; Christensen, Marvin; ...

2017-03-23

Orchestration of every National Ignition Facility (NIF) shot cycle is managed by the Integrated Computer Control System (ICCS), which uses a scalable software architecture running code on more than 1950 front-end processors, embedded controllers, and supervisory servers. The ICCS operates laser and industrial control hardware containing 66 000 control and monitor points to ensure that all of NIF’s laser beams arrive at the target within 30 ps of each other and are aligned to a pointing accuracy of less than 50 μm root-mean-square, while ensuring that a host of diagnostic instruments record data in a few billionths of a second.more » NIF’s automated control subsystems are built from a common object-oriented software framework that distributes the software across the computer network and achieves interoperation between different software languages and target architectures. A large suite of business and scientific software tools supports experimental planning, experimental setup, facility configuration, and post-shot analysis. Standard business services using open-source software, commercial workflow tools, and database and messaging technologies have been developed. An information technology infrastructure consisting of servers, network devices, and storage provides the foundation for these systems. Thus, this work is an overview of the control and information systems used to support a wide variety of experiments during the National Ignition Campaign.« less

Control and Information Systems for the National Ignition Facility

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

Brunton, Gordon; Casey, Allan; Christensen, Marvin

Orchestration of every National Ignition Facility (NIF) shot cycle is managed by the Integrated Computer Control System (ICCS), which uses a scalable software architecture running code on more than 1950 front-end processors, embedded controllers, and supervisory servers. The ICCS operates laser and industrial control hardware containing 66 000 control and monitor points to ensure that all of NIF’s laser beams arrive at the target within 30 ps of each other and are aligned to a pointing accuracy of less than 50 μm root-mean-square, while ensuring that a host of diagnostic instruments record data in a few billionths of a second.more » NIF’s automated control subsystems are built from a common object-oriented software framework that distributes the software across the computer network and achieves interoperation between different software languages and target architectures. A large suite of business and scientific software tools supports experimental planning, experimental setup, facility configuration, and post-shot analysis. Standard business services using open-source software, commercial workflow tools, and database and messaging technologies have been developed. An information technology infrastructure consisting of servers, network devices, and storage provides the foundation for these systems. Thus, this work is an overview of the control and information systems used to support a wide variety of experiments during the National Ignition Campaign.« less

The Human Exposure Model (HEM): A Tool to Support Rapid Assessment of Human Health Impacts from Near-Field Consumer Product Exposures

EPA Science Inventory

The US EPA is developing an open and publically available software program called the Human Exposure Model (HEM) to provide near-field exposure information for Life Cycle Impact Assessments (LCIAs). Historically, LCIAs have often omitted impacts from near-field sources of exposur...

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

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

ERIC Educational Resources Information Center

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

2013-01-01

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

BATSE spectroscopy analysis system

NASA Technical Reports Server (NTRS)

Schaefer, Bradley E.; Bansal, Sandhia; Basu, Anju; Brisco, Phil; Cline, Thomas L.; Friend, Elliott; Laubenthal, Nancy; Panduranga, E. S.; Parkar, Nuru; Rust, Brad

1992-01-01

The Burst and Transient Source Experiment (BATSE) Spectroscopy Analysis System (BSAS) is the software system which is the primary tool for the analysis of spectral data from BATSE. As such, Guest Investigators and the community as a whole need to know its basic properties and characteristics. Described here are the characteristics of the BATSE spectroscopy detectors and the BSAS.

CellProfiler Tracer: exploring and validating high-throughput, time-lapse microscopy image data.

PubMed

Bray, Mark-Anthony; Carpenter, Anne E

2015-11-04

Time-lapse analysis of cellular images is an important and growing need in biology. Algorithms for cell tracking are widely available; what researchers have been missing is a single open-source software package to visualize standard tracking output (from software like CellProfiler) in a way that allows convenient assessment of track quality, especially for researchers tuning tracking parameters for high-content time-lapse experiments. This makes quality assessment and algorithm adjustment a substantial challenge, particularly when dealing with hundreds of time-lapse movies collected in a high-throughput manner. We present CellProfiler Tracer, a free and open-source tool that complements the object tracking functionality of the CellProfiler biological image analysis package. Tracer allows multi-parametric morphological data to be visualized on object tracks, providing visualizations that have already been validated within the scientific community for time-lapse experiments, and combining them with simple graph-based measures for highlighting possible tracking artifacts. CellProfiler Tracer is a useful, free tool for inspection and quality control of object tracking data, available from http://www.cellprofiler.org/tracer/.

The New Meteor Radar at Penn State: Design and First Observations

NASA Technical Reports Server (NTRS)

Urbina, J.; Seal, R.; Dyrud, L.

2011-01-01

In an effort to provide new and improved meteor radar sensing capabilities, Penn State has been developing advanced instruments and technologies for future meteor radars, with primary objectives of making such instruments more capable and more cost effective in order to study the basic properties of the global meteor flux, such as average mass, velocity, and chemical composition. Using low-cost field programmable gate arrays (FPGAs), combined with open source software tools, we describe a design methodology enabling one to develop state-of-the art radar instrumentation, by developing a generalized instrumentation core that can be customized using specialized output stage hardware. Furthermore, using object-oriented programming (OOP) techniques and open-source tools, we illustrate a technique to provide a cost-effective, generalized software framework to uniquely define an instrument s functionality through a customizable interface, implemented by the designer. The new instrument is intended to provide instantaneous profiles of atmospheric parameters and climatology on a daily basis throughout the year. An overview of the instrument design concepts and some of the emerging technologies developed for this meteor radar are presented.

Self-service for software development projects and HPC activities

NASA Astrophysics Data System (ADS)

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

2014-05-01

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

The Earth System Documentation (ES-DOC) Software Process

NASA Astrophysics Data System (ADS)

Greenslade, M. A.; Murphy, S.; Treshansky, A.; DeLuca, C.; Guilyardi, E.; Denvil, S.

2013-12-01

Earth System Documentation (ES-DOC) is an international project supplying high-quality tools & services in support of earth system documentation creation, analysis and dissemination. It is nurturing a sustainable standards based documentation eco-system that aims to become an integral part of the next generation of exa-scale dataset archives. ES-DOC leverages open source software, and applies a software development methodology that places end-user narratives at the heart of all it does. ES-DOC has initially focused upon nurturing the Earth System Model (ESM) documentation eco-system and currently supporting the following projects: * Coupled Model Inter-comparison Project Phase 5 (CMIP5); * Dynamical Core Model Inter-comparison Project (DCMIP); * National Climate Predictions and Projections Platforms Quantitative Evaluation of Downscaling Workshop. This talk will demonstrate that ES-DOC implements a relatively mature software development process. Taking a pragmatic Agile process as inspiration, ES-DOC: * Iteratively develops and releases working software; * Captures user requirements via a narrative based approach; * Uses online collaboration tools (e.g. Earth System CoG) to manage progress; * Prototypes applications to validate their feasibility; * Leverages meta-programming techniques where appropriate; * Automates testing whenever sensibly feasible; * Streamlines complex deployments to a single command; * Extensively leverages GitHub and Pivotal Tracker; * Enforces strict separation of the UI from underlying API's; * Conducts code reviews.

GMODWeb: a web framework for the generic model organism database

PubMed Central

O'Connor, Brian D; Day, Allen; Cain, Scott; Arnaiz, Olivier; Sperling, Linda; Stein, Lincoln D

2008-01-01

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from . PMID:18570664

BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments

DOE PAGES

Thomas, Brandon R.; Chylek, Lily A.; Colvin, Joshua; ...

2015-11-09

Rule-based models are analyzed with specialized simulators, such as those provided by the BioNetGen and NFsim open-source software packages. Here in this paper, we present BioNetFit, a general-purpose fitting tool that is compatible with BioNetGen and NFsim. BioNetFit is designed to take advantage of distributed computing resources. This feature facilitates fitting (i.e. optimization of parameter values for consistency with data) when simulations are computationally expensive.

The Geoinformatica free and open source software stack

NASA Astrophysics Data System (ADS)

Jolma, A.

2012-04-01

The Geoinformatica free and open source software (FOSS) stack is based mainly on three established FOSS components, namely GDAL, GTK+, and Perl. GDAL provides access to a very large selection of geospatial data formats and data sources, a generic geospatial data model, and a large collection of geospatial analytical and processing functionality. GTK+ and the Cairo graphics library provide generic graphics and graphical user interface capabilities. Perl is a programming language, for which there is a very large set of FOSS modules for a wide range of purposes and which can be used as an integrative tool for building applications. In the Geoinformatica stack, data storages such as FOSS RDBMS PostgreSQL with its geospatial extension PostGIS can be used below the three above mentioned components. The top layer of Geoinformatica consists of a C library and several Perl modules. The C library comprises a general purpose raster algebra library, hydrological terrain analysis functions, and visualization code. The Perl modules define a generic visualized geospatial data layer and subclasses for raster and vector data and graphs. The hydrological terrain functions are already rather old and they suffer for example from the requirement of in-memory rasters. Newer research conducted using the platform include basic geospatial simulation modeling, visualization of ecological data, linking with a Bayesian network engine for spatial risk assessment in coastal areas, and developing standards-based distributed water resources information systems in Internet. The Geoinformatica stack constitutes a platform for geospatial research, which is targeted towards custom analytical tools, prototyping and linking with external libraries. Writing custom analytical tools is supported by the Perl language and the large collection of tools that are available especially in GDAL and Perl modules. Prototyping is supported by the GTK+ library, the GUI tools, and the support for object-oriented programming in Perl. New feature types, geospatial layer classes, and tools as extensions with specific features can be defined, used, and studied. Linking with external libraries is possible using the Perl foreign function interface tools or with generic tools such as Swig. We are interested in implementing and testing linking Geoinformatica with existing or new more specific hydrological FOSS.

Building Interactive Visualizations for Geochronological Data

NASA Astrophysics Data System (ADS)

Zeringue, J.; Bowring, J. F.; McLean, N. M.; Pastor, F.

2014-12-01

Since the early 1990s, Ken Ludwig's Isoplot software has been the tool of choice for visualization and analysis of isotopic data used for geochronology. The software is an add-in to Microsoft Excel that allows users to generate visual representations of data. However, recent changes to Excel have made Isoplot more difficult to use and maintain, and the software is no longer supported. In the last several years, the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES), at the College of Charleston, has worked collaboratively with geochronologists to develop U-Pb_Redux, a software product that provides some of Isoplot's functionality for U-Pb geochronology. However, the community needs a full and complete Isoplot replacement that is open source, platform independent, and not dependent on proprietary software. This temporary lapse in tooling also presents a tremendous opportunity for scientific computing in the earth sciences. When Isoplot was written for Excel, it gained much of the platform's flexibility and power but also was burdened with its limitations. For example, Isoplot could not be used outside of Excel, could not be cross-platform (so long as Excel wasn't), could not be embedded in other applications, and only static images could be produced. Nonetheless this software was and still is a powerful tool that has served the community for more than two decades and the trade-offs were more than acceptable. In 2014, we seek to gain flexibility not available with Excel. We propose that the next generation of charting software be reusable, platform-agnostic, and interactive. This new software should allow scientists to easily explore—not just passively view—their data. Beginning in the fall of 2013, researchers at CIRDLES began planning for and prototyping a 21st-century replacement for Isoplot, which we call Topsoil, an anagram of Isoplot. This work is being conducted in the public domain at https://github.com/CIRDLES/topsoil. We welcome and encourage community participation and contributions.

Development of a comprehensive software engineering environment

NASA Technical Reports Server (NTRS)

Hartrum, Thomas C.; Lamont, Gary B.

1987-01-01

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

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

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

PubMed Central

2011-01-01

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

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

PubMed

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

2011-05-17

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

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

PubMed

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

2012-04-05

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

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

PubMed Central

2012-01-01

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

The Automated Instrumentation and Monitoring System (AIMS): Design and Architecture. 3.2

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Schmidt, Melisa; Schulbach, Cathy; Bailey, David (Technical Monitor)

1997-01-01

Whether a researcher is designing the 'next parallel programming paradigm', another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of such information can help computer and software architects to capture, and therefore, exploit behavioral variations among/within various parallel programs to take advantage of specific hardware characteristics. A software tool-set that facilitates performance evaluation of parallel applications on multiprocessors has been put together at NASA Ames Research Center under the sponsorship of NASA's High Performance Computing and Communications Program over the past five years. The Automated Instrumentation and Monitoring Systematic has three major software components: a source code instrumentor which automatically inserts active event recorders into program source code before compilation; a run-time performance monitoring library which collects performance data; and a visualization tool-set which reconstructs program execution based on the data collected. Besides being used as a prototype for developing new techniques for instrumenting, monitoring and presenting parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Currently, the execution of FORTRAN and C programs on the Intel Paragon and PALM workstations can be automatically instrumented and monitored. Performance data thus collected can be displayed graphically on various workstations. The process of performance tuning with AIMS will be illustrated using various NAB Parallel Benchmarks. This report includes a description of the internal architecture of AIMS and a listing of the source code.

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

Gabriele, Fatuzzo; Michele, Mangiameli, E-mail: amichele.mangiameli@dica.unict.it; Giuseppe, Mussumeci

The laser scanning is a technology that allows in a short time to run the relief geometric objects with a high level of detail and completeness, based on the signal emitted by the laser and the corresponding return signal. When the incident laser radiation hits the object to detect, then the radiation is reflected. The purpose is to build a three-dimensional digital model that allows to reconstruct the reality of the object and to conduct studies regarding the design, restoration and/or conservation. When the laser scanner is equipped with a digital camera, the result of the measurement process is amore » set of points in XYZ coordinates showing a high density and accuracy with radiometric and RGB tones. In this case, the set of measured points is called “point cloud” and allows the reconstruction of the Digital Surface Model. Even the post-processing is usually performed by closed source software, which is characterized by Copyright restricting the free use, free and open source software can increase the performance by far. Indeed, this latter can be freely used providing the possibility to display and even custom the source code. The experience started at the Faculty of Engineering in Catania is aimed at finding a valuable free and open source tool, MeshLab (Italian Software for data processing), to be compared with a reference closed source software for data processing, i.e. RapidForm. In this work, we compare the results obtained with MeshLab and Rapidform through the planning of the survey and the acquisition of the point cloud of a morphologically complex statue.« less

Evolving software reengineering technology for the emerging innovative-competitive era

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

Design pattern mining using distributed learning automata and DNA sequence alignment.

PubMed

Esmaeilpour, Mansour; Naderifar, Vahideh; Shukur, Zarina

2014-01-01

Over the last decade, design patterns have been used extensively to generate reusable solutions to frequently encountered problems in software engineering and object oriented programming. A design pattern is a repeatable software design solution that provides a template for solving various instances of a general problem. This paper describes a new method for pattern mining, isolating design patterns and relationship between them; and a related tool, DLA-DNA for all implemented pattern and all projects used for evaluation. DLA-DNA achieves acceptable precision and recall instead of other evaluated tools based on distributed learning automata (DLA) and deoxyribonucleic acid (DNA) sequences alignment. The proposed method mines structural design patterns in the object oriented source code and extracts the strong and weak relationships between them, enabling analyzers and programmers to determine the dependency rate of each object, component, and other section of the code for parameter passing and modular programming. The proposed model can detect design patterns better that available other tools those are Pinot, PTIDEJ and DPJF; and the strengths of their relationships. The result demonstrate that whenever the source code is build standard and non-standard, based on the design patterns, then the result of the proposed method is near to DPJF and better that Pinot and PTIDEJ. The proposed model is tested on the several source codes and is compared with other related models and available tools those the results show the precision and recall of the proposed method, averagely 20% and 9.6% are more than Pinot, 27% and 31% are more than PTIDEJ and 3.3% and 2% are more than DPJF respectively. The primary idea of the proposed method is organized in two following steps: the first step, elemental design patterns are identified, while at the second step, is composed to recognize actual design patterns.

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

PubMed

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

2010-06-01

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

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

PubMed Central

Solernou, Albert

2018-01-01

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

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

PubMed

Ranke, Johannes; Wöltjen, Janina; Meinecke, Stefan

2018-01-01

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

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

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

A 3D interactive multi-object segmentation tool using local robust statistics driven active contours.

PubMed

Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, Allen

2012-08-01

Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. In the past, much work has been dedicated only to the algorithmic development. Nevertheless, for clinical end users, a well designed algorithm with an interactive software is necessary for an algorithm to be utilized in their daily work. Furthermore, the software would better be open sourced in order to be used and validated by not only the authors but also the entire community. Therefore, the contribution of the present work is twofolds: first, we propose a new robust statistics based conformal metric and the conformal area driven multiple active contour framework, to simultaneously extract multiple targets from MR and CT medical imagery in 3D. Second, an open source graphically interactive 3D segmentation tool based on the aforementioned contour evolution is implemented and is publicly available for end users on multiple platforms. In using this software for the segmentation task, the process is initiated by the user drawn strokes (seeds) in the target region in the image. Then, the local robust statistics are used to describe the object features, and such features are learned adaptively from the seeds under a non-parametric estimation scheme. Subsequently, several active contours evolve simultaneously with their interactions being motivated by the principles of action and reaction-this not only guarantees mutual exclusiveness among the contours, but also no longer relies upon the assumption that the multiple objects fill the entire image domain, which was tacitly or explicitly assumed in many previous works. In doing so, the contours interact and converge to equilibrium at the desired positions of the desired multiple objects. Furthermore, with the aim of not only validating the algorithm and the software, but also demonstrating how the tool is to be used, we provide the reader reproducible experiments that demonstrate the capability of the proposed segmentation tool on several public available data sets. Copyright © 2012 Elsevier B.V. All rights reserved.

A 3D Interactive Multi-object Segmentation Tool using Local Robust Statistics Driven Active Contours

PubMed Central

Gao, Yi; Kikinis, Ron; Bouix, Sylvain; Shenton, Martha; Tannenbaum, Allen

2012-01-01

Extracting anatomical and functional significant structures renders one of the important tasks for both the theoretical study of the medical image analysis, and the clinical and practical community. In the past, much work has been dedicated only to the algorithmic development. Nevertheless, for clinical end users, a well designed algorithm with an interactive software is necessary for an algorithm to be utilized in their daily work. Furthermore, the software would better be open sourced in order to be used and validated by not only the authors but also the entire community. Therefore, the contribution of the present work is twofolds: First, we propose a new robust statistics based conformal metric and the conformal area driven multiple active contour framework, to simultaneously extract multiple targets from MR and CT medical imagery in 3D. Second, an open source graphically interactive 3D segmentation tool based on the aforementioned contour evolution is implemented and is publicly available for end users on multiple platforms. In using this software for the segmentation task, the process is initiated by the user drawn strokes (seeds) in the target region in the image. Then, the local robust statistics are used to describe the object features, and such features are learned adaptively from the seeds under a non-parametric estimation scheme. Subsequently, several active contours evolve simultaneously with their interactions being motivated by the principles of action and reaction — This not only guarantees mutual exclusiveness among the contours, but also no longer relies upon the assumption that the multiple objects fill the entire image domain, which was tacitly or explicitly assumed in many previous works. In doing so, the contours interact and converge to equilibrium at the desired positions of the desired multiple objects. Furthermore, with the aim of not only validating the algorithm and the software, but also demonstrating how the tool is to be used, we provide the reader reproducible experiments that demonstrate the capability of the proposed segmentation tool on several public available data sets. PMID:22831773

Fault Tree Analysis Application for Safety and Reliability

NASA Technical Reports Server (NTRS)

Wallace, Dolores R.

2003-01-01

Many commercial software tools exist for fault tree analysis (FTA), an accepted method for mitigating risk in systems. The method embedded in the tools identifies a root as use in system components, but when software is identified as a root cause, it does not build trees into the software component. No commercial software tools have been built specifically for development and analysis of software fault trees. Research indicates that the methods of FTA could be applied to software, but the method is not practical without automated tool support. With appropriate automated tool support, software fault tree analysis (SFTA) may be a practical technique for identifying the underlying cause of software faults that may lead to critical system failures. We strive to demonstrate that existing commercial tools for FTA can be adapted for use with SFTA, and that applied to a safety-critical system, SFTA can be used to identify serious potential problems long before integrator and system testing.

Open source tracking and analysis of adult Drosophila locomotion in Buridan's paradigm with and without visual targets.

PubMed

Colomb, Julien; Reiter, Lutz; Blaszkiewicz, Jedrzej; Wessnitzer, Jan; Brembs, Bjoern

2012-01-01

Insects have been among the most widely used model systems for studying the control of locomotion by nervous systems. In Drosophila, we implemented a simple test for locomotion: in Buridan's paradigm, flies walk back and forth between two inaccessible visual targets [1]. Until today, the lack of easily accessible tools for tracking the fly position and analyzing its trajectory has probably contributed to the slow acceptance of Buridan's paradigm. We present here a package of open source software designed to track a single animal walking in a homogenous environment (Buritrack) and to analyze its trajectory. The Centroid Trajectory Analysis (CeTrAn) software is coded in the open source statistics project R. It extracts eleven metrics and includes correlation analyses and a Principal Components Analysis (PCA). It was designed to be easily customized to personal requirements. In combination with inexpensive hardware, these tools can readily be used for teaching and research purposes. We demonstrate the capabilities of our package by measuring the locomotor behavior of adult Drosophila melanogaster (whose wings were clipped), either in the presence or in the absence of visual targets, and comparing the latter to different computer-generated data. The analysis of the trajectories confirms that flies are centrophobic and shows that inaccessible visual targets can alter the orientation of the flies without changing their overall patterns of activity. Using computer generated data, the analysis software was tested, and chance values for some metrics (as well as chance value for their correlation) were set. Our results prompt the hypothesis that fixation behavior is observed only if negative phototaxis can overcome the propensity of the flies to avoid the center of the platform. Together with our companion paper, we provide new tools to promote Open Science as well as the collection and analysis of digital behavioral data.

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

PubMed

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

2015-11-01

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

Rocker: Open source, easy-to-use tool for AUC and enrichment calculations and ROC visualization.

PubMed

Lätti, Sakari; Niinivehmas, Sanna; Pentikäinen, Olli T

2016-01-01

Receiver operating characteristics (ROC) curve with the calculation of area under curve (AUC) is a useful tool to evaluate the performance of biomedical and chemoinformatics data. For example, in virtual drug screening ROC curves are very often used to visualize the efficiency of the used application to separate active ligands from inactive molecules. Unfortunately, most of the available tools for ROC analysis are implemented into commercially available software packages, or are plugins in statistical software, which are not always the easiest to use. Here, we present Rocker, a simple ROC curve visualization tool that can be used for the generation of publication quality images. Rocker also includes an automatic calculation of the AUC for the ROC curve and Boltzmann-enhanced discrimination of ROC (BEDROC). Furthermore, in virtual screening campaigns it is often important to understand the early enrichment of active ligand identification, for this Rocker offers automated calculation routine. To enable further development of Rocker, it is freely available (MIT-GPL license) for use and modifications from our web-site (http://www.jyu.fi/rocker).

CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.