The Intelligence Problem of Policymakers in Counterinsurgency: Asking And Answering the Right Questions

DTIC Science & Technology

2013-12-01

explosive device ISR intelligence, surveillance and reconnaissance J2 joint staff intelligence section NATO North Atlantic Treaty Organization OSINT open...commonly referring to the technical means of collection to the exclusion of HUMINT, open source intelligence ( OSINT ), and other information coming...is using to gain popular support or to delegitimize the supported government. The 10th Mountain Division determined OSINT was an important component

Digital Textbooks. Research Brief

ERIC Educational Resources Information Center

Johnston, Howard

2011-01-01

Despite their growing popularity, digital alternatives to conventional textbooks are stirring up controversy. With the introduction of tablet computers, and the growing trend toward "cloud computing" and "open source" software, the trend is accelerating because costs are coming down and free or inexpensive materials are becoming more available.…

psiTurk: An open-source framework for conducting replicable behavioral experiments online.

PubMed

Gureckis, Todd M; Martin, Jay; McDonnell, John; Rich, Alexander S; Markant, Doug; Coenen, Anna; Halpern, David; Hamrick, Jessica B; Chan, Patricia

2016-09-01

Online data collection has begun to revolutionize the behavioral sciences. However, conducting carefully controlled behavioral experiments online introduces a number of new of technical and scientific challenges. The project described in this paper, psiTurk, is an open-source platform which helps researchers develop experiment designs which can be conducted over the Internet. The tool primarily interfaces with Amazon's Mechanical Turk, a popular crowd-sourcing labor market. This paper describes the basic architecture of the system and introduces new users to the overall goals. psiTurk aims to reduce the technical hurdles for researchers developing online experiments while improving the transparency and collaborative nature of the behavioral sciences.

DeNovoGUI: An Open Source Graphical User Interface for de Novo Sequencing of Tandem Mass Spectra

PubMed Central

2013-01-01

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com. PMID:24295440

DeNovoGUI: an open source graphical user interface for de novo sequencing of tandem mass spectra.

PubMed

Muth, Thilo; Weilnböck, Lisa; Rapp, Erdmann; Huber, Christian G; Martens, Lennart; Vaudel, Marc; Barsnes, Harald

2014-02-07

De novo sequencing is a popular technique in proteomics for identifying peptides from tandem mass spectra without having to rely on a protein sequence database. Despite the strong potential of de novo sequencing algorithms, their adoption threshold remains quite high. We here present a user-friendly and lightweight graphical user interface called DeNovoGUI for running parallelized versions of the freely available de novo sequencing software PepNovo+, greatly simplifying the use of de novo sequencing in proteomics. Our platform-independent software is freely available under the permissible Apache2 open source license. Source code, binaries, and additional documentation are available at http://denovogui.googlecode.com .

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

Mousetrap: An integrated, open-source mouse-tracking package.

PubMed

Kieslich, Pascal J; Henninger, Felix

2017-10-01

Mouse-tracking - the analysis of mouse movements in computerized experiments - is becoming increasingly popular in the cognitive sciences. Mouse movements are taken as an indicator of commitment to or conflict between choice options during the decision process. Using mouse-tracking, researchers have gained insight into the temporal development of cognitive processes across a growing number of psychological domains. In the current article, we present software that offers easy and convenient means of recording and analyzing mouse movements in computerized laboratory experiments. In particular, we introduce and demonstrate the mousetrap plugin that adds mouse-tracking to OpenSesame, a popular general-purpose graphical experiment builder. By integrating with this existing experimental software, mousetrap allows for the creation of mouse-tracking studies through a graphical interface, without requiring programming skills. Thus, researchers can benefit from the core features of a validated software package and the many extensions available for it (e.g., the integration with auxiliary hardware such as eye-tracking, or the support of interactive experiments). In addition, the recorded data can be imported directly into the statistical programming language R using the mousetrap package, which greatly facilitates analysis. Mousetrap is cross-platform, open-source and available free of charge from https://github.com/pascalkieslich/mousetrap-os .

Decision-Theoretic Methods in Simulation Optimization

DTIC Science & Technology

2014-09-24

freely available, and is also being considered for use by Netflix . • [Scott et al., 2011] provides an easily computed approximation to the knowledge...Area, such as Netflix . It has received a great deal of attention from the com- munity, and is already quite popular on the open-source software

A Review of Meta-Analysis Packages in R

ERIC Educational Resources Information Center

Polanin, Joshua R.; Hennessy, Emily A.; Tanner-Smith, Emily E.

2017-01-01

Meta-analysis is a statistical technique that allows an analyst to synthesize effect sizes from multiple primary studies. To estimate meta-analysis models, the open-source statistical environment R is quickly becoming a popular choice. The meta-analytic community has contributed to this growth by developing numerous packages specific to…

Playing, Debugging, Learning: A Proposal between Game and Instructional Designs via Extended Prototyping

ERIC Educational Resources Information Center

Gandolfi, Enrico

2018-01-01

This article investigates the phenomenon of open and participative development (e.g. beta testing, Kickstarter projects)--i.e. extended prototyping--in digital entertainment as a potential source of insights for instructional interventions. Despite the increasing popularity of this practice and the potential implications for educators and…

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

Developing and Benchmarking Native Linux Applications on Android

NASA Astrophysics Data System (ADS)

Batyuk, Leonid; Schmidt, Aubrey-Derrick; Schmidt, Hans-Gunther; Camtepe, Ahmet; Albayrak, Sahin

Smartphones get increasingly popular where more and more smartphone platforms emerge. Special attention was gained by the open source platform Android which was presented by the Open Handset Alliance (OHA) hosting members like Google, Motorola, and HTC. Android uses a Linux kernel and a stripped-down userland with a custom Java VM set on top. The resulting system joins the advantages of both environments, while third-parties are intended to develop only Java applications at the moment.

MUFFSgenMC: An Open Source MUon Flexible Framework for Spectral GENeration for Monte Carlo Applications

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

Chatzidakis, Stylianos; Greulich, Christopher

A cosmic ray Muon Flexible Framework for Spectral GENeration for Monte Carlo Applications (MUFFSgenMC) has been developed to support state-of-the-art cosmic ray muon tomographic applications. The flexible framework allows for easy and fast creation of source terms for popular Monte Carlo applications like GEANT4 and MCNP. This code framework simplifies the process of simulations used for cosmic ray muon tomography.

Developing a GIS for CO2 analysis using lightweight, open source components

NASA Astrophysics Data System (ADS)

Verma, R.; Goodale, C. E.; Hart, A. F.; Kulawik, S. S.; Law, E.; Osterman, G. B.; Braverman, A.; Nguyen, H. M.; Mattmann, C. A.; Crichton, D. J.; Eldering, A.; Castano, R.; Gunson, M. R.

2012-12-01

There are advantages to approaching the realm of geographic information systems (GIS) using lightweight, open source components in place of a more traditional web map service (WMS) solution. Rapid prototyping, schema-less data storage, the flexible interchange of components, and open source community support are just some of the benefits. In our effort to develop an application supporting the geospatial and temporal rendering of remote sensing carbon-dioxide (CO2) data for the CO2 Virtual Science Data Environment project, we have connected heterogeneous open source components together to form a GIS. Utilizing widely popular open source components including the schema-less database MongoDB, Leaflet interactive maps, the HighCharts JavaScript graphing library, and Python Bottle web-services, we have constructed a system for rapidly visualizing CO2 data with reduced up-front development costs. These components can be aggregated together, resulting in a configurable stack capable of replicating features provided by more standard GIS technologies. The approach we have taken is not meant to replace the more established GIS solutions, but to instead offer a rapid way to provide GIS features early in the development of an application and to offer a path towards utilizing more capable GIS technology in the future.

Factor Analysis Using "R"

ERIC Educational Resources Information Center

Beaujean, A. Alexander

2013-01-01

"R" (R Development Core Team, 2011) is a very powerful tool to analyze data, that is gaining in popularity due to its costs (its free) and flexibility (its open-source). This article gives a general introduction to using "R" (i.e., loading the program, using functions, importing data). Then, using data from Canivez, Konold, Collins, and Wilson…

The SAMI2 Open Source Project

NASA Astrophysics Data System (ADS)

Huba, J. D.; Joyce, G.

2001-05-01

In the past decade, the Open Source Model for software development has gained popularity and has had numerous major achievements: emacs, Linux, the Gimp, and Python, to name a few. The basic idea is to provide the source code of the model or application, a tutorial on its use, and a feedback mechanism with the community so that the model can be tested, improved, and archived. Given the success of the Open Source Model, we believe it may prove valuable in the development of scientific research codes. With this in mind, we are `Open Sourcing' the low to mid-latitude ionospheric model that has recently been developed at the Naval Research Laboratory: SAMI2 (Sami2 is Another Model of the Ionosphere). The model is comprehensive and uses modern numerical techniques. The structure and design of SAMI2 make it relatively easy to understand and modify: the numerical algorithms are simple and direct, and the code is reasonably well-written. Furthermore, SAMI2 is designed to run on personal computers; prohibitive computational resources are not necessary, thereby making the model accessible and usable by virtually all researchers. For these reasons, SAMI2 is an excellent candidate to explore and test the open source modeling paradigm in space physics research. We will discuss various topics associated with this project. Research supported by the Office of Naval Research.

Dog Movie Stars and Dog Breed Popularity: A Case Study in Media Influence on Choice

PubMed Central

Ghirlanda, Stefano; Acerbi, Alberto; Herzog, Harold

2014-01-01

Fashions and fads are important phenomena that influence many individual choices. They are ubiquitous in human societies, and have recently been used as a source of data to test models of cultural dynamics. Although a few statistical regularities have been observed in fashion cycles, their empirical characterization is still incomplete. Here we consider the impact of mass media on popular culture, showing that the release of movies featuring dogs is often associated with an increase in the popularity of featured breeds, for up to 10 years after movie release. We also find that a movie's impact on breed popularity correlates with the estimated number of viewers during the movie's opening weekend—a proxy of the movie's reach among the general public. Movies' influence on breed popularity was strongest in the early 20th century, and has declined since. We reach these conclusions through a new, widely applicable method to measure the cultural impact of events, capable of disentangling the event's effect from ongoing cultural trends. PMID:25208271

Dog movie stars and dog breed popularity: a case study in media influence on choice.

PubMed

Ghirlanda, Stefano; Acerbi, Alberto; Herzog, Harold

2014-01-01

Fashions and fads are important phenomena that influence many individual choices. They are ubiquitous in human societies, and have recently been used as a source of data to test models of cultural dynamics. Although a few statistical regularities have been observed in fashion cycles, their empirical characterization is still incomplete. Here we consider the impact of mass media on popular culture, showing that the release of movies featuring dogs is often associated with an increase in the popularity of featured breeds, for up to 10 years after movie release. We also find that a movie's impact on breed popularity correlates with the estimated number of viewers during the movie's opening weekend--a proxy of the movie's reach among the general public. Movies' influence on breed popularity was strongest in the early 20th century, and has declined since. We reach these conclusions through a new, widely applicable method to measure the cultural impact of events, capable of disentangling the event's effect from ongoing cultural trends.

Adding tools to the open source toolbox: The Internet

NASA Technical Reports Server (NTRS)

Porth, Tricia

1994-01-01

The Internet offers researchers additional sources of information not easily available from traditional sources such as print volumes or commercial data bases. Internet tools such as e-mail and file transfer protocol (ftp) speed up the way researchers communicate and transmit data. Mosaic, one of the newest additions to the Internet toolbox, allows users to combine tools such as ftp, gopher, wide area information server, and the world wide web with multimedia capabilities. Mosaic has quickly become a popular means of making information available on the Internet because it is versatile and easily customizable.

Quantifying Uncertainty in Expert Judgment: Initial Results

DTIC Science & Technology

2013-03-01

lines of source code were added in . ---------- C++ = 32%; JavaScript = 29%; XML = 15%; C = 7%; CSS = 7%; Java = 5%; Oth- er = 5% LOC = 927,266...much total effort in person years has been spent on this project? CMU/SEI-2013-TR-001 | 33 5 MySQL , the most popular Open Source SQL...as MySQL , Oracle, PostgreSQL, MS SQL Server, ODBC, or Interbase. Features include email reminders, iCal/vCal import/export, re- mote subscriptions

Open Source Virtual Worlds and Low Cost Sensors for Physical Rehab of Patients with Chronic Diseases

NASA Astrophysics Data System (ADS)

Romero, Salvador J.; Fernandez-Luque, Luis; Sevillano, José L.; Vognild, Lars

For patients with chronic diseases, exercise is a key part of rehab to deal better with their illness. Some of them do rehabilitation at home with telemedicine systems. However, keeping to their exercising program is challenging and many abandon the rehabilitation. We postulate that information technologies for socializing and serious games can encourage patients to keep doing physical exercise and rehab. In this paper we present Virtual Valley, a low cost telemedicine system for home exercising, based on open source virtual worlds and utilizing popular low cost motion controllers (e.g. Wii Remote) and medical sensors. Virtual Valley allows patient to socialize, learn, and play group based serious games while exercising.

VAGUE: a graphical user interface for the Velvet assembler.

PubMed

Powell, David R; Seemann, Torsten

2013-01-15

Velvet is a popular open-source de novo genome assembly software tool, which is run from the Unix command line. Most of the problems experienced by new users of Velvet revolve around constructing syntactically and semantically correct command lines, getting input files into acceptable formats and assessing the output. Here, we present Velvet Assembler Graphical User Environment (VAGUE), a multi-platform graphical front-end for Velvet. VAGUE aims to make sequence assembly accessible to a wider audience and to facilitate better usage amongst existing users of Velvet. VAGUE is implemented in JRuby and targets the Java Virtual Machine. It is available under an open-source GPLv2 licence from http://www.vicbioinformatics.com/. torsten.seemann@monash.edu.

How Educational Ideas Catch On: The Promotion of Popular Education Innovations and the Role of Evidence

ERIC Educational Resources Information Center

Carrier, Nathalie

2017-01-01

Background: Within the wider education industry, a large quantity of ideas, practices and products are routinely promoted as useful innovations. These innovations span many forms such as software applications, open source courseware, online learning platforms and web 2.0 technologies. Coupled with this promotion, there is increasing interest and…

The Use of Distance Learning in the Educational Process Content and Structure of Educational Platforms--Analysis of the Platform Educans

ERIC Educational Resources Information Center

Igado, Manuel Fandos

2010-01-01

This work provides some considerations that complements the scarcity of researches this field of knowledge of the e-learning specifically referred to secondary education. Distance training programmes (both open source code and not) are becoming increasingly more popular, especially in higher level education. However, there are very few cases of…

Development of an Innovative Interactive Virtual Classroom System for K-12 Education Using Google App Engine

ERIC Educational Resources Information Center

Mumba, Frackson; Zhu, Mengxia

2013-01-01

This paper presents a Simulation-based interactive Virtual ClassRoom web system (SVCR: www.vclasie.com) powered by the state-of-the-art cloud computing technology from Google SVCR integrates popular free open-source math, science and engineering simulations and provides functions such as secure user access control and management of courses,…

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.

An Open Source Web Map Server Implementation For California and the Digital Earth: Lessons Learned

NASA Technical Reports Server (NTRS)

Sullivan, D. V.; Sheffner, E. J.; Skiles, J. W.; Brass, J. A.; Condon, Estelle (Technical Monitor)

2000-01-01

This paper describes an Open Source implementation of the Open GIS Consortium's Web Map interface. It is based on the very popular Apache WWW Server, the Sun Microsystems Java ServIet Development Kit, and a C language shared library interface to a spatial datastore. This server was initially written as a proof of concept, to support a National Aeronautics and Space Administration (NASA) Digital Earth test bed demonstration. It will also find use in the California Land Science Information Partnership (CaLSIP), a joint program between NASA and the state of California. At least one WebMap enabled server will be installed in every one of the state's 58 counties. This server will form a basis for a simple, easily maintained installation for those entities that do not yet require one of the larger, more expensive, commercial offerings.

ggCyto: Next Generation Open-Source Visualization Software for Cytometry.

PubMed

Van, Phu; Jiang, Wenxin; Gottardo, Raphael; Finak, Greg

2018-06-01

Open source software for computational cytometry has gained in popularity over the past few years. Efforts such as FlowCAP, the Lyoplate and Euroflow projects have highlighted the importance of efforts to standardize both experimental and computational aspects of cytometry data analysis. The R/BioConductor platform hosts the largest collection of open source cytometry software covering all aspects of data analysis and providing infrastructure to represent and analyze cytometry data with all relevant experimental, gating, and cell population annotations enabling fully reproducible data analysis. Data visualization frameworks to support this infrastructure have lagged behind. ggCyto is a new open-source BioConductor software package for cytometry data visualization built on ggplot2 that enables ggplot-like functionality with the core BioConductor flow cytometry data structures. Amongst its features are the ability to transform data and axes on-the-fly using cytometry-specific transformations, plot faceting by experimental meta-data variables, and partial matching of channel, marker and cell populations names to the contents of the BioConductor cytometry data structures. We demonstrate the salient features of the package using publicly available cytometry data with complete reproducible examples in a supplementary material vignette. https://bioconductor.org/packages/devel/bioc/html/ggcyto.html. gfinak@fredhutch.org. Supplementary data are available at Bioinformatics online and at http://rglab.org/ggcyto/.

Simulation with Python on transverse modes of the symmetric confocal resonator

NASA Astrophysics Data System (ADS)

Wang, Qing Hua; Qi, Jing; Ji, Yun Jing; Song, Yang; Li, Zhenhua

2017-08-01

Python is a popular open-source programming language that can be used to simulate various optical phenomena. We have developed a suite of programs to help teach the course of laser principle. The complicated transverse modes of the symmetric confocal resonator can be visualized in personal computers, which is significant to help the students understand the pattern distribution of laser resonator.

A ROSE-based OpenMP 3.0 Research Compiler Supporting Multiple Runtime Libraries

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

Liao, C; Quinlan, D; Panas, T

2010-01-25

OpenMP is a popular and evolving programming model for shared-memory platforms. It relies on compilers for optimal performance and to target modern hardware architectures. A variety of extensible and robust research compilers are key to OpenMP's sustainable success in the future. In this paper, we present our efforts to build an OpenMP 3.0 research compiler for C, C++, and Fortran; using the ROSE source-to-source compiler framework. Our goal is to support OpenMP research for ourselves and others. We have extended ROSE's internal representation to handle all of the OpenMP 3.0 constructs and facilitate their manipulation. Since OpenMP research is oftenmore » complicated by the tight coupling of the compiler translations and the runtime system, we present a set of rules to define a common OpenMP runtime library (XOMP) on top of multiple runtime libraries. These rules additionally define how to build a set of translations targeting XOMP. Our work demonstrates how to reuse OpenMP translations across different runtime libraries. This work simplifies OpenMP research by decoupling the problematic dependence between the compiler translations and the runtime libraries. We present an evaluation of our work by demonstrating an analysis tool for OpenMP correctness. We also show how XOMP can be defined using both GOMP and Omni and present comparative performance results against other OpenMP compilers.« less

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Giannozzi, P.; Andreussi, O.; Brumme, T.; Bunau, O.; Buongiorno Nardelli, M.; Calandra, M.; Car, R.; Cavazzoni, C.; Ceresoli, D.; Cococcioni, M.; Colonna, N.; Carnimeo, I.; Dal Corso, A.; de Gironcoli, S.; Delugas, P.; DiStasio, R. A., Jr.; Ferretti, A.; Floris, A.; Fratesi, G.; Fugallo, G.; Gebauer, R.; Gerstmann, U.; Giustino, F.; Gorni, T.; Jia, J.; Kawamura, M.; Ko, H.-Y.; Kokalj, A.; Küçükbenli, E.; Lazzeri, M.; Marsili, M.; Marzari, N.; Mauri, F.; Nguyen, N. L.; Nguyen, H.-V.; Otero-de-la-Roza, A.; Paulatto, L.; Poncé, S.; Rocca, D.; Sabatini, R.; Santra, B.; Schlipf, M.; Seitsonen, A. P.; Smogunov, A.; Timrov, I.; Thonhauser, T.; Umari, P.; Vast, N.; Wu, X.; Baroni, S.

2017-11-01

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Giannozzi, P; Andreussi, O; Brumme, T; Bunau, O; Buongiorno Nardelli, M; Calandra, M; Car, R; Cavazzoni, C; Ceresoli, D; Cococcioni, M; Colonna, N; Carnimeo, I; Dal Corso, A; de Gironcoli, S; Delugas, P; DiStasio, R A; Ferretti, A; Floris, A; Fratesi, G; Fugallo, G; Gebauer, R; Gerstmann, U; Giustino, F; Gorni, T; Jia, J; Kawamura, M; Ko, H-Y; Kokalj, A; Küçükbenli, E; Lazzeri, M; Marsili, M; Marzari, N; Mauri, F; Nguyen, N L; Nguyen, H-V; Otero-de-la-Roza, A; Paulatto, L; Poncé, S; Rocca, D; Sabatini, R; Santra, B; Schlipf, M; Seitsonen, A P; Smogunov, A; Timrov, I; Thonhauser, T; Umari, P; Vast, N; Wu, X; Baroni, S

2017-10-24

Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

Andreussi, Oliviero; Brumme, Thomas; Bunau, Oana; Buongiorno Nardelli, Marco; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Cococcioni, Matteo; Colonna, Nicola; Carnimeo, Ivan; Dal Corso, Andrea; de Gironcoli, Stefano; Delugas, Pietro; DiStasio, Robert; Ferretti, Andrea; Floris, Andrea; Fratesi, Guido; Fugallo, Giorgia; Gebauer, Ralph; Gerstmann, Uwe; Giustino, Feliciano; Gorni, Tommaso; Jia, Junteng; Kawamura, Mitsuaki; Ko, Hsin-Yu; Kokalj, Anton; Küçükbenli, Emine; Lazzeri, Michele; Marsili, Margherita; Marzari, Nicola; Mauri, Francesco; Nguyen, Ngoc Linh; Nguyen, Huy-Viet; Otero-de-la-Roza, Alberto; Paulatto, Lorenzo; Poncé, Samuel; Giannozzi, Paolo; Rocca, Dario; Sabatini, Riccardo; Santra, Biswajit; Schlipf, Martin; Seitsonen, Ari Paavo; Smogunov, Alexander; Timrov, Iurii; Thonhauser, Timo; Umari, Paolo; Vast, Nathalie; Wu, Xifan; Baroni, Stefano

2017-09-27

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software. © 2017 IOP Publishing Ltd.

Do Open Source LMSs Support Personalization? A Comparative Evaluation

NASA Astrophysics Data System (ADS)

Kerkiri, Tania; Paleologou, Angela-Maria

A number of parameters that support the LMSs capabilities towards content personalization are presented and substantiated. These parameters constitute critical criteria for an exhaustive investigation of the personalization capabilities of the most popular open source LMSs. Results are comparatively shown and commented upon, thus highlighting a course of conduct for the implementation of new personalization methodologies for these LMSs, aligned at their existing infrastructure, to maintain support of the numerous educational institutions entrusting major part of their curricula to them. Meanwhile, new capabilities arise as drawn from a more efficient description of the existing resources -especially when organized into widely available repositories- that lead to qualitatively advanced learner-oriented courses which would ideally meet the challenge of combining personification of demand and personalization of thematic content at once.

Two-step web-mining approach to study geology/geophysics-related open-source software projects

NASA Astrophysics Data System (ADS)

Behrends, Knut; Conze, Ronald

2013-04-01

Geology/geophysics is a highly interdisciplinary science, overlapping with, for instance, physics, biology and chemistry. In today's software-intensive work environments, geoscientists often encounter new open-source software from scientific fields that are only remotely related to the own field of expertise. We show how web-mining techniques can help to carry out systematic discovery and evaluation of such software. In a first step, we downloaded ~500 abstracts (each consisting of ~1 kb UTF-8 text) from agu-fm12.abstractcentral.com. This web site hosts the abstracts of all publications presented at AGU Fall Meeting 2012, the world's largest annual geology/geophysics conference. All abstracts belonged to the category "Earth and Space Science Informatics", an interdisciplinary label cross-cutting many disciplines such as "deep biosphere", "atmospheric research", and "mineral physics". Each publication was represented by a highly structured record with ~20 short data attributes, the largest authorship-record being the unstructured "abstract" field. We processed texts of the abstracts with the statistics software "R" to calculate a corpus and a term-document matrix. Using R package "tm", we applied text-mining techniques to filter data and develop hypotheses about software-development activities happening in various geology/geophysics fields. Analyzing the term-document matrix with basic techniques (e.g., word frequencies, co-occurences, weighting) as well as more complex methods (clustering, classification) several key pieces of information were extracted. For example, text-mining can be used to identify scientists who are also developers of open-source scientific software, and the names of their programming projects and codes can also be identified. In a second step, based on the intermediate results found by processing the conference-abstracts, any new hypotheses can be tested in another webmining subproject: by merging the dataset with open data from github.com and stackoverflow.com. These popular, developer-centric websites have powerful application-programmer interfaces, and follow an open-data policy. In this regard, these sites offer a web-accessible reservoir of information that can be tapped to study questions such as: which open source software projects are eminent in the various geoscience fields? What are the most popular programming languages? How are they trending? Are there any interesting temporal patterns in committer activities? How large are programming teams and how do they change over time? What free software packages exist in the vast realms of related fields? Does the software from these fields have capabilities that might still be useful to me as a researcher, or can help me perform my work better? Are there any open-source projects that might be commercially interesting? This evaluation strategy reveals programming projects that tend to be new. As many important legacy codes are not hosted on open-source code-repositories, the presented search method might overlook some older projects.

PACS for Bhutan: a cost effective open source architecture for emerging countries.

PubMed

Ratib, Osman; Roduit, Nicolas; Nidup, Dechen; De Geer, Gerard; Rosset, Antoine; Geissbuhler, Antoine

2016-10-01

This paper reports the design and implementation of an innovative and cost-effective imaging management infrastructure suitable for radiology centres in emerging countries. It was implemented in the main referring hospital of Bhutan equipped with a CT, an MRI, digital radiology, and a suite of several ultrasound units. They lacked the necessary informatics infrastructure for image archiving and interpretation and needed a system for distribution of images to clinical wards. The solution developed for this project combines several open source software platforms in a robust and versatile archiving and communication system connected to analysis workstations equipped with a FDA-certified version of the highly popular Open-Source software. The whole system was implemented on standard off-the-shelf hardware. The system was installed in three days, and training of the radiologists as well as the technical and IT staff was provided onsite to ensure full ownership of the system by the local team. Radiologists were rapidly capable of reading and interpreting studies on the diagnostic workstations, which had a significant benefit on their workflow and ability to perform diagnostic tasks more efficiently. Furthermore, images were also made available to several clinical units on standard desktop computers through a web-based viewer. • Open source imaging informatics platforms can provide cost-effective alternatives for PACS • Robust and cost-effective open architecture can provide adequate solutions for emerging countries • Imaging informatics is often lacking in hospitals equipped with digital modalities.

An Open-source Meteorological Operational System and its Installation in Portuguese- speaking Countries

NASA Astrophysics Data System (ADS)

Almeida, W. G.; Ferreira, A. L.; Mendes, M. V.; Ribeiro, A.; Yoksas, T.

2007-05-01

CPTEC, a division of Brazil’s INPE, has been using several open-source software packages for a variety of tasks in its Data Division. Among these tools are ones traditionally used in research and educational communities such as GrADs (Grid Analysis and Display System from the Center for Ocean-Land-Atmosphere Studies (COLA)), the Local Data Manager (LDM) and GEMPAK (from Unidata), andl operational tools such the Automatic File Distributor (AFD) that are popular among National Meteorological Services. In addition, some tools developed locally at CPTEC are also being made available as open-source packages. One package is being used to manage the data from Automatic Weather Stations that INPE operates. This system uses only open- source tools such as MySQL database, PERL scripts and Java programs for web access, and Unidata’s Internet Data Distribution (IDD) system and AFD for data delivery. All of these packages are get bundled into a low-cost and easy to install and package called the Meteorological Data Operational System. Recently, in a cooperation with the SICLIMAD project, this system has been modified for use by Portuguese- speaking countries in Africa to manage data from many Automatic Weather Stations that are being installed in these countries under SICLIMAD sponsorship. In this presentation we describe the tools included-in and and architecture-of the Meteorological Data Operational System.

IQM: An Extensible and Portable Open Source Application for Image and Signal Analysis in Java

PubMed Central

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM’s image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis. PMID:25612319

IQM: an extensible and portable open source application for image and signal analysis in Java.

PubMed

Kainz, Philipp; Mayrhofer-Reinhartshuber, Michael; Ahammer, Helmut

2015-01-01

Image and signal analysis applications are substantial in scientific research. Both open source and commercial packages provide a wide range of functions for image and signal analysis, which are sometimes supported very well by the communities in the corresponding fields. Commercial software packages have the major drawback of being expensive and having undisclosed source code, which hampers extending the functionality if there is no plugin interface or similar option available. However, both variants cannot cover all possible use cases and sometimes custom developments are unavoidable, requiring open source applications. In this paper we describe IQM, a completely free, portable and open source (GNU GPLv3) image and signal analysis application written in pure Java. IQM does not depend on any natively installed libraries and is therefore runnable out-of-the-box. Currently, a continuously growing repertoire of 50 image and 16 signal analysis algorithms is provided. The modular functional architecture based on the three-tier model is described along the most important functionality. Extensibility is achieved using operator plugins, and the development of more complex workflows is provided by a Groovy script interface to the JVM. We demonstrate IQM's image and signal processing capabilities in a proof-of-principle analysis and provide example implementations to illustrate the plugin framework and the scripting interface. IQM integrates with the popular ImageJ image processing software and is aiming at complementing functionality rather than competing with existing open source software. Machine learning can be integrated into more complex algorithms via the WEKA software package as well, enabling the development of transparent and robust methods for image and signal analysis.

VisIt: An End-User Tool for Visualizing and Analyzing Very Large Data

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

Childs, Hank; Brugger, Eric; Whitlock, Brad

2012-11-01

VisIt is a popular open source tool for visualizing and analyzing big data. It owes its success to its foci of increasing data understanding, large data support, and providing a robust and usable product, as well as its underlying design that fits today's supercomputing landscape. This report, which draws heavily from an earlier publication at the SciDAC Conference in 2011 describes the VisIt project and its accomplishments.

Open source EMR software: profiling, insights and hands-on analysis.

PubMed

Kiah, M L M; Haiqi, Ahmed; Zaidan, B B; Zaidan, A A

2014-11-01

The use of open source software in health informatics is increasingly advocated by authors in the literature. Although there is no clear evidence of the superiority of the current open source applications in the healthcare field, the number of available open source applications online is growing and they are gaining greater prominence. This repertoire of open source options is of a great value for any future-planner interested in adopting an electronic medical/health record system, whether selecting an existent application or building a new one. The following questions arise. How do the available open source options compare to each other with respect to functionality, usability and security? Can an implementer of an open source application find sufficient support both as a user and as a developer, and to what extent? Does the available literature provide adequate answers to such questions? This review attempts to shed some light on these aspects. The objective of this study is to provide more comprehensive guidance from an implementer perspective toward the available alternatives of open source healthcare software, particularly in the field of electronic medical/health records. The design of this study is twofold. In the first part, we profile the published literature on a sample of existent and active open source software in the healthcare area. The purpose of this part is to provide a summary of the available guides and studies relative to the sampled systems, and to identify any gaps in the published literature with respect to our research questions. In the second part, we investigate those alternative systems relative to a set of metrics, by actually installing the software and reporting a hands-on experience of the installation process, usability, as well as other factors. The literature covers many aspects of open source software implementation and utilization in healthcare practice. Roughly, those aspects could be distilled into a basic taxonomy, making the literature landscape more perceivable. Nevertheless, the surveyed articles fall short of fulfilling the targeted objective of providing clear reference to potential implementers. The hands-on study contributed a more detailed comparative guide relative to our set of assessment measures. Overall, no system seems to satisfy an industry-standard measure, particularly in security and interoperability. The systems, as software applications, feel similar from a usability perspective and share a common set of functionality, though they vary considerably in community support and activity. More detailed analysis of popular open source software can benefit the potential implementers of electronic health/medical records systems. The number of examined systems and the measures by which to compare them vary across studies, but still rewarding insights start to emerge. Our work is one step toward that goal. Our overall conclusion is that open source options in the medical field are still far behind the highly acknowledged open source products in other domains, e.g. operating systems market share. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

JBioWH: an open-source Java framework for bioinformatics data integration

PubMed Central

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh PMID:23846595

JBioWH: an open-source Java framework for bioinformatics data integration.

PubMed

Vera, Roberto; Perez-Riverol, Yasset; Perez, Sonia; Ligeti, Balázs; Kertész-Farkas, Attila; Pongor, Sándor

2013-01-01

The Java BioWareHouse (JBioWH) project is an open-source platform-independent programming framework that allows a user to build his/her own integrated database from the most popular data sources. JBioWH can be used for intensive querying of multiple data sources and the creation of streamlined task-specific data sets on local PCs. JBioWH is based on a MySQL relational database scheme and includes JAVA API parser functions for retrieving data from 20 public databases (e.g. NCBI, KEGG, etc.). It also includes a client desktop application for (non-programmer) users to query data. In addition, JBioWH can be tailored for use in specific circumstances, including the handling of massive queries for high-throughput analyses or CPU intensive calculations. The framework is provided with complete documentation and application examples and it can be downloaded from the Project Web site at http://code.google.com/p/jbiowh. A MySQL server is available for demonstration purposes at hydrax.icgeb.trieste.it:3307. Database URL: http://code.google.com/p/jbiowh.

Performance Evaluation of Block Acquisition and Tracking Algorithms Using an Open Source GPS Receiver Platform

NASA Technical Reports Server (NTRS)

Ramachandran, Ganesh K.; Akopian, David; Heckler, Gregory W.; Winternitz, Luke B.

2011-01-01

Location technologies have many applications in wireless communications, military and space missions, etc. US Global Positioning System (GPS) and other existing and emerging Global Navigation Satellite Systems (GNSS) are expected to provide accurate location information to enable such applications. While GNSS systems perform very well in strong signal conditions, their operation in many urban, indoor, and space applications is not robust or even impossible due to weak signals and strong distortions. The search for less costly, faster and more sensitive receivers is still in progress. As the research community addresses more and more complicated phenomena there exists a demand on flexible multimode reference receivers, associated SDKs, and development platforms which may accelerate and facilitate the research. One of such concepts is the software GPS/GNSS receiver (GPS SDR) which permits a facilitated access to algorithmic libraries and a possibility to integrate more advanced algorithms without hardware and essential software updates. The GNU-SDR and GPS-SDR open source receiver platforms are such popular examples. This paper evaluates the performance of recently proposed block-corelator techniques for acquisition and tracking of GPS signals using open source GPS-SDR platform.

Leveraging human oversight and intervention in large-scale parallel processing of open-source data

NASA Astrophysics Data System (ADS)

Casini, Enrico; Suri, Niranjan; Bradshaw, Jeffrey M.

2015-05-01

The popularity of cloud computing along with the increased availability of cheap storage have led to the necessity of elaboration and transformation of large volumes of open-source data, all in parallel. One way to handle such extensive volumes of information properly is to take advantage of distributed computing frameworks like Map-Reduce. Unfortunately, an entirely automated approach that excludes human intervention is often unpredictable and error prone. Highly accurate data processing and decision-making can be achieved by supporting an automatic process through human collaboration, in a variety of environments such as warfare, cyber security and threat monitoring. Although this mutual participation seems easily exploitable, human-machine collaboration in the field of data analysis presents several challenges. First, due to the asynchronous nature of human intervention, it is necessary to verify that once a correction is made, all the necessary reprocessing is done in chain. Second, it is often needed to minimize the amount of reprocessing in order to optimize the usage of resources due to limited availability. In order to improve on these strict requirements, this paper introduces improvements to an innovative approach for human-machine collaboration in the processing of large amounts of open-source data in parallel.

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration.

PubMed

Dryden, Michael D M; Wheeler, Aaron R

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as "black boxes," giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat's voltammetric measurements are much more sensitive than those of "CheapStat" (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial "black box" potentiostat. Likewise, in head-to-head tests, DStat's potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the "open source" movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools.

Open-Source Sequence Clustering Methods Improve the State Of the Art.

PubMed

Kopylova, Evguenia; Navas-Molina, Jose A; Mercier, Céline; Xu, Zhenjiang Zech; Mahé, Frédéric; He, Yan; Zhou, Hong-Wei; Rognes, Torbjørn; Caporaso, J Gregory; Knight, Rob

2016-01-01

Sequence clustering is a common early step in amplicon-based microbial community analysis, when raw sequencing reads are clustered into operational taxonomic units (OTUs) to reduce the run time of subsequent analysis steps. Here, we evaluated the performance of recently released state-of-the-art open-source clustering software products, namely, OTUCLUST, Swarm, SUMACLUST, and SortMeRNA, against current principal options (UCLUST and USEARCH) in QIIME, hierarchical clustering methods in mothur, and USEARCH's most recent clustering algorithm, UPARSE. All the latest open-source tools showed promising results, reporting up to 60% fewer spurious OTUs than UCLUST, indicating that the underlying clustering algorithm can vastly reduce the number of these derived OTUs. Furthermore, we observed that stringent quality filtering, such as is done in UPARSE, can cause a significant underestimation of species abundance and diversity, leading to incorrect biological results. Swarm, SUMACLUST, and SortMeRNA have been included in the QIIME 1.9.0 release. IMPORTANCE Massive collections of next-generation sequencing data call for fast, accurate, and easily accessible bioinformatics algorithms to perform sequence clustering. A comprehensive benchmark is presented, including open-source tools and the popular USEARCH suite. Simulated, mock, and environmental communities were used to analyze sensitivity, selectivity, species diversity (alpha and beta), and taxonomic composition. The results demonstrate that recent clustering algorithms can significantly improve accuracy and preserve estimated diversity without the application of aggressive filtering. Moreover, these tools are all open source, apply multiple levels of multithreading, and scale to the demands of modern next-generation sequencing data, which is essential for the analysis of massive multidisciplinary studies such as the Earth Microbiome Project (EMP) (J. A. Gilbert, J. K. Jansson, and R. Knight, BMC Biol 12:69, 2014, http://dx.doi.org/10.1186/s12915-014-0069-1).

Efficient Comparison between Windows and Linux Platform Applicable in a Virtual Architectural Walkthrough Application

NASA Astrophysics Data System (ADS)

Thubaasini, P.; Rusnida, R.; Rohani, S. M.

This paper describes Linux, an open source platform used to develop and run a virtual architectural walkthrough application. It proposes some qualitative reflections and observations on the nature of Linux in the concept of Virtual Reality (VR) and on the most popular and important claims associated with the open source approach. The ultimate goal of this paper is to measure and evaluate the performance of Linux used to build the virtual architectural walkthrough and develop a proof of concept based on the result obtain through this project. Besides that, this study reveals the benefits of using Linux in the field of virtual reality and reflects a basic comparison and evaluation between Windows and Linux base operating system. Windows platform is use as a baseline to evaluate the performance of Linux. The performance of Linux is measured based on three main criteria which is frame rate, image quality and also mouse motion.

Optical 3-Way Handshake (O3WHS) Protocol Simulation in OMNeT++

DTIC Science & Technology

2017-06-01

PERSON Vinod K Mishra a. REPORT Unclassified b. ABSTRACT Unclassified c . THIS PAGE Unclassified 19b. TELEPHONE NUMBER (Include area code) 410...popular program called OMNeT++2 for that purpose. It is an open-source discrete event simulator tool written in C ++ language. It has been chiefly...References 1. Von Lehmen A, Doverspike R, Clapp G, Freimuth DM, Gannett J, Kolarov A, Kobrinski H, Makaya C , Mavrogiorgis E, Pastor J, Rauch M

Putting Home Data Management into Perspective

DTIC Science & Technology

2009-12-01

approaches. However, users of home and personal storage live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop-down lists of recently...users of home and personal storage live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop-down lists of recently-opened Word documents...live it. Popular interfaces (e.g., iTunes , iPhoto, and even drop- down lists of recently-opened Word documents) allow users to navigate file

An Introduction to Drupal: Fast and Furious

NASA Astrophysics Data System (ADS)

Erdmann, C.

2010-10-01

Drupal is a free open source content management system (CMS) and web application framework that is gaining in popularity. Part of Drupal's popularity stems from the flexibility that both developers and users have when working with the system. Drupal also has an enthusiastic and innovative community, with developers that contribute to the core system and who add additional modules for all to use. The result is a stable core system that can be customized to suit a variety of needs, including those of libraries. The purpose of this paper is to introduce Drupal to the astronomy library community by providing some background on the project and its use within libraries. Basic instructions on installation and use of the system, within the context of the ESO Library, will also be explained.

SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.

PubMed

Blattmann, Peter; Heusel, Moritz; Aebersold, Ruedi

2016-01-01

SWATH-MS is an acquisition and analysis technique of targeted proteomics that enables measuring several thousand proteins with high reproducibility and accuracy across many samples. OpenSWATH is popular open-source software for peptide identification and quantification from SWATH-MS data. For downstream statistical and quantitative analysis there exist different tools such as MSstats, mapDIA and aLFQ. However, the transfer of data from OpenSWATH to the downstream statistical tools is currently technically challenging. Here we introduce the R/Bioconductor package SWATH2stats, which allows convenient processing of the data into a format directly readable by the downstream analysis tools. In addition, SWATH2stats allows annotation, analyzing the variation and the reproducibility of the measurements, FDR estimation, and advanced filtering before submitting the processed data to downstream tools. These functionalities are important to quickly analyze the quality of the SWATH-MS data. Hence, SWATH2stats is a new open-source tool that summarizes several practical functionalities for analyzing, processing, and converting SWATH-MS data and thus facilitates the efficient analysis of large-scale SWATH/DIA datasets.

CISUS: an integrated 3D ultrasound system for IGT using a modular tracking API

NASA Astrophysics Data System (ADS)

Boctor, Emad M.; Viswanathan, Anand; Pieper, Steve; Choti, Michael A.; Taylor, Russell H.; Kikinis, Ron; Fichtinger, Gabor

2004-05-01

Ultrasound has become popular in clinical/surgical applications, both as the primary image guidance modality and also in conjunction with other modalities like CT or MRI. Three dimensional ultrasound (3DUS) systems have also demonstrated usefulness in image-guided therapy (IGT). At the same time, however, current lack of open-source and open-architecture multi-modal medical visualization systems prevents 3DUS from fulfilling its potential. Several stand-alone 3DUS systems, like Stradx or In-Vivo exist today. Although these systems have been found to be useful in real clinical setting, it is difficult to augment their functionality and integrate them in versatile IGT systems. To address these limitations, a robotic/freehand 3DUS open environment (CISUS) is being integrated into the 3D Slicer, an open-source research tool developed for medical image analysis and surgical planning. In addition, the system capitalizes on generic application programming interfaces (APIs) for tracking devices and robotic control. The resulting platform-independent open-source system may serve as a valuable tool to the image guided surgery community. Other researchers could straightforwardly integrate the generic CISUS system along with other functionalities (i.e. dual view visualization, registration, real-time tracking, segmentation, etc) to rapidly create their medical/surgical applications. Our current driving clinical application is robotically assisted and freehand 3DUS-guided liver ablation, which is fully being integrated under the CISUS-3D Slicer. Initial functionality and pre-clinical feasibility are demonstrated on phantom and ex-vivo animal models.

VIVO Open Source Software: Connecting Facilities to Promote Discovery and Further Research.

NASA Astrophysics Data System (ADS)

Gross, M. B.; Rowan, L. R.; Mayernik, M. S.; Daniels, M. D.; Stott, D.; Allison, J.; Maull, K. E.; Krafft, D. B.; Khan, H.

2016-12-01

EarthCollab (http://earthcube.org/group/earthcollab), a National Science Foundation (NSF) EarthCube Building Block project, has adapted an open source semantic web application, VIVO, for use within the earth science domain. EarthCollab is a partnership between UNAVCO, an NSF facility supporting research through geodetic services, the Earth Observing Laboratory (EOL) at the National Center for Atmospheric Research (NCAR), and Cornell University, where VIVO was created to highlight the scholarly output of researchers at universities. Two public sites have been released: Connect UNAVCO (connect.unavco.org) and Arctic Data Connects (vivo.eol.ucar.edu). The core VIVO software and ontology have been extended to work better with concepts necessary for capturing work within UNAVCO's and EOL's province such as principal investigators for continuous GPS/GNSS stations at UNAVCO and keywords describing cruise datasets at EOL. The sites increase discoverability of large and diverse data archives by linking data with people, research, and field projects. Disambiguation is a major challenge when using VIVO and open data when "anyone can say anything about anything." Concepts and controlled vocabularies help to build consistent and easily searchable connections within VIVO. We use aspects of subject heading services such as FAST and LOC, as well as AGU and GSA fields of research and subject areas to reveal connections, especially with VIVO instances at other institutions. VIVO works effectively with persistent IDs and the projects strive to utilize publication and data DOIs, ORCIDs for people, and ISNI and GRID for organizations. ORCID, an open source project, is very useful for disambiguation and unlike other identifier systems for people developed by publishers, makes public data available via an API. VIVO utilizes Solr and Freemarker, which are open source search engine and templating technologies, respectively. Additionally, a handful of popular open source libraries and applications are being used in the project such as D3.js, jQuery, Leaflet, and Elasticsearch. Our implementation of these open source projects within VIVO is available for adaptation by other institutions using VIVO via GitHub (git.io/vG9AJ).

Global ISR: Toward a Comprehensive Defense Against Unauthorized Code Execution

DTIC Science & Technology

2010-10-01

implementation using two of the most popular open- source servers: the Apache web server, and the MySQL database server. For Apache, we measure the effect that...utility ab. T o ta l T im e ( s e c ) 0 500 1000 1500 2000 2500 3000 Native Null ISR ISR−MP Fig. 3. The MySQL test-insert bench- mark measures...various SQL operations. The figure draws total execution time as reported by the benchmark utility. Finally, we benchmarked a MySQL database server using

DStat: A Versatile, Open-Source Potentiostat for Electroanalysis and Integration

PubMed Central

Dryden, Michael D. M.; Wheeler, Aaron R.

2015-01-01

Most electroanalytical techniques require the precise control of the potentials in an electrochemical cell using a potentiostat. Commercial potentiostats function as “black boxes,” giving limited information about their circuitry and behaviour which can make development of new measurement techniques and integration with other instruments challenging. Recently, a number of lab-built potentiostats have emerged with various design goals including low manufacturing cost and field-portability, but notably lacking is an accessible potentiostat designed for general lab use, focusing on measurement quality combined with ease of use and versatility. To fill this gap, we introduce DStat (http://microfluidics.utoronto.ca/dstat), an open-source, general-purpose potentiostat for use alone or integrated with other instruments. DStat offers picoampere current measurement capabilities, a compact USB-powered design, and user-friendly cross-platform software. DStat is easy and inexpensive to build, may be modified freely, and achieves good performance at low current levels not accessible to other lab-built instruments. In head-to-head tests, DStat’s voltammetric measurements are much more sensitive than those of “CheapStat” (a popular open-source potentiostat described previously), and are comparable to those of a compact commercial “black box” potentiostat. Likewise, in head-to-head tests, DStat’s potentiometric precision is similar to that of a commercial pH meter. Most importantly, the versatility of DStat was demonstrated through integration with the open-source DropBot digital microfluidics platform. In sum, we propose that DStat is a valuable contribution to the “open source” movement in analytical science, which is allowing users to adapt their tools to their experiments rather than alter their experiments to be compatible with their tools. PMID:26510100

ERPLAB: an open-source toolbox for the analysis of event-related potentials

PubMed Central

Lopez-Calderon, Javier; Luck, Steven J.

2014-01-01

ERPLAB toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP) data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB’s EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB’s tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user’s guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations. PMID:24782741

ERPLAB: an open-source toolbox for the analysis of event-related potentials.

PubMed

Lopez-Calderon, Javier; Luck, Steven J

2014-01-01

ERPLAB toolbox is a freely available, open-source toolbox for processing and analyzing event-related potential (ERP) data in the MATLAB environment. ERPLAB is closely integrated with EEGLAB, a popular open-source toolbox that provides many EEG preprocessing steps and an excellent user interface design. ERPLAB adds to EEGLAB's EEG processing functions, providing additional tools for filtering, artifact detection, re-referencing, and sorting of events, among others. ERPLAB also provides robust tools for averaging EEG segments together to create averaged ERPs, for creating difference waves and other recombinations of ERP waveforms through algebraic expressions, for filtering and re-referencing the averaged ERPs, for plotting ERP waveforms and scalp maps, and for quantifying several types of amplitudes and latencies. ERPLAB's tools can be accessed either from an easy-to-learn graphical user interface or from MATLAB scripts, and a command history function makes it easy for users with no programming experience to write scripts. Consequently, ERPLAB provides both ease of use and virtually unlimited power and flexibility, making it appropriate for the analysis of both simple and complex ERP experiments. Several forms of documentation are available, including a detailed user's guide, a step-by-step tutorial, a scripting guide, and a set of video-based demonstrations.

Defining popular iconic metaphor.

PubMed

Columbus, Peter J; Boerger, Michael A

2002-04-01

Popular Iconic Metaphor is added to the cognitive linguistic lexicon of figurative language. Popular Iconic Metaphors employ real or fictional celebrities of popular culture as source domains in figurative discourse. Some borders of Popular Iconic Metaphor are identified, and Elvis Presley is offered as a prototype example of a popular iconic source domain, due to his ubiquity in American popular culture, which affords his figurative usage in ways consistent with decision heuristics in everyday life. Further study of Popular Iconic Metaphors may serve to illuminate how figurative expressions emerge in their localized contexts, structure conduct and experience, and affect mediation of cultural and personal meanings.

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory.

PubMed

Marchetti, Luca; Manca, Vincenzo

2015-04-15

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R. The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it. luca.marchetti@univr.it, marchetti@cosbi.eu Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Functional Interaction Network Construction and Analysis for Disease Discovery.

PubMed

Wu, Guanming; Haw, Robin

2017-01-01

Network-based approaches project seemingly unrelated genes or proteins onto a large-scale network context, therefore providing a holistic visualization and analysis platform for genomic data generated from high-throughput experiments, reducing the dimensionality of data via using network modules and increasing the statistic analysis power. Based on the Reactome database, the most popular and comprehensive open-source biological pathway knowledgebase, we have developed a highly reliable protein functional interaction network covering around 60 % of total human genes and an app called ReactomeFIViz for Cytoscape, the most popular biological network visualization and analysis platform. In this chapter, we describe the detailed procedures on how this functional interaction network is constructed by integrating multiple external data sources, extracting functional interactions from human curated pathway databases, building a machine learning classifier called a Naïve Bayesian Classifier, predicting interactions based on the trained Naïve Bayesian Classifier, and finally constructing the functional interaction database. We also provide an example on how to use ReactomeFIViz for performing network-based data analysis for a list of genes.

Improving Students' Educational Experience by Harnessing Digital Technology: elgg in the ODL Environment

ERIC Educational Resources Information Center

Tung, Lai Cheng

2013-01-01

Given the rising popularity of both open and distance learning (ODL) and social networking tools, it seems logical to merge and harness these two popular technologies with the goal of improving student educational experience. The integration seems to hold tremendous promise for the open and distance learning mode. To reduce the gap in the…

Scalable Regression Tree Learning on Hadoop using OpenPlanet

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

Yin, Wei; Simmhan, Yogesh; Prasanna, Viktor

As scientific and engineering domains attempt to effectively analyze the deluge of data arriving from sensors and instruments, machine learning is becoming a key data mining tool to build prediction models. Regression tree is a popular learning model that combines decision trees and linear regression to forecast numerical target variables based on a set of input features. Map Reduce is well suited for addressing such data intensive learning applications, and a proprietary regression tree algorithm, PLANET, using MapReduce has been proposed earlier. In this paper, we describe an open source implement of this algorithm, OpenPlanet, on the Hadoop framework usingmore » a hybrid approach. Further, we evaluate the performance of OpenPlanet using realworld datasets from the Smart Power Grid domain to perform energy use forecasting, and propose tuning strategies of Hadoop parameters to improve the performance of the default configuration by 75% for a training dataset of 17 million tuples on a 64-core Hadoop cluster on FutureGrid.« less

Psynteract: A flexible, cross-platform, open framework for interactive experiments.

PubMed

Henninger, Felix; Kieslich, Pascal J; Hilbig, Benjamin E

2017-10-01

We introduce a novel platform for interactive studies, that is, any form of study in which participants' experiences depend not only on their own responses, but also on those of other participants who complete the same study in parallel, for example a prisoner's dilemma or an ultimatum game. The software thus especially serves the rapidly growing field of strategic interaction research within psychology and behavioral economics. In contrast to all available software packages, our platform does not handle stimulus display and response collection itself. Instead, we provide a mechanism to extend existing experimental software to incorporate interactive functionality. This approach allows us to draw upon the capabilities already available, such as accuracy of temporal measurement, integration with auxiliary hardware such as eye-trackers or (neuro-)physiological apparatus, and recent advances in experimental software, for example capturing response dynamics through mouse-tracking. Through integration with OpenSesame, an open-source graphical experiment builder, studies can be assembled via a drag-and-drop interface requiring little or no further programming skills. In addition, by using the same communication mechanism across software packages, we also enable interoperability between systems. Our source code, which provides support for all major operating systems and several popular experimental packages, can be freely used and distributed under an open source license. The communication protocols underlying its functionality are also well documented and easily adapted to further platforms. Code and documentation are available at https://github.com/psynteract/ .

Open Source Hardware for DIY Environmental Sensing

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Hicks, S. D.; Damiano, S. G.; Montgomery, D. S.

2014-12-01

The Arduino open source electronics platform has been very popular within the DIY (Do It Yourself) community for several years, and it is now providing environmental science researchers with an inexpensive alternative to commercial data logging and transmission hardware. Here we present the designs for our latest series of custom Arduino-based dataloggers, which include wireless communication options like self-meshing radio networks and cellular phone modules. The main Arduino board uses a custom interface board to connect to various research-grade sensors to take readings of turbidity, dissolved oxygen, water depth and conductivity, soil moisture, solar radiation, and other parameters. Sensors with SDI-12 communications can be directly interfaced to the logger using our open Arduino-SDI-12 software library (https://github.com/StroudCenter/Arduino-SDI-12). Different deployment options are shown, like rugged enclosures to house the loggers and rigs for mounting the sensors in both fresh water and marine environments. After the data has been collected and transmitted by the logger, the data is received by a mySQL-PHP stack running on a web server that can be accessed from anywhere in the world. Once there, the data can be visualized on web pages or served though REST requests and Water One Flow (WOF) services. Since one of the main benefits of using open source hardware is the easy collaboration between users, we are introducing a new web platform for discussion and sharing of ideas and plans for hardware and software designs used with DIY environmental sensors and data loggers.

DasPy – Open Source Multivariate Land Data Assimilation Framework with High Performance Computing

NASA Astrophysics Data System (ADS)

Han, Xujun; Li, Xin; Montzka, Carsten; Kollet, Stefan; Vereecken, Harry; Hendricks Franssen, Harrie-Jan

2015-04-01

Data assimilation has become a popular method to integrate observations from multiple sources with land surface models to improve predictions of the water and energy cycles of the soil-vegetation-atmosphere continuum. In recent years, several land data assimilation systems have been developed in different research agencies. Because of the software availability or adaptability, these systems are not easy to apply for the purpose of multivariate land data assimilation research. Multivariate data assimilation refers to the simultaneous assimilation of observation data for multiple model state variables into a simulation model. Our main motivation was to develop an open source multivariate land data assimilation framework (DasPy) which is implemented using the Python script language mixed with C++ and Fortran language. This system has been evaluated in several soil moisture, L-band brightness temperature and land surface temperature assimilation studies. The implementation allows also parameter estimation (soil properties and/or leaf area index) on the basis of the joint state and parameter estimation approach. LETKF (Local Ensemble Transform Kalman Filter) is implemented as the main data assimilation algorithm, and uncertainties in the data assimilation can be represented by perturbed atmospheric forcings, perturbed soil and vegetation properties and model initial conditions. The CLM4.5 (Community Land Model) was integrated as the model operator. The CMEM (Community Microwave Emission Modelling Platform), COSMIC (COsmic-ray Soil Moisture Interaction Code) and the two source formulation were integrated as observation operators for assimilation of L-band passive microwave, cosmic-ray soil moisture probe and land surface temperature measurements, respectively. DasPy is parallelized using the hybrid MPI (Message Passing Interface) and OpenMP (Open Multi-Processing) techniques. All the input and output data flow is organized efficiently using the commonly used NetCDF file format. Online 1D and 2D visualization of data assimilation results is also implemented to facilitate the post simulation analysis. In summary, DasPy is a ready to use open source parallel multivariate land data assimilation framework.

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.

Navigating protected genomics data with UCSC Genome Browser in a Box.

PubMed

Haeussler, Maximilian; Raney, Brian J; Hinrichs, Angie S; Clawson, Hiram; Zweig, Ann S; Karolchik, Donna; Casper, Jonathan; Speir, Matthew L; Haussler, David; Kent, W James

2015-03-01

Genome Browser in a Box (GBiB) is a small virtual machine version of the popular University of California Santa Cruz (UCSC) Genome Browser that can be run on a researcher's own computer. Once GBiB is installed, a standard web browser is used to access the virtual server and add personal data files from the local hard disk. Annotation data are loaded on demand through the Internet from UCSC or can be downloaded to the local computer for faster access. Software downloads and installation instructions are freely available for non-commercial use at https://genome-store.ucsc.edu/. GBiB requires the installation of open-source software VirtualBox, available for all major operating systems, and the UCSC Genome Browser, which is open source and free for non-commercial use. Commercial use of GBiB and the Genome Browser requires a license (http://genome.ucsc.edu/license/). © The Author 2014. Published by Oxford University Press.

PIVOT: platform for interactive analysis and visualization of transcriptomics data.

PubMed

Zhu, Qin; Fisher, Stephen A; Dueck, Hannah; Middleton, Sarah; Khaladkar, Mugdha; Kim, Junhyong

2018-01-05

Many R packages have been developed for transcriptome analysis but their use often requires familiarity with R and integrating results of different packages requires scripts to wrangle the datatypes. Furthermore, exploratory data analyses often generate multiple derived datasets such as data subsets or data transformations, which can be difficult to track. Here we present PIVOT, an R-based platform that wraps open source transcriptome analysis packages with a uniform user interface and graphical data management that allows non-programmers to interactively explore transcriptomics data. PIVOT supports more than 40 popular open source packages for transcriptome analysis and provides an extensive set of tools for statistical data manipulations. A graph-based visual interface is used to represent the links between derived datasets, allowing easy tracking of data versions. PIVOT further supports automatic report generation, publication-quality plots, and program/data state saving, such that all analysis can be saved, shared and reproduced. PIVOT will allow researchers with broad background to easily access sophisticated transcriptome analysis tools and interactively explore transcriptome datasets.

Slicer Method Comparison Using Open-source 3D Printer

NASA Astrophysics Data System (ADS)

Ariffin, M. K. A. Mohd; Sukindar, N. A.; Baharudin, B. T. H. T.; Jaafar, C. N. A.; Ismail, M. I. S.

2018-01-01

Open-source 3D printer has been one of the popular choices in fabricating 3D models. This technology is easily accessible and low in cost. However, several studies have been made to improve the performance of this low-cost technology in term of the accuracy of the parts finish. This study is focusing on the selection of slicer mode between CuraEngine and Slic3r. The effect on this slicer has been observe in terms of accuracy and surface visualization. The result shows that if the accuracy is the top priority, CuraEngine is the better option to use as contribute more accuracy as well as less filament is needed compared to the Slice3r. Slice3r may be very useful for complicated parts such as hanging structure due to excessive material which act as support material. The study provides basic platform for the user to have an idea which option to be used in fabricating 3D model.

It’s an app. It’s a hypervisor. It’s a hypapp. : Design and Implementation of an eXtensible and Modular Hypervisor Framework

DTIC Science & Technology

2012-06-26

existing commercial-grade virtualization solutions (e.g., Xen, Linux KVM, VMware, or L4 ), but generally do not require such rich functional- ity [9...ports multiprocessor configuration on both AMD and Intel x86 platforms. Xen [8], KVM [27], VMware [39], NOVA [33], Virtual- box‡‡ and L4 are some...popular general purpose (open-source) hypervisors and microkernels which have been used for var- ious hypervisor based research [9,15,26,30,32,34,45

Explicit B-spline regularization in diffeomorphic image registration

PubMed Central

Tustison, Nicholas J.; Avants, Brian B.

2013-01-01

Diffeomorphic mappings are central to image registration due largely to their topological properties and success in providing biologically plausible solutions to deformation and morphological estimation problems. Popular diffeomorphic image registration algorithms include those characterized by time-varying and constant velocity fields, and symmetrical considerations. Prior information in the form of regularization is used to enforce transform plausibility taking the form of physics-based constraints or through some approximation thereof, e.g., Gaussian smoothing of the vector fields [a la Thirion's Demons (Thirion, 1998)]. In the context of the original Demons' framework, the so-called directly manipulated free-form deformation (DMFFD) (Tustison et al., 2009) can be viewed as a smoothing alternative in which explicit regularization is achieved through fast B-spline approximation. This characterization can be used to provide B-spline “flavored” diffeomorphic image registration solutions with several advantages. Implementation is open source and available through the Insight Toolkit and our Advanced Normalization Tools (ANTs) repository. A thorough comparative evaluation with the well-known SyN algorithm (Avants et al., 2008), implemented within the same framework, and its B-spline analog is performed using open labeled brain data and open source evaluation tools. PMID:24409140

Application of Emerging Open-source Embedded Systems for Enabling Low-cost Wireless Mini-observatory Nodes in the Coastal Zone

NASA Astrophysics Data System (ADS)

Glazer, B. T.

2016-02-01

Here, we describe the development of novel, low-cost, open-source instrumentation to enable wireless data transfer of biogeochemical sensors in the coastal zone. The platform is centered upon the Beaglebone Black single board computer. Process-inquiry in environmental sciences suffers from undersampling; enabling sustained and unattended data collection typically involves expensive instrumentation and infrastructure deployed as cabled observatories with little flexibility in deployment location following initial installation. High cost of commercially-available or custom electronic packages have not only limited the number of sensor node sites that can be targeted by reasonably well-funded academic researchers, but have also entirely prohibited widespread engagement with K-12, public non-profit, and `citizen scientist' STEM audiences. The new platform under development represents a balanced blend of research-grade sensors and low-cost open-source electronics that are easily assembled. Custom, robust, open-source code that remains customizable for specific node configurations can match a specific deployment's measurement needs, depending on the scientific research priorities. We have demonstrated prototype capabilities and versatility through lab testing and field deployments of multiple sensor nodes with multiple sensor inputs, all of which are streaming near-real-time data over wireless RF links to a shore-based base station. On shore, first-pass data processing QA/QC takes place and near-real-time plots are made available on the World Wide Web. Specifically, we have worked closely with an environmental and cultural management and restoration non-profit organization, and middle and high school science classes, engaging their interest in STEM application to local watershed processes. Ultimately, continued successful development of this pilot project can lead to a coastal oceanographic analogue of the popular Weather Underground personal weather station model.

Analysing concurrent transcranial magnetic stimulation and electroencephalographic data: A review and introduction to the open-source TESA software.

PubMed

Rogasch, Nigel C; Sullivan, Caley; Thomson, Richard H; Rose, Nathan S; Bailey, Neil W; Fitzgerald, Paul B; Farzan, Faranak; Hernandez-Pavon, Julio C

2017-02-15

The concurrent use of transcranial magnetic stimulation with electroencephalography (TMS-EEG) is growing in popularity as a method for assessing various cortical properties such as excitability, oscillations and connectivity. However, this combination of methods is technically challenging, resulting in artifacts both during recording and following typical EEG analysis methods, which can distort the underlying neural signal. In this article, we review the causes of artifacts in EEG recordings resulting from TMS, as well as artifacts introduced during analysis (e.g. as the result of filtering over high-frequency, large amplitude artifacts). We then discuss methods for removing artifacts, and ways of designing pipelines to minimise analysis-related artifacts. Finally, we introduce the TMS-EEG signal analyser (TESA), an open-source extension for EEGLAB, which includes functions that are specific for TMS-EEG analysis, such as removing and interpolating the TMS pulse artifact, removing and minimising TMS-evoked muscle activity, and analysing TMS-evoked potentials. The aims of TESA are to provide users with easy access to current TMS-EEG analysis methods and to encourage direct comparisons of these methods and pipelines. It is hoped that providing open-source functions will aid in both improving and standardising analysis across the field of TMS-EEG research. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

An open-source textbook for teaching climate-related risk analysis using the R computing environment

NASA Astrophysics Data System (ADS)

Applegate, P. J.; Keller, K.

2015-12-01

Greenhouse gas emissions lead to increased surface air temperatures and sea level rise. In turn, sea level rise increases the risks of flooding for people living near the world's coastlines. Our own research on assessing sea level rise-related risks emphasizes both Earth science and statistics. At the same time, the free, open-source computing environment R is growing in popularity among statisticians and scientists due to its flexibility and graphics capabilities, as well as its large library of existing functions. We have developed a set of laboratory exercises that introduce students to the Earth science and statistical concepts needed for assessing the risks presented by climate change, particularly sea-level rise. These exercises will be published as a free, open-source textbook on the Web. Each exercise begins with a description of the Earth science and/or statistical concepts that the exercise teaches, with references to key journal articles where appropriate. Next, students are asked to examine in detail a piece of existing R code, and the exercise text provides a clear explanation of how the code works. Finally, students are asked to modify the existing code to produce a well-defined outcome. We discuss our experiences in developing the exercises over two separate semesters at Penn State, plus using R Markdown to interweave explanatory text with sample code and figures in the textbook.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments.

PubMed

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E; Rost, Burkhard; Goldberg, Tatyana

2016-11-15

The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is 'web ready': written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/Supplementary information: Supplementary data are available at Bioinformatics online. msa@bio.sh. © The Author 2016. Published by Oxford University Press.

MSAViewer: interactive JavaScript visualization of multiple sequence alignments

PubMed Central

Yachdav, Guy; Wilzbach, Sebastian; Rauscher, Benedikt; Sheridan, Robert; Sillitoe, Ian; Procter, James; Lewis, Suzanna E.; Rost, Burkhard; Goldberg, Tatyana

2016-01-01

Summary: The MSAViewer is a quick and easy visualization and analysis JavaScript component for Multiple Sequence Alignment data of any size. Core features include interactive navigation through the alignment, application of popular color schemes, sorting, selecting and filtering. The MSAViewer is ‘web ready’: written entirely in JavaScript, compatible with modern web browsers and does not require any specialized software. The MSAViewer is part of the BioJS collection of components. Availability and Implementation: The MSAViewer is released as open source software under the Boost Software License 1.0. Documentation, source code and the viewer are available at http://msa.biojs.net/. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: msa@bio.sh PMID:27412096

Sensing Slow Mobility and Interesting Locations for Lombardy Region (italy): a Case Study Using Pointwise Geolocated Open Data

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Oxoli, D.; Zurbarán, M. A.

2016-06-01

During the past years Web 2.0 technologies have caused the emergence of platforms where users can share data related to their activities which in some cases are then publicly released with open licenses. Popular categories for this include community platforms where users can upload GPS tracks collected during slow travel activities (e.g. hiking, biking and horse riding) and platforms where users share their geolocated photos. However, due to the high heterogeneity of the information available on the Web, the sole use of these user-generated contents makes it an ambitious challenge to understand slow mobility flows as well as to detect the most visited locations in a region. Exploiting the available data on community sharing websites allows to collect near real-time open data streams and enables rigorous spatial-temporal analysis. This work presents an approach for collecting, unifying and analysing pointwise geolocated open data available from different sources with the aim of identifying the main locations and destinations of slow mobility activities. For this purpose, we collected pointwise open data from the Wikiloc platform, Twitter, Flickr and Foursquare. The analysis was confined to the data uploaded in Lombardy Region (Northern Italy) - corresponding to millions of pointwise data. Collected data was processed through the use of Free and Open Source Software (FOSS) in order to organize them into a suitable database. This allowed to run statistical analyses on data distribution in both time and space by enabling the detection of users' slow mobility preferences as well as places of interest at a regional scale.

Web catalog of oceanographic data using GeoNetwork

NASA Astrophysics Data System (ADS)

Marinova, Veselka; Stefanov, Asen

2017-04-01

Most of the data collected, analyzed and used by Bulgarian oceanographic data center (BgODC) from scientific cruises, argo floats, ferry boxes and real time operating systems are spatially oriented and need to be displayed on the map. The challenge is to make spatial information more accessible to users, decision makers and scientists. In order to meet this challenge, BgODC concentrate its efforts on improving dynamic and standardized access to their geospatial data as well as those from various related organizations and institutions. BgODC currently is implementing a project to create a geospatial portal for distributing metadata and search, exchange and harvesting spatial data. There are many open source software solutions able to create such spatial data infrastructure (SDI). Finally, the GeoNetwork open source is chosen, as it is already widespread. This software is free, effective and "cheap" solution for implementing SDI at organization level. It is platform independent and runs under many operating systems. Filling of the catalog goes through these practical steps: • Managing and storing data reliably within MS SQL spatial data base; • Registration of maps and data of various formats and sources in GeoServer (most popular open source geospatial server embedded with GeoNetwork) ; • Filling added meta data and publishing geospatial data at the desktop of GeoNetwork. GeoServer and GeoNetwork are based on Java so they require installing of a servlet engine like Tomcat. The experience gained from the use of GeoNetwork Open Source confirms that the catalog meets the requirements for data management and is flexible enough to customize. Building the catalog facilitates sustainable data exchange between end users. The catalog is a big step towards implementation of the INSPIRE directive due to availability of many features necessary for producing "INSPIRE compliant" metadata records. The catalog now contains all available GIS data provided by BgODC for Internet access. Searching data within the catalog is based upon geographic extent, theme type and free text search.

Teaching for Social Change--Mission "Possible"? Cultural Studies Approaches to Teaching Popular Culture.

ERIC Educational Resources Information Center

Banning, Marlia

It is an open question whether popular culture courses are effective sites in which to instill the kinds of critical media literacies that might contribute to students acting in support of social justice in their everyday lives. A course called "The Uses of Popular Culture" focuses on contemporary multicultural American society to…

Patterns and sources of alcohol consumption preceding alcohol-affected attendances to a New Zealand hospital emergency department.

PubMed

Das, Manidipa; Stewart, Rebecca; Ardagh, Michael; Deely, Joanne M; Dodd, Stuart; Bartholomew, Nadia V; Pearson, Scott; Spearing, Ruth; Williams, Tracey; Than, Martin

2014-08-29

To perform a descriptive study of the drinking behaviour (amounts, types, sources of alcohol consumed) preceding alcohol-affected presentations to Christchurch Hospital Emergency Department (ED). Over 336 hours in the ED, patients with recent alcohol consumption or alcohol-related attendances were identified, classified as alcohol-affected or alcohol- unaffected, and invited to consent to answering questions on types, amounts and sources of alcohol consumed in the drinking session preceding or implicated in their ED attendance. Demographic information and level of intoxication were also recorded. Data were summarised descriptively. Alcohol-affected patients were more frequently young (16-25 years) and male. Median alcohol consumption was 14 (range 1 to 71) standard drinks. Beer was the most popular beverage (34%), but spirits (23%), ready-to-drink mixes (21%) and wine (20%) were also popular. Liquor stores (45%) were the most popular source of alcohol, followed by on-licence premises (25%), and supermarkets (21%). The popularity of different types of beverages and their source varied according to patient age and gender. Consumption of large amounts, as well as allegedly 'safe' amounts, of a range of alcoholic beverages, most commonly from an off-licence source, contributed to alcohol-affected presentations to the ED. Beverage and source popularity varied by age and gender.

Popularizing dissent: A civil society perspective.

PubMed

Motion, Judy; Leitch, Shirley; Weaver, C Kay

2015-05-01

This article theorizes civil society groups' attempts to popularize opposition to genetic modification in New Zealand as deliberative interventions that seek to open up public participation in science-society governance. In this case, the popularization strategies were designed to intensify concerns about social justice and democratic incursions, mobilize dissent and offer meaningful mechanisms for navigating and participating in public protest. Such civic popularization efforts, we argue, are more likely to succeed when popularity and politicization strategies are judiciously integrated to escalate controversy, re-negotiate power relations and provoke agency and action. © The Author(s) 2014.

A High Precision $3.50 Open Source 3D Printed Rain Gauge Calibrator

NASA Astrophysics Data System (ADS)

Lopez Alcala, J. M.; Udell, C.; Selker, J. S.

2017-12-01

Currently available rain gauge calibrators tend to be designed for specific rain gauges, are expensive, employ low-precision water reservoirs, and do not offer the flexibility needed to test the ever more popular small-aperture rain gauges. The objective of this project was to develop and validate a freely downloadable, open-source, 3D printed rain gauge calibrator that can be adjusted for a wide range of gauges. The proposed calibrator provides for applying low, medium, and high intensity flow, and allows the user to modify the design to conform to unique system specifications based on parametric design, which may be modified and printed using CAD software. To overcome the fact that different 3D printers yield different print qualities, we devised a simple post-printing step that controlled critical dimensions to assure robust performance. Specifically, the three orifices of the calibrator are drilled to reach the three target flow rates. Laboratory tests showed that flow rates were consistent between prints, and between trials of each part, while the total applied water was precisely controlled by the use of a volumetric flask as the reservoir.

IdentiPy: An Extensible Search Engine for Protein Identification in Shotgun Proteomics.

PubMed

Levitsky, Lev I; Ivanov, Mark V; Lobas, Anna A; Bubis, Julia A; Tarasova, Irina A; Solovyeva, Elizaveta M; Pridatchenko, Marina L; Gorshkov, Mikhail V

2018-06-18

We present an open-source, extensible search engine for shotgun proteomics. Implemented in Python programming language, IdentiPy shows competitive processing speed and sensitivity compared with the state-of-the-art search engines. It is equipped with a user-friendly web interface, IdentiPy Server, enabling the use of a single server installation accessed from multiple workstations. Using a simplified version of X!Tandem scoring algorithm and its novel "autotune" feature, IdentiPy outperforms the popular alternatives on high-resolution data sets. Autotune adjusts the search parameters for the particular data set, resulting in improved search efficiency and simplifying the user experience. IdentiPy with the autotune feature shows higher sensitivity compared with the evaluated search engines. IdentiPy Server has built-in postprocessing and protein inference procedures and provides graphic visualization of the statistical properties of the data set and the search results. It is open-source and can be freely extended to use third-party scoring functions or processing algorithms and allows customization of the search workflow for specialized applications.

Visualization of N-body Simulations in Virtual Worlds

NASA Astrophysics Data System (ADS)

Knop, Robert A.; Ames, J.; Djorgovski, G.; Farr, W.; Hut, P.; Johnson, A.; McMillan, S.; Nakasone, A.; Vesperini, E.

2010-01-01

We report on work to use virtual worlds for visualizing the results of N-body calculations, on three levels. First, we have written a demonstration 3-body solver entirely in the scripting language of the popularly used virtual world Second Life. Second, we have written a physics module for the open source virtual world OpenSim that performs N-body calculations as the physics engine for the server, allowing natural 3-d visualization of the solution as the solution is being performed. Finally, we give an initial report on the potential use of virtual worlds to visualize calculations which have previously been performed, or which are being performed in other processes and reported to the virtual world server. This work has been performed as part of the Meta-Institute of Computational Astrophysics (MICA). http://www.mica-vw.org

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets.

PubMed

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; Del-Toro, Noemi; Dianes, Jose A; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE.The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX "complete" submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

PRIDE Inspector Toolsuite: Moving Toward a Universal Visualization Tool for Proteomics Data Standard Formats and Quality Assessment of ProteomeXchange Datasets*

PubMed Central

Perez-Riverol, Yasset; Xu, Qing-Wei; Wang, Rui; Uszkoreit, Julian; Griss, Johannes; Sanchez, Aniel; Reisinger, Florian; Csordas, Attila; Ternent, Tobias; del-Toro, Noemi; Dianes, Jose A.; Eisenacher, Martin; Hermjakob, Henning; Vizcaíno, Juan Antonio

2016-01-01

The original PRIDE Inspector tool was developed as an open source standalone tool to enable the visualization and validation of mass-spectrometry (MS)-based proteomics data before data submission or already publicly available in the Proteomics Identifications (PRIDE) database. The initial implementation of the tool focused on visualizing PRIDE data by supporting the PRIDE XML format and a direct access to private (password protected) and public experiments in PRIDE. The ProteomeXchange (PX) Consortium has been set up to enable a better integration of existing public proteomics repositories, maximizing its benefit to the scientific community through the implementation of standard submission and dissemination pipelines. Within the Consortium, PRIDE is focused on supporting submissions of tandem MS data. The increasing use and popularity of the new Proteomics Standards Initiative (PSI) data standards such as mzIdentML and mzTab, and the diversity of workflows supported by the PX resources, prompted us to design and implement a new suite of algorithms and libraries that would build upon the success of the original PRIDE Inspector and would enable users to visualize and validate PX “complete” submissions. The PRIDE Inspector Toolsuite supports the handling and visualization of different experimental output files, ranging from spectra (mzML, mzXML, and the most popular peak lists formats) and peptide and protein identification results (mzIdentML, PRIDE XML, mzTab) to quantification data (mzTab, PRIDE XML), using a modular and extensible set of open-source, cross-platform libraries. We believe that the PRIDE Inspector Toolsuite represents a milestone in the visualization and quality assessment of proteomics data. It is freely available at http://github.com/PRIDE-Toolsuite/. PMID:26545397

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.

In-car countermeasures open window and music revisited on the real road: popular but hardly effective against driver sleepiness.

PubMed

Schwarz, Johanna F A; Ingre, Michael; Fors, Carina; Anund, Anna; Kecklund, Göran; Taillard, Jacques; Philip, Pierre; Åkerstedt, Torbjörn

2012-10-01

This study investigated the effects of two very commonly used countermeasures against driver sleepiness, opening the window and listening to music, on subjective and physiological sleepiness measures during real road driving. In total, 24 individuals participated in the study. Sixteen participants received intermittent 10-min intervals of: (i) open window (2 cm opened); and (ii) listening to music, during both day and night driving on an open motorway. Both subjective sleepiness and physiological sleepiness (blink duration) was estimated to be significantly reduced when subjects listened to music, but the effect was only minor compared with the pronounced effects of night driving and driving duration. Open window had no attenuating effect on either sleepiness measure. No significant long-term effects beyond the actual countermeasure application intervals occurred, as shown by comparison to the control group (n = 8). Thus, despite their popularity, opening the window and listening to music cannot be recommended as sole countermeasures against driver sleepiness. © 2012 European Sleep Research Society.

Marriage and Retirement: Advice to Couples in Popular Literature.

ERIC Educational Resources Information Center

Harbert, Ellen M.; And Others

Though academic research has shown retirement to be viewed by retirees as a satisfying time in life, popular opinion holds that retirement is a difficult adjustment for a couple. This study was undertaken to find out more about one source of popular opinion, the popular press. All popular books and magazine articles on the topic of marriage and…

The Development of Wireless Body Area Network for Motion Sensing Application

NASA Astrophysics Data System (ADS)

Puspitaningayu, P.; Widodo, A.; Yundra, E.; Ramadhany, F.; Arianto, L.; Habibie, D.

2018-04-01

The information era has driven the society into the digitally-controlled lifestyle. Wireless body area networks (WBAN) as the specific scope of wireless sensor networks (WSN) is consistently growing into bigger applications. Currently, people are able to monitor their medical parameters by simply using small electronics devices attached to their body and connected to the authorities. On top of that, this time, smart phones are typically equipped with sensors such as accelerometer, gyroscope, barometric pressure, heart rate monitor, etc. It means that the sensing yet the signal processing can be performed by a single device. Moreover, Android opens lot wider opportunities for new applications as the most popular open-sourced smart phone platform. This paper is intended to show the development of motion sensing application which focused on analysing data from accelerometer and gyroscope. Beside reads the sensors, this application also has the ability to convert the sensors’ numerical value into graphs.

Performance of Reynolds Averaged Navier-Stokes Models in Predicting Separated Flows: Study of the Hump Flow Model Problem

NASA Technical Reports Server (NTRS)

Cappelli, Daniele; Mansour, Nagi N.

2012-01-01

Separation can be seen in most aerodynamic flows, but accurate prediction of separated flows is still a challenging problem for computational fluid dynamics (CFD) tools. The behavior of several Reynolds Averaged Navier-Stokes (RANS) models in predicting the separated ow over a wall-mounted hump is studied. The strengths and weaknesses of the most popular RANS models (Spalart-Allmaras, k-epsilon, k-omega, k-omega-SST) are evaluated using the open source software OpenFOAM. The hump ow modeled in this work has been documented in the 2004 CFD Validation Workshop on Synthetic Jets and Turbulent Separation Control. Only the baseline case is treated; the slot flow control cases are not considered in this paper. Particular attention is given to predicting the size of the recirculation bubble, the position of the reattachment point, and the velocity profiles downstream of the hump.

E-learning and blended learning in textile engineering education: a closed feedback loop approach

NASA Astrophysics Data System (ADS)

Charitopoulos, A.; Vassiliadis, S.; Rangoussi, M.; Koulouriotis, D.

2017-10-01

E-learning has gained a significant role in typical education and in professional training, thanks to the flexibility it offers to the time and location parameters of the education event framework. Purely e-learning scenarios are mostly limited either to Open University-type higher education institutions or to graduate level or professional degrees; blended learning scenarios are progressively becoming popular thanks to their balanced approach. The aim of the present work is to propose approaches that exploit the e-learning and the blended-learning scenarios for Textile Engineering education programmes, especially for multi-institutional ones. The “E-Team” European MSc degree programme organized by AUTEX is used as a case study. The proposed solution is based on (i) a free and open-source e-learning platform (moodle) and (ii) blended learning educational scenarios. Educational challenges addressed include student engagement, student error / failure handling, as well as collaborative learning promotion and support.

Combining Open-Source Packages for Planetary Exploration

NASA Astrophysics Data System (ADS)

Schmidt, Albrecht; Grieger, Björn; Völk, Stefan

2015-04-01

The science planning of the ESA Rosetta mission has presented challenges which were addressed with combining various open-source software packages, such as the SPICE toolkit, the Python language and the Web graphics library three.js. The challenge was to compute certain parameters from a pool of trajectories and (possible) attitudes to describe the behaviour of the spacecraft. To be able to do this declaratively and efficiently, a C library was implemented that allows to interface the SPICE toolkit for geometrical computations from the Python language and process as much data as possible during one subroutine call. To minimise the lines of code one has to write special care was taken to ensure that the bindings were idiomatic and thus integrate well into the Python language and ecosystem. When done well, this very much simplifies the structure of the code and facilitates the testing for correctness by automatic test suites and visual inspections. For rapid visualisation and confirmation of correctness of results, the geometries were visualised with the three.js library, a popular Javascript library for displaying three-dimensional graphics in a Web browser. Programmatically, this was achieved by generating data files from SPICE sources that were included into templated HTML and displayed by a browser, thus made easily accessible to interested parties at large. As feedback came and new ideas were to be explored, the authors benefited greatly from the design of the Python-to-SPICE library which allowed the expression of algorithms to be concise and easier to communicate. In summary, by combining several well-established open-source tools, we were able to put together a flexible computation and visualisation environment that helped communicate and build confidence in planning ideas.

cp-R, an interface the R programming language for clinical laboratory method comparisons.

PubMed

Holmes, Daniel T

2015-02-01

Clinical scientists frequently need to compare two different bioanalytical methods as part of assay validation/monitoring. As a matter necessity, regression methods for quantitative comparison in clinical chemistry, hematology and other clinical laboratory disciplines must allow for error in both the x and y variables. Traditionally the methods popularized by 1) Deming and 2) Passing and Bablok have been recommended. While commercial tools exist, no simple open source tool is available. The purpose of this work was to develop and entirely open-source GUI-driven program for bioanalytical method comparisons capable of performing these regression methods and able to produce highly customized graphical output. The GUI is written in python and PyQt4 with R scripts performing regression and graphical functions. The program can be run from source code or as a pre-compiled binary executable. The software performs three forms of regression and offers weighting where applicable. Confidence bands of the regression are calculated using bootstrapping for Deming and Passing Bablok methods. Users can customize regression plots according to the tools available in R and can produced output in any of: jpg, png, tiff, bmp at any desired resolution or ps and pdf vector formats. Bland Altman plots and some regression diagnostic plots are also generated. Correctness of regression parameter estimates was confirmed against existing R packages. The program allows for rapid and highly customizable graphical output capable of conforming to the publication requirements of any clinical chemistry journal. Quick method comparisons can also be performed and cut and paste into spreadsheet or word processing applications. We present a simple and intuitive open source tool for quantitative method comparison in a clinical laboratory environment. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Designing a Resource Evolution Support System for Open Knowledge Communities

ERIC Educational Resources Information Center

Yang, Xianmin; Yu, Shengquan

2015-01-01

The continuous generation and evolution of digital learning resources is important for promoting open learning and meeting the personalized needs of learners. In the Web 2.0 era, open and collaborative authoring is becoming a popular method by which to create vast personalized learning resources in open knowledge communities (OKCs). However, the…

A Web Portal-Based Time-Aware KML Animation Tool for Exploring Spatiotemporal Dynamics of Hydrological Events

NASA Astrophysics Data System (ADS)

Bao, X.; Cai, X.; Liu, Y.

2009-12-01

Understanding spatiotemporal dynamics of hydrological events such as storms and droughts is highly valuable for decision making on disaster mitigation and recovery. Virtual Globe-based technologies such as Google Earth and Open Geospatial Consortium KML standards show great promises for collaborative exploration of such events using visual analytical approaches. However, currently there are two barriers for wider usage of such approaches. First, there lacks an easy way to use open source tools to convert legacy or existing data formats such as shapefiles, geotiff, or web services-based data sources to KML and to produce time-aware KML files. Second, an integrated web portal-based time-aware animation tool is currently not available. Thus users usually share their files in the portal but have no means to visually explore them without leaving the portal environment which the users are familiar with. We develop a web portal-based time-aware KML animation tool for viewing extreme hydrologic events. The tool is based on Google Earth JavaScript API and Java Portlet standard 2.0 JSR-286, and it is currently deployable in one of the most popular open source portal frameworks, namely Liferay. We have also developed an open source toolkit kml-soc-ncsa (http://code.google.com/p/kml-soc-ncsa/) to facilitate the conversion of multiple formats into KML and the creation of time-aware KML files. We illustrate our tool using some example cases, in which drought and storm events with both time and space dimension can be explored in this web-based KML animation portlet. The tool provides an easy-to-use web browser-based portal environment for multiple users to collaboratively share and explore their time-aware KML files as well as improving the understanding of the spatiotemporal dynamics of the hydrological events.

Wonder and the clinical encounter.

PubMed

Evans, H M

2012-04-01

In terms of intervening in embodied experience, medical treatment is wonder-full in its ambition and its metaphysical presumption; yet, wonder's role in clinical medicine has received little philosophical attention. In this paper, I propose, to doctors and others in routine clinical life, the value of an openness to wonder and to the sense of wonder. Key to this is the identity of the central ethical challenges facing most clinicians, which is not the high-tech drama of the popular conceptions of medical ethics but, rather, the routine of patients' undramatic but unremitting demands for the clinician's time and respectful attention. Wonder (conceived as an intense and transfiguring attentiveness) is a ubiquitous ethical source, an alternative to the more familiar respect for rational autonomy, a source of renewal galvanizing diagnostic imagination, and a timely recalling of the embodied agency of both patient and clinician.

Synchrotron-based ambient pressure X-ray photoelectron spectroscopy of hydrogen and helium

DOE PAGES

Zhong, Jian-Qiang; Wang, Mengen; Hoffmann, William H.; ...

2018-03-01

Contrary to popular belief, it is possible to obtain X-ray photoelectron spectra for elements lighter than lithium, namely hydrogen and helium. The literature is plagued with claims of this impossibility, which holds true for lab-based X-ray sources. However, this limitation is merely technical and is related mostly to the low X-ray photoionization cross-sections of the 1s orbitals of hydrogen and helium. Here, we show that, using ambient pressure X-ray photoelectron spectroscopy (XPS), a bright-enough X-ray source allows the study of these elusive elements. This has important implications in the understanding of the limitations of one of the most useful techniquesmore » in materials science, and moreover, it potentially opens the possibility of using XPS to directly study the most abundant element in the universe.« less

HGDB: A web retrieving cardiovascular-associated gene data.

PubMed

Noorabad-Ghahroodi, Faezeh; Abdi, Samaneh; Zand, Amir Hossein; Najafi, Mohammad

2017-04-01

The use of data obtained from high throughput techniques in genetics studies is an essential subject in biology. The system approaches of networking and enriching may improve the data management. Here, we annotated the molecular features for cardiovascular-associated genes and presented the HGDB search-based database (www.hgdb.ir). The initial seed data was primarily used from Gene Ontology and was automatically enriched with other molecular features. The data was managed in a SQL popular and open source. The search tabs on the HGDB homepage were applied for ID/Name Gene, chromosome, cell organelle and all gene options. The search results were presented on the gene text-based and source link-based descriptions. The HGDB is a friendly website to present gene data in the cardiovascular field. Copyright © 2017 Elsevier B.V. All rights reserved.

Synchrotron-based ambient pressure X-ray photoelectron spectroscopy of hydrogen and helium

NASA Astrophysics Data System (ADS)

Zhong, Jian-Qiang; Wang, Mengen; Hoffmann, William H.; van Spronsen, Matthijs A.; Lu, Deyu; Boscoboinik, J. Anibal

2018-02-01

Contrary to popular belief, it is possible to obtain X-ray photoelectron spectra for elements lighter than lithium, namely hydrogen and helium. The literature is plagued with claims of this impossibility, which holds true for lab-based X-ray sources. However, this limitation is merely technical and is related mostly to the low X-ray photoionization cross-sections of the 1s orbitals of hydrogen and helium. In this letter, we show that, using ambient pressure X-ray photoelectron spectroscopy (XPS), a bright-enough X-ray source allows the study of these elusive elements. This has important implications in the understanding of the limitations of one of the most useful techniques in materials science, and moreover, it potentially opens the possibility of using XPS to directly study the most abundant element in the universe.

Synchrotron-based ambient pressure X-ray photoelectron spectroscopy of hydrogen and helium

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

Zhong, Jian-Qiang; Wang, Mengen; Hoffmann, William H.

Contrary to popular belief, it is possible to obtain X-ray photoelectron spectra for elements lighter than lithium, namely hydrogen and helium. The literature is plagued with claims of this impossibility, which holds true for lab-based X-ray sources. However, this limitation is merely technical and is related mostly to the low X-ray photoionization cross-sections of the 1s orbitals of hydrogen and helium. Here, we show that, using ambient pressure X-ray photoelectron spectroscopy (XPS), a bright-enough X-ray source allows the study of these elusive elements. This has important implications in the understanding of the limitations of one of the most useful techniquesmore » in materials science, and moreover, it potentially opens the possibility of using XPS to directly study the most abundant element in the universe.« less

Further Development of Verification Check-Cases for Six- Degree-of-Freedom Flight Vehicle Simulations

NASA Technical Reports Server (NTRS)

Jackson, E. Bruce; Madden, Michael M.; Shelton, Robert; Jackson, A. A.; Castro, Manuel P.; Noble, Deleena M.; Zimmerman, Curtis J.; Shidner, Jeremy D.; White, Joseph P.; Dutta, Doumyo;

Thermo-msf-parser: an open source Java library to parse and visualize Thermo Proteome Discoverer msf files.

PubMed

Colaert, Niklaas; Barsnes, Harald; Vaudel, Marc; Helsens, Kenny; Timmerman, Evy; Sickmann, Albert; Gevaert, Kris; Martens, Lennart

2011-08-05

The Thermo Proteome Discoverer program integrates both peptide identification and quantification into a single workflow for peptide-centric proteomics. Furthermore, its close integration with Thermo mass spectrometers has made it increasingly popular in the field. Here, we present a Java library to parse the msf files that constitute the output of Proteome Discoverer. The parser is also implemented as a graphical user interface allowing convenient access to the information found in the msf files, and in Rover, a program to analyze and validate quantitative proteomics information. All code, binaries, and documentation is freely available at http://thermo-msf-parser.googlecode.com.

GEOMAGIA50: An archeointensity database with PHP and MySQL

NASA Astrophysics Data System (ADS)

Korhonen, K.; Donadini, F.; Riisager, P.; Pesonen, L. J.

2008-04-01

The GEOMAGIA50 database stores 3798 archeomagnetic and paleomagnetic intensity determinations dated to the past 50,000 years. It also stores details of the measurement setup for each determination, which are used for ranking the data according to prescribed reliability criteria. The ranking system aims to alleviate the data reliability problem inherent in this kind of data. GEOMAGIA50 is based on two popular open source technologies. The MySQL database management system is used for storing the data, whereas the functionality and user interface are provided by server-side PHP scripts. This technical brief gives a detailed description of GEOMAGIA50 from a technical viewpoint.

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

Using Popular Culture in Developmental Writing

ERIC Educational Resources Information Center

Barnes, Sharon L.

2006-01-01

Using popular culture in my developmental writing course has prompted me to reconsider what it means to create successful developmental writing assignments. Having slipped into the questionable habit of assuming that removing complexity makes an assignment appropriate for developing writers, I pared down a fairly open-ended "media…

Panorama: A Targeted Proteomics Knowledge Base

PubMed Central

2015-01-01

Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline,1 an increasingly popular Windows client software tool for targeted proteomics experiments. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates distributed collaboration and secure sharing of published and unpublished data via a web-browser interface. It is fully integrated with the Skyline workflow and supports publishing a document directly to a Panorama server from the Skyline user interface. Panorama captures the complete Skyline document information content in a relational database schema. Curated results published to Panorama can be aggregated and exported as chromatogram libraries. These libraries can be used in Skyline to pick optimal targets in new experiments and to validate peak identification of target peptides. Panorama is open-source and freely available. It is distributed as part of LabKey Server,2 an open source biomedical research data management system. Laboratories and organizations can set up Panorama locally by downloading and installing the software on their own servers. They can also request freely hosted projects on https://panoramaweb.org, a Panorama server maintained by the Department of Genome Sciences at the University of Washington. PMID:25102069

Open source integrated modeling environment Delta Shell

NASA Astrophysics Data System (ADS)

Donchyts, G.; Baart, F.; Jagers, B.; van Putten, H.

2012-04-01

In the last decade, integrated modelling has become a very popular topic in environmental modelling since it helps solving problems, which is difficult to model using a single model. However, managing complexity of integrated models and minimizing time required for their setup remains a challenging task. The integrated modelling environment Delta Shell simplifies this task. The software components of Delta Shell are easy to reuse separately from each other as well as a part of integrated environment that can run in a command-line or a graphical user interface mode. The most components of the Delta Shell are developed using C# programming language and include libraries used to define, save and visualize various scientific data structures as well as coupled model configurations. Here we present two examples showing how Delta Shell simplifies process of setting up integrated models from the end user and developer perspectives. The first example shows coupling of a rainfall-runoff, a river flow and a run-time control models. The second example shows how coastal morphological database integrates with the coastal morphological model (XBeach) and a custom nourishment designer. Delta Shell is also available as open-source software released under LGPL license and accessible via http://oss.deltares.nl.

Architectures for Rainfall Property Estimation From Polarimetric Radar

NASA Astrophysics Data System (ADS)

Collis, S. M.; Giangrande, S. E.; Helmus, J.; Troemel, S.

2014-12-01

Radars that transmit and receive signals in polarizations aligned both horizontal and vertical to the horizon collect a number of measurements. The relation both between these measurements and between measurements and desired microphysical quantities (such as rainfall rate) is complicated due to a number of scattering mechanisms. The result is that there ends up being an intractable number of often incompatible techniques for extracting geophysical insight. This presentation will discuss methods developed by the Atmospheric Measurement Climate (ARM) Research Facility to streamline the creation of application chains for retrieving rainfall properties for the purposes of fine scale model evaluation. By using a Common Data Model (CDM) approach and working in the popular open source Python scientific environment analysis techniques such as Linear Programming (LP) can be bought to bear on the task of retrieving insight from radar signals. This presentation will outline how we have used these techniques to detangle polarimetric phase signals, estimate a three-dimensional precipitation field and then objectively compare to cloud resolving model derived rainfall fields from the NASA/DoE Mid-Latitude Continental Convective Clouds Experiment (MC3E). All techniques show will be available, open source, in the Python-ARM Radar Toolkit (Py-ART).

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

DasPy 1.0 - the Open Source Multivariate Land Data Assimilation Framework in combination with the Community Land Model 4.5

NASA Astrophysics Data System (ADS)

Han, X.; Li, X.; He, G.; Kumbhar, P.; Montzka, C.; Kollet, S.; Miyoshi, T.; Rosolem, R.; Zhang, Y.; Vereecken, H.; Franssen, H.-J. H.

2015-08-01

Data assimilation has become a popular method to integrate observations from multiple sources with land surface models to improve predictions of the water and energy cycles of the soil-vegetation-atmosphere continuum. Multivariate data assimilation refers to the simultaneous assimilation of observation data from multiple model state variables into a simulation model. In recent years, several land data assimilation systems have been developed in different research agencies. Because of the software availability or adaptability, these systems are not easy to apply for the purpose of multivariate land data assimilation research. We developed an open source multivariate land data assimilation framework (DasPy) which is implemented using the Python script language mixed with the C++ and Fortran programming languages. LETKF (Local Ensemble Transform Kalman Filter) is implemented as the main data assimilation algorithm, and uncertainties in the data assimilation can be introduced by perturbed atmospheric forcing data, and represented by perturbed soil and vegetation parameters and model initial conditions. The Community Land Model (CLM) was integrated as the model operator. The implementation allows also parameter estimation (soil properties and/or leaf area index) on the basis of the joint state and parameter estimation approach. The Community Microwave Emission Modelling platform (CMEM), COsmic-ray Soil Moisture Interaction Code (COSMIC) and the Two-Source Formulation (TSF) were integrated as observation operators for the assimilation of L-band passive microwave, cosmic-ray soil moisture probe and land surface temperature measurements, respectively. DasPy has been evaluated in several assimilation studies of neutron count intensity (soil moisture), L-band brightness temperature and land surface temperature. DasPy is parallelized using the hybrid Message Passing Interface and Open Multi-Processing techniques. All the input and output data flows are organized efficiently using the commonly used NetCDF file format. Online 1-D and 2-D visualization of data assimilation results is also implemented to facilitate the post simulation analysis. In summary, DasPy is a ready to use open source parallel multivariate land data assimilation framework.

Conversion of HSPF Legacy Model to a Platform-Independent, Open-Source Language

NASA Astrophysics Data System (ADS)

Heaphy, R. T.; Burke, M. P.; Love, J. T.

2015-12-01

Since its initial development over 30 years ago, the Hydrologic Simulation Program - FORTAN (HSPF) model has been used worldwide to support water quality planning and management. In the United States, HSPF receives widespread endorsement as a regulatory tool at all levels of government and is a core component of the EPA's Better Assessment Science Integrating Point and Nonpoint Sources (BASINS) system, which was developed to support nationwide Total Maximum Daily Load (TMDL) analysis. However, the model's legacy code and data management systems have limitations in their ability to integrate with modern software, hardware, and leverage parallel computing, which have left voids in optimization, pre-, and post-processing tools. Advances in technology and our scientific understanding of environmental processes that have occurred over the last 30 years mandate that upgrades be made to HSPF to allow it to evolve and continue to be a premiere tool for water resource planners. This work aims to mitigate the challenges currently facing HSPF through two primary tasks: (1) convert code to a modern widely accepted, open-source, high-performance computing (hpc) code; and (2) convert model input and output files to modern widely accepted, open-source, data model, library, and binary file format. Python was chosen as the new language for the code conversion. It is an interpreted, object-oriented, hpc code with dynamic semantics that has become one of the most popular open-source languages. While python code execution can be slow compared to compiled, statically typed programming languages, such as C and FORTRAN, the integration of Numba (a just-in-time specializing compiler) has allowed this challenge to be overcome. For the legacy model data management conversion, HDF5 was chosen to store the model input and output. The code conversion for HSPF's hydrologic and hydraulic modules has been completed. The converted code has been tested against HSPF's suite of "test" runs and shown good agreement and similar execution times while using the Numba compiler. Continued verification of the accuracy of the converted code against more complex legacy applications and improvement upon execution times by incorporating an intelligent network change detection tool is currently underway, and preliminary results will be presented.

Inexpensive, Low Power, Open-Source Data Logging in the Field

NASA Astrophysics Data System (ADS)

Sandell, C. T.; Wickert, A. D.

2016-12-01

Collecting a robust data set of environmental conditions with commercial equipment is often cost prohibitive. I present the ALog, a general-purpose, inexpensive, low-power, open-source data logger that has proven its durability on long-term deployments in the harsh conditions of high altitude glaciers and humid river deltas. The ALog was developed to fill the need for a capable, rugged, easy-to-use, inexpensive, open-source hardware targeted at long-term remote deployment in nearly any environment. Building on the popular Arduino platform, the hardware features a high-precision clock, full size SD card slot for high-volume data storage, screw terminals, six analog inputs, two digital inputs, one digital interrupt, 3.3V and 5V power outputs, and SPI and I2C communication capability. The design is focused on extremely low power consumption allowing the Alog to be deployed for years on a single set of common alkaline batteries. The power efficiency of the Alog eliminates the difficulties associated with field power collection including additional hardware and installation costs, dependence on weather conditions, possible equipment failure, and the transport of bulky/heavy equipment to a remote site. Battery power increases suitable data collection sites (too shaded for photovoltaics) and allows for low profile installation options (including underground). The ALog has gone through continuous development with over four years of successful data collection in hydrologic field research. Over this time, software support for a wide range of sensors has been made available such as ultrasonic rangefinders (for water level, snow accumulation and glacial melt), temperature sensors (air and groundwater), humidity sensors, pyranometers, inclinometers, rain gauges, soil moisture and water potential sensors, resistance-based tools to measure frost heave, and cameras that trigger on events. The software developed for use with the ALog allows simple integration of established commercial sensors, including example implementation code so users with limited programming knowledge can get up and running with ease. All development files including design schematics, circuit board layouts, and source code files are open-source to further eliminate barriers to its use and allow community development contribution.

Weiqi games as a tree: Zipf's law of openings and beyond

NASA Astrophysics Data System (ADS)

Xu, Li-Gong; Li, Ming-Xia; Zhou, Wei-Xing

2015-06-01

Weiqi is one of the most complex board games played by two persons. The placement strategies adopted by Weiqi players are often used to analog the philosophy of human wars. Contrary to the western chess, Weiqi games are less studied by academics partially because Weiqi is popular only in East Asia, especially in China, Japan and Korea. Here, we propose to construct a directed tree using a database of extensive Weiqi games and perform a quantitative analysis of the Weiqi tree. We find that the popularity distribution of Weiqi openings with the same number of moves is distributed according to a power law and the tail exponent increases with the number of moves. Intriguingly, the superposition of the popularity distributions of Weiqi openings with a number of moves not higher than a given number also has a power-law tail in which the tail exponent increases with the number of moves, and the superposed distribution approaches the Zipf law. These findings are the same as for chess and support the conjecture that the popularity distribution of board game openings follows the Zipf law with a universal exponent. We also find that the distribution of out-degrees has a power-law form, the distribution of branching ratios has a very complicated pattern, and the distribution of uniqueness scores defined by the path lengths from the root vertex to the leaf vertices exhibits a unimodal shape. Our work provides a promising direction for the study of the decision-making process of Weiqi playing from the perspective of directed branching tree.

Popularity of Russian information sources of medical education.

PubMed

Vasilyeva, Irina V; Arseniev, Sergey B

2014-01-01

The aim of the present study is to analyze the popularity of information sources of medical educational sites <webmedinfo.ru>, medical information portal <meduniver.com>, medical portal for students <6years.net>, electronic library of medical literature <booksmed.com>, <medliter.ru> and <medbook.net.ru>. Three sites (<www.webmedinfo.ru>, <meduniver.com> and <6years.net>) provide sources of medical literature, educational videos, medical histories, medical papers and medical popular literature. And three other sites (<www.booksmed.com>, <www.medliter.ru> and <www.medbook.net.ru>) provide sources for electronic medical books on various subjects. Using on-line programs Alexa and Cy-pr we have analyzed the website's rating and identified the main data and time-varying data of the sites. Calculated Alexa Rank rating was determined for each site. Our study has shown that the most popular information sources of medical education among the six studied sites for Russian users is <meduniver.com>; the site <booksmed.com> is at the second place referring to the Alexa Rank rating and the site <webmedinfo.ru> is at the second place referring to the citation index in Yandex. The most popular medical site of electronic medical books is <booksmed.com>.

BASKET on-board software library

NASA Astrophysics Data System (ADS)

Luntzer, Armin; Ottensamer, Roland; Kerschbaum, Franz

2014-07-01

The University of Vienna is a provider of on-board data processing software with focus on data compression, such as used on board the highly successful Herschel/PACS instrument, as well as in the small BRITE-Constellation fleet of cube-sats. Current contributions are made to CHEOPS, SAFARI and PLATO. The effort was taken to review the various functions developed for Herschel and provide a consolidated software library to facilitate the work for future missions. This library is a shopping basket of algorithms. Its contents are separated into four classes: auxiliary functions (e.g. circular buffers), preprocessing functions (e.g. for calibration), lossless data compression (arithmetic or Rice coding) and lossy reduction steps (ramp fitting etc.). The "BASKET" has all functionality that is needed to create an on-board data processing chain. All sources are written in C, supplemented by optimized versions in assembly, targeting popular CPU architectures for space applications. BASKET is open source and constantly growing

The ImageJ ecosystem: an open platform for biomedical image analysis

PubMed Central

Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W.

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available – from commercial to academic, special-purpose to Swiss army knife, small to large–but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts life science, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. PMID:26153368

The ImageJ ecosystem: An open platform for biomedical image analysis.

PubMed

Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

When Educational Resources Are Open

ERIC Educational Resources Information Center

Breck, Judy

2007-01-01

This article is a partial look at what the future of education might be if educational resources become open online. Intertwingularity is discussed as a general term for what OER will do online. Predictions about an open education future are based on nine quotations from books by popular writers about our networked age. When the network mechanisms…

Universal electronics for miniature and automated chemical assays.

PubMed

Urban, Pawel L

2015-02-21

This minireview discusses universal electronic modules (generic programmable units) and their use by analytical chemists to construct inexpensive, miniature or automated devices. Recently, open-source platforms have gained considerable popularity among tech-savvy chemists because their implementation often does not require expert knowledge and investment of funds. Thus, chemistry students and researchers can easily start implementing them after a few hours of reading tutorials and trial-and-error. Single-board microcontrollers and micro-computers such as Arduino, Teensy, Raspberry Pi or BeagleBone enable collecting experimental data with high precision as well as efficient control of electric potentials and actuation of mechanical systems. They are readily programmed using high-level languages, such as C, C++, JavaScript or Python. They can also be coupled with mobile consumer electronics, including smartphones as well as teleinformatic networks. More demanding analytical tasks require fast signal processing. Field-programmable gate arrays enable efficient and inexpensive prototyping of high-performance analytical platforms, thus becoming increasingly popular among analytical chemists. This minireview discusses the advantages and drawbacks of universal electronic modules, considering their application in prototyping and manufacture of intelligent analytical instrumentation.

Short-Term Solar Forecasting Performance of Popular Machine Learning Algorithms: Preprint

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

Florita, Anthony R; Elgindy, Tarek; Hodge, Brian S

A framework for assessing the performance of short-term solar forecasting is presented in conjunction with a range of numerical results using global horizontal irradiation (GHI) from the open-source Surface Radiation Budget (SURFRAD) data network. A suite of popular machine learning algorithms is compared according to a set of statistically distinct metrics and benchmarked against the persistence-of-cloudiness forecast and a cloud motion forecast. Results show significant improvement compared to the benchmarks with trade-offs among the machine learning algorithms depending on the desired error metric. Training inputs include time series observations of GHI for a history of years, historical weather and atmosphericmore » measurements, and corresponding date and time stamps such that training sensitivities might be inferred. Prediction outputs are GHI forecasts for 1, 2, 3, and 4 hours ahead of the issue time, and they are made for every month of the year for 7 locations. Photovoltaic power and energy outputs can then be made using the solar forecasts to better understand power system impacts.« less

Cordova: Web-based management of genetic variation data

PubMed Central

Ephraim, Sean S.; Anand, Nikhil; DeLuca, Adam P.; Taylor, Kyle R.; Kolbe, Diana L.; Simpson, Allen C.; Azaiez, Hela; Sloan, Christina M.; Shearer, A. Eliot; Hallier, Andrea R.; Casavant, Thomas L.; Scheetz, Todd E.; Smith, Richard J. H.; Braun, Terry A.

2014-01-01

Summary: Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician–scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Availability and implementation: Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Contact: sean.ephraim@gmail.com or terry-braun@uiowa.edu PMID:25123904

Content management systems and E-commerce: a comparative case study

NASA Astrophysics Data System (ADS)

Al Rasheed, Amal A.; El-Masri, Samir D.

2011-12-01

The need for CMS's to create and edit e-commerce websites has increased with the growing importance of e-commerce. In this paper, the various features essential for e-commerce CMS's are explored. The aim of the paper was to find the best CMS solution for e-commerce which includes the best of both CMS and store management. Accordingly, we conducted a study on three popular open source CMS's for e-commerce: VirtueMart from Joomla!, Ubercart from Drupal, and Magento. We took into account features like hosting and installation, performance, support/community, content management, add on modules and functional features. We concluded with improvements that could be made in order to alleviate problems.

UpSetR: an R package for the visualization of intersecting sets and their properties.

PubMed

Conway, Jake R; Lex, Alexander; Gehlenborg, Nils

2017-09-15

Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/ . nils@hms.harvard.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Integrating Space Communication Network Capabilities via Web Portal Technologies

NASA Technical Reports Server (NTRS)

Johnston, Mark D.; Lee, Carlyn-Ann; Lau, Chi-Wung; Cheung, Kar-Ming; Levesque, Michael; Carruth, Butch; Coffman, Adam; Wallace, Mike

2014-01-01

We have developed a service portal prototype as part of an investigation into the feasibility of using Java portlet technology as a means of providing integrated access to NASA communications network services. Portal servers provide an attractive platform for this role due to the various built-in collaboration applications they can provide, combined with the possibility to develop custom inter-operating portlets to extent their functionality while preserving common presentation and behavior. This paper describes various options for integration of network services related to planning and scheduling, and results based on use of a popular open-source portal framework. Plans are underway to develop an operational SCaN Service Portal, building on the experiences reported here.

Reasoning Strategies in the Context of Engineering Design with Everyday Materials

ERIC Educational Resources Information Center

Worsley, Marcelo; Blikstein, Paulo

2016-01-01

"Making" represents an increasingly popular label for describing a form of engineering design. While making is growing in popularity, there are still open questions about the strategies that students are using in these activities. Assessing and improving learning in making/ engineering design contexts require that we have a better…

Handedness and "Open-Earedness": Strong Right-Handers Are Less Likely to Prefer Less Popular Musical Genres

ERIC Educational Resources Information Center

Christman, Stephen D.

2013-01-01

Research shows that strong right-handedness is associated with decreased cognitive flexibility and decreased tendencies to update beliefs, arising from decreased interhemispheric interaction. In the current study, strong right-handedness was associated with decreased overall liking of less popular musical genres (with the specific genres of…

Development of an Information Security Awareness Training Program for the Royal Saudi Naval Forces (RSNF)

DTIC Science & Technology

2003-06-01

security faculty. This program offers great teaching along with the ability to master the material needed for the two most popular certifications in...then move on to an overview of some popular networks. The Open Systems Interconnect model (OSI) will be introduced to trainees to make them understand...several different network types, this part explains the two most popular types of networks: LANs and WANs. 2.1.4. Time: 30 Minutes 32 2.2. Network

Let Us Take a Yale Open Course: A Chinese View of Open Educational Resources Provided by Institutions in the West

ERIC Educational Resources Information Center

Xia, J.

2013-01-01

This research examines selected online comments from open courses available on Chinese websites. These courses were created by universities in the West as an effort to build open educational resources (OER) and were recently translated into Chinese and were relocated to some popular Chinese websites. This research aimed to understand why the…

Toward a Puerto Rican popular nosology: nervios and ataque de nervios.

PubMed

Guarnaccia, Peter J; Lewis-Fernández, Roberto; Marano, Melissa Rivera

2003-09-01

This paper is about naming illnesses--about who determines what categories are used and the implications of these determinations. The central concerns of medical/psychiatric anthropology have been to understand popular categories of and systems for classification of illness, to examine the relationship of illness categories to cultural understandings of the body, and to interpret the role of categories of illness in mediating between the personal and social spheres. At the same time, the paper also discusses the interplay of popular categories and psychiatric diagnoses. This paper examines the multiple experiences of nervios among Puerto Ricans in Puerto Rico and New York City. Our contention is that nervios is more than a diffuse idiom of distress, and that there are different categories and experiences of nervios which provide insights into how distress is experienced and expressed by Puerto Ricans and point to different social sources of suffering. The data in this paper come from the responses to a series of open-ended questions which tapped into people's general conceptions of nervios and ataques de nervios. These questions were incorporated into follow-up interviews to an epidemiological study of the mental health of adults in Puerto Rico. The results suggest ways to incorporate these different categories of nervios into future research and clinical work with different Latino groups in the United States and in their home countries.

TRENTOOL: A Matlab open source toolbox to analyse information flow in time series data with transfer entropy

PubMed Central

2011-01-01

Background Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. Results In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. Conclusions TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox. PMID:22098775

Inexpensive, Low Power, Open-Source Data Logging hardware development

NASA Astrophysics Data System (ADS)

Sandell, C. T.; Schulz, B.; Wickert, A. D.

2017-12-01

Over the past six years, we have developed a suite of open-source, low-cost, and lightweight data loggers for scientific research. These loggers employ the popular and easy-to-use Arduino programming environment, but consist of custom hardware optimized for field research. They may be connected to a broad and expanding range of off-the-shelf sensors, with software support built in directly to the "ALog" library. Three main models exist: The ALog (for Autonomous or Arduino Logger) is the extreme low-power model for years-long deployments with only primary AA or D batteries. The ALog shield is a stripped-down ALog that nests with a standard Arduino board for prototyping or education. The TLog (for Telemetering Logger) contains an embedded radio with 500 m range and a GPS for communications and precision timekeeping. This enables meshed networks of loggers that can send their data back to an internet-connected "home base" logger for near-real-time field data retrieval. All boards feature feature a high-precision clock, full size SD card slot for high-volume data storage, large screw terminals to connect sensors, interrupts, SPI and I2C communication capability, and 3.3V/5V power outputs. The ALog and TLog have fourteen 16-bit analog inputs with a precision voltage reference for precise analog measurements. Their components are rated -40 to +85 degrees C, and they have been tested in harsh field conditions. These low-cost and open-source data loggers have enabled our research group to collect field data across North and South America on a limited budget, support student projects, and build toward better future scientific data systems.

TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy.

PubMed

Lindner, Michael; Vicente, Raul; Priesemann, Viola; Wibral, Michael

2011-11-18

Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.

An Alternative Approach: Openness in Education over the Last 100 Years

ERIC Educational Resources Information Center

Baker, Fredrick W.

2017-01-01

What is the nature of openness, and what role has it played in education over the years? The concept of openness has traditionally been very difficult to define, and its history in education has often been ignored, obscured, or misrepresented in the literature, media, and popular culture. This paper provides an operational definition of openness…

WHAT IS A MOMENT ARM? CALCULATING MUSCLE EFFECTIVENESS IN BIOMECHANICAL MODELS USING GENERALIZED COORDINATES

PubMed Central

Seth, Ajay; Delp, Scott L.

2015-01-01

Biomechanics researchers often use multibody models to represent biological systems. However, the mapping from biology to mechanics and back can be problematic. OpenSim is a popular open source tool used for this purpose, mapping between biological specifications and an underlying generalized coordinate multibody system called Simbody. One quantity of interest to biomechanical researchers and clinicians is “muscle moment arm,” a measure of the effectiveness of a muscle at contributing to a particular motion over a range of configurations. OpenSim can automatically calculate these quantities for any muscle once a model has been built. For simple cases, this calculation is the same as the conventional moment arm calculation in mechanical engineering. But a muscle may span several joints (e.g., wrist, neck, back) and may follow a convoluted path over various curved surfaces. A biological joint may require several bodies or even a mechanism to accurately represent in the multibody model (e.g., knee, shoulder). In these situations we need a careful definition of muscle moment arm that is analogous to the mechanical engineering concept, yet generalized to be of use to biomedical researchers. Here we present some biomechanical modeling challenges and how they are resolved in OpenSim and Simbody to yield biologically meaningful muscle moment arms. PMID:25905111

WHAT IS A MOMENT ARM? CALCULATING MUSCLE EFFECTIVENESS IN BIOMECHANICAL MODELS USING GENERALIZED COORDINATES.

PubMed

Sherman, Michael A; Seth, Ajay; Delp, Scott L

2013-08-01

Biomechanics researchers often use multibody models to represent biological systems. However, the mapping from biology to mechanics and back can be problematic. OpenSim is a popular open source tool used for this purpose, mapping between biological specifications and an underlying generalized coordinate multibody system called Simbody. One quantity of interest to biomechanical researchers and clinicians is "muscle moment arm," a measure of the effectiveness of a muscle at contributing to a particular motion over a range of configurations. OpenSim can automatically calculate these quantities for any muscle once a model has been built. For simple cases, this calculation is the same as the conventional moment arm calculation in mechanical engineering. But a muscle may span several joints (e.g., wrist, neck, back) and may follow a convoluted path over various curved surfaces. A biological joint may require several bodies or even a mechanism to accurately represent in the multibody model (e.g., knee, shoulder). In these situations we need a careful definition of muscle moment arm that is analogous to the mechanical engineering concept, yet generalized to be of use to biomedical researchers. Here we present some biomechanical modeling challenges and how they are resolved in OpenSim and Simbody to yield biologically meaningful muscle moment arms.

Multilevel Parallelization of AutoDock 4.2.

PubMed

Norgan, Andrew P; Coffman, Paul K; Kocher, Jean-Pierre A; Katzmann, David J; Sosa, Carlos P

2011-04-28

Virtual (computational) screening is an increasingly important tool for drug discovery. AutoDock is a popular open-source application for performing molecular docking, the prediction of ligand-receptor interactions. AutoDock is a serial application, though several previous efforts have parallelized various aspects of the program. In this paper, we report on a multi-level parallelization of AutoDock 4.2 (mpAD4). Using MPI and OpenMP, AutoDock 4.2 was parallelized for use on MPI-enabled systems and to multithread the execution of individual docking jobs. In addition, code was implemented to reduce input/output (I/O) traffic by reusing grid maps at each node from docking to docking. Performance of mpAD4 was examined on two multiprocessor computers. Using MPI with OpenMP multithreading, mpAD4 scales with near linearity on the multiprocessor systems tested. In situations where I/O is limiting, reuse of grid maps reduces both system I/O and overall screening time. Multithreading of AutoDock's Lamarkian Genetic Algorithm with OpenMP increases the speed of execution of individual docking jobs, and when combined with MPI parallelization can significantly reduce the execution time of virtual screens. This work is significant in that mpAD4 speeds the execution of certain molecular docking workloads and allows the user to optimize the degree of system-level (MPI) and node-level (OpenMP) parallelization to best fit both workloads and computational resources.

Empennage Noise Shielding Benefits for an Open Rotor Transport

NASA Technical Reports Server (NTRS)

Berton, Jeffrey J.

2012-01-01

NASA sets aggressive, strategic, civil aircraft performance and environmental goals and develops ambitious technology roadmaps to guide its research efforts. NASA has adopted a phased approach for community noise reduction of civil aircraft. While the goal of the near-term first phase focuses primarily on source noise reduction, the goal of the second phase relies heavily on presumed architecture changes of future aircraft. The departure from conventional airplane configurations to designs that incorporate some type of propulsion noise shielding is anticipated to provide an additional 10 cumulative EPNdB of noise reduction. One candidate propulsion system for these advanced aircraft is the open rotor engine. In some planned applications, twin open rotor propulsors are located on the aft fuselage, with the vehicle s empennage shielding some of their acoustic signature from observers on the ground. This study focuses on predicting the noise certification benefits of a notional open rotor aircraft with tail structures shielding a portion of the rotor noise. The measured noise of an open rotor test article--collected with and without an acoustic barrier wall--is the basis of the prediction. The results are used to help validate NASA s reliance on acoustic shielding to achieve the second phase of its community noise reduction goals. The noise measurements are also compared to a popular empirical diffraction correlation often used at NASA to predict acoustic shielding.

Scoping out the International Spy Museum

ERIC Educational Resources Information Center

Radosh, Ronald

2010-01-01

The International Spy Museum in Washington, D.C.--a private museum that opened in July 2002 at the cost of $40 million--is rated as one of the most visited and popular tourist destinations in the nation's capital, despite stiff competition from the various public museums that are part of the Smithsonian. The popularity of the Spy Museum has a…

Popular science publishing in contemporary China.

PubMed

Wu, Guosheng; Qiu, Hui

2013-07-01

Since the 1950s China's popular science publishing has been the business of the government, and subject to its will. China adopted a system of planned economies, as the Soviet Union did, until the 1980s when a policy of reform and opening-up was adopted. During the period of the planned economies, popular science publishing was not a commercial but a governmental enterprise. More than 100 million copies of the most representative publication of this period, One Hundred Thousand Whys, have been distributed. The Unmoved Mover Series of the 1990s was a milestone in the new era. What is significant about this series is that it broke through the prevailing mode of science-popularization as 'serving for industrial and agricultural production, serving for ideology'. China's popular science publishing has its defects, genetically and culturally. In an age of marketization, popular science books are frequently applauded by the experts, but not enjoyed by general readers.

AutoBayes Program Synthesis System System Internals

NASA Technical Reports Server (NTRS)

Schumann, Johann Martin

2011-01-01

This lecture combines the theoretical background of schema based program synthesis with the hands-on study of a powerful, open-source program synthesis system (Auto-Bayes). Schema-based program synthesis is a popular approach toward program synthesis. The lecture will provide an introduction into this topic and discuss how this technology can be used to generate customized algorithms. The synthesis of advanced numerical algorithms requires the availability of a powerful symbolic (algebra) system. Its task is to symbolically solve equations, simplify expressions, or to symbolically calculate derivatives (among others) such that the synthesized algorithms become as efficient as possible. We will discuss the use and importance of the symbolic system for synthesis. Any synthesis system is a large and complex piece of code. In this lecture, we will study Autobayes in detail. AutoBayes has been developed at NASA Ames and has been made open source. It takes a compact statistical specification and generates a customized data analysis algorithm (in C/C++) from it. AutoBayes is written in SWI Prolog and many concepts from rewriting, logic, functional, and symbolic programming. We will discuss the system architecture, the schema libary and the extensive support infra-structure. Practical hands-on experiments and exercises will enable the student to get insight into a realistic program synthesis system and provides knowledge to use, modify, and extend Autobayes.

Teachers' Roles in Light of Massive Open Online Courses (MOOCs): Evolution and Challenges in Higher Distance Education

ERIC Educational Resources Information Center

Gil-Jaurena, Inés; Domínguez, Daniel

2018-01-01

This article analyses the challenges teachers face when entering a digital and open online environment in higher education. Massive open online courses (MOOCs) have become a popular phenomenon, making online learning more visible in the educational agenda; therefore, it is appropriate to analyse their expansion and diversification to help inform…

WASS: An open-source pipeline for 3D stereo reconstruction of ocean waves

NASA Astrophysics Data System (ADS)

Bergamasco, Filippo; Torsello, Andrea; Sclavo, Mauro; Barbariol, Francesco; Benetazzo, Alvise

2017-10-01

Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community and industry. Indeed, recent advances of both computer vision algorithms and computer processing power now allow the study of the spatio-temporal wave field with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner, so that the implementation of a sea-waves 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well tested software package that automates the reconstruction process from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS (http://www.dais.unive.it/wass), an Open-Source stereo processing pipeline for sea waves 3D reconstruction. Our tool completely automates all the steps required to estimate dense point clouds from stereo images. Namely, it computes the extrinsic parameters of the stereo rig so that no delicate calibration has to be performed on the field. It implements a fast 3D dense stereo reconstruction procedure based on the consolidated OpenCV library and, lastly, it includes set of filtering techniques both on the disparity map and the produced point cloud to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface. In this paper, we describe the architecture of WASS and the internal algorithms involved. The pipeline workflow is shown step-by-step and demonstrated on real datasets acquired at sea.

YouTube Professors: Scholars as Online Video Stars

ERIC Educational Resources Information Center

Young, Jeffrey R.

2008-01-01

This article takes a look at the rising popularity of professors as the latest YouTube stars. The popularity of their appearances on YouTube and other video-sharing sites is making it possible for classrooms to be opened up and making teaching--which once took place behind closed doors--a more public art. Web video has generated a new form of…

What the White "Squaws" Want from Black Hawk: Gendering the Fan-Celebrity Relationship

ERIC Educational Resources Information Center

Helton, Tena L.

2010-01-01

Americans in the East were great fans of Black Hawk, whose popularity on tour overtook that of Andrew Jackson's parallel tour of the Northeast. Undoubtedly, then, Black Hawk was a celebrity. He remained popular even in 1837, when he attended Catlin's gallery opening in New York, which included his 1832 painting of Black Hawk. Black Hawk may also…

Resources for Popular Culture in Ancient, Medieval and Renaissance Humanities.

ERIC Educational Resources Information Center

Schroeder, Fred E. H.

1996-01-01

Notes that there are few readily accessible resources for teachers who wish to include popular culture in their ancient, medieval, or renaissance history lessons. Goes on to partially remedy this situation by providing a review of print sources of information on popular culture. Also mentions useful films and artifacts. (DSK)

Cordova: web-based management of genetic variation data.

PubMed

Ephraim, Sean S; Anand, Nikhil; DeLuca, Adam P; Taylor, Kyle R; Kolbe, Diana L; Simpson, Allen C; Azaiez, Hela; Sloan, Christina M; Shearer, A Eliot; Hallier, Andrea R; Casavant, Thomas L; Scheetz, Todd E; Smith, Richard J H; Braun, Terry A

2014-12-01

Cordova is an out-of-the-box solution for building and maintaining an online database of genetic variations integrated with pathogenicity prediction results from popular algorithms. Our primary motivation for developing this system is to aid researchers and clinician-scientists in determining the clinical significance of genetic variations. To achieve this goal, Cordova provides an interface to review and manually or computationally curate genetic variation data as well as share it for clinical diagnostics and the advancement of research. Cordova is open source under the MIT license and is freely available for download at https://github.com/clcg/cordova. Published by Oxford University Press. This work is written by US Government employees and is in the public domain in the US.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.

PubMed

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig's scalability over many computing nodes and illustrate its use with example scripts. Available under the open source MIT license at http://sourceforge.net/projects/seqpig/

Research on private cloud computing based on analysis on typical opensource platform: a case study with Eucalyptus and Wavemaker

NASA Astrophysics Data System (ADS)

Yu, Xiaoyuan; Yuan, Jian; Chen, Shi

2013-03-01

Cloud computing is one of the most popular topics in the IT industry and is recently being adopted by many companies. It has four development models, as: public cloud, community cloud, hybrid cloud and private cloud. Except others, private cloud can be implemented in a private network, and delivers some benefits of cloud computing without pitfalls. This paper makes a comparison of typical open source platforms through which we can implement a private cloud. After this comparison, we choose Eucalyptus and Wavemaker to do a case study on the private cloud. We also do some performance estimation of cloud platform services and development of prototype software as cloud services.

UpSetR: an R package for the visualization of intersecting sets and their properties

PubMed Central

Conway, Jake R.; Lex, Alexander; Gehlenborg, Nils

2017-01-01

Abstract Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed. Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties. Availability and implementation: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/. Contact: nils@hms.harvard.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28645171

Cloud prediction of protein structure and function with PredictProtein for Debian.

PubMed

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Staniewski, Cedric; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome.

Cloud Prediction of Protein Structure and Function with PredictProtein for Debian

PubMed Central

Kaján, László; Yachdav, Guy; Vicedo, Esmeralda; Steinegger, Martin; Mirdita, Milot; Angermüller, Christof; Böhm, Ariane; Domke, Simon; Ertl, Julia; Mertes, Christian; Reisinger, Eva; Rost, Burkhard

2013-01-01

We report the release of PredictProtein for the Debian operating system and derivatives, such as Ubuntu, Bio-Linux, and Cloud BioLinux. The PredictProtein suite is available as a standard set of open source Debian packages. The release covers the most popular prediction methods from the Rost Lab, including methods for the prediction of secondary structure and solvent accessibility (profphd), nuclear localization signals (predictnls), and intrinsically disordered regions (norsnet). We also present two case studies that successfully utilize PredictProtein packages for high performance computing in the cloud: the first analyzes protein disorder for whole organisms, and the second analyzes the effect of all possible single sequence variants in protein coding regions of the human genome. PMID:23971032

Web-based decision support and visualization tools for water quality management in the Chesapeake Bay watershed

USGS Publications Warehouse

Mullinix, C.; Hearn, P.; Zhang, H.; Aguinaldo, J.

2009-01-01

Federal, State, and local water quality managers charged with restoring the Chesapeake Bay ecosystem require tools to maximize the impact of their limited resources. To address this need, the U.S. Geological Survey (USGS) and the Environmental Protection Agency's Chesapeake Bay Program (CBP) are developing a suite of Web-based tools called the Chesapeake Online Assessment Support Toolkit (COAST). The goal of COAST is to help CBP partners identify geographic areas where restoration activities would have the greatest effect, select the appropriate management strategies, and improve coordination and prioritization among partners. As part of the COAST suite of tools focused on environmental restoration, a water quality management visualization component called the Nutrient Yields Mapper (NYM) tool is being developed by USGS. The NYM tool is a web application that uses watershed yield estimates from USGS SPAtially Referenced Regressions On Watershed (SPARROW) attributes model (Schwarz et al., 2006) [6] to allow water quality managers to identify important sources of nitrogen and phosphorous within the Chesapeake Bay watershed. The NYM tool utilizes new open source technologies that have become popular in geospatial web development, including components such as OpenLayers and GeoServer. This paper presents examples of water quality data analysis based on nutrient type, source, yield, and area of interest using the NYM tool for the Chesapeake Bay watershed. In addition, we describe examples of map-based techniques for identifying high and low nutrient yield areas; web map engines; and data visualization and data management techniques.

A Kind of Optimization Method of Loading Documents in OpenOffice.org

NASA Astrophysics Data System (ADS)

Lan, Yuqing; Li, Li; Zhou, Wenbin

As a giant in open source community, OpenOffice.org has become the most popular office suite within Linux community. But OpenOffice.org is relatively slow while loading documents. Research shows that the most time consuming part is importing one page of whole document. If there are many pages in a document, the accumulation of time consumed can be astonishing. Therefore, this paper proposes a solution, which has improved the speed of loading documents through asynchronous importing mechanism: a document is not imported as a whole, but only part of the document is imported at first for display, then mechanism in the background is started to asynchronously import the remaining parts, and insert it into the drawing queue of OpenOffice.org for display. In this way, the problem can be solved and users don't have to wait for a long time. Application start-up time testing tool has been used to test the time consumed in loading different pages of documents before and after optimization of OpenOffice.org, then, we adopt the regression theory to analyse the correlation between the page number of documents and the loading time. In addition, visual modeling of the experimental data are acquired with the aid of matlab. An obvious increase in loading speed can be seen after a comparison of the time consumed to load a document before and after the solution is adopted. And then, using Microsoft Office compared with the optimized OpenOffice.org, their loading speeds are almost same. The results of the experiments show the effectiveness of this solution.

Organizing Astronomy Popularization and Teacher Training Workshops in Nigeria: A paradigm shift in Sourcing funds

NASA Astrophysics Data System (ADS)

Chukwudi Okpala, Kingsley; Iheanyi Okere, Bonaventure

2015-08-01

Funding for astronomy popularization and workshops has become a huge challenge in recent times especially for developing countries like Nigeria. However, a modification of the primary and secondary school curriculum to include space science topics in the school system has led to a ripe desire by the relevant agencies/corporate bodies to make commitments towards the astronomy popularization activities as part of their social responsibility. Considering the size of Nigeria, there is need for a shift in paradigm for sourcing resources to tackle the dart of funds for organizing educational activities in a sustainable manner. Recently a teacher training and science popularization workshop was organized as a first in a series of subsequent workshops geared towards having a sustainable means of popularizing astronomy for development in Nigeria. Principally, the key lies in the partnership with schools and other corporate bodies in addition to the usual governmental actions. Experiences from this workshop will be enumerated with the hope of inspiring the same success in similar societies.

2015 Hans O. Mauksch Address: How Departments Can Respond to the Changing Popularity of the Sociology Major

ERIC Educational Resources Information Center

Sweet, Stephen

2016-01-01

While the popularity of the psychology major and the sociology major were comparable in 1970, sociology witnessed a decline while psychology witnessed expansion. This article considers strategies of expanding the popularity of the sociology major, considering data from a variety of sources. Primary recommendations are to configure programs to…

Understanding User Behavioral Patterns in Open Knowledge Communities

ERIC Educational Resources Information Center

Yang, Xianmin; Song, Shuqiang; Zhao, Xinshuo; Yu, Shengquan

2018-01-01

Open knowledge communities (OKCs) have become popular in the era of knowledge economy. This study aimed to explore how users collaboratively create and share knowledge in OKCs. In particular, this research identified the behavior distribution and behavioral patterns of users by conducting frequency distribution and lag sequential analyses. Some…

Exploring Engaging Gamification Mechanics in Massive Online Open Courses

ERIC Educational Resources Information Center

Chang, Jen-Wei; Wei, Hung-Yu

2016-01-01

Massive open online courses (MOOCs) have developed rapidly and become tremendously popular because of their plentiful gamification designs, such as reputation points, rewards, and goal setting. Although previous studies have mentioned a broad range of gamification designs that might influence MOOC learner engagement, most gamified MOOCs fail to…

Design of numerical model for thermoacoustic devices using OpenFOAM

NASA Astrophysics Data System (ADS)

Tisovsky, Tomas; Vit, Tomas

2017-09-01

Thermoacoustic devices are increasingly popular especially because of their construction simplicity and the ability to easily convert waste heat into the form of usable energy. Aim of this paper is to introduce some of the effective procedures for creating a complex mathematical model of thermoacoustic devices in OpenFOAM.

Fixing Higher Education through Technology: Canadian Media Coverage of Massive Open Online Courses

ERIC Educational Resources Information Center

Dumitrica, Delia

2017-01-01

The popularization of massive open online courses (MOOCs) has been shrouded in promises of disruption and radical change in education. In Canada, official partnerships struck by higher education institutions with platform providers such as "Coursera", "Udacity" and "edX" were publicized by dailies and professional…

Toward Cost-Effective Fingerprinting Methodology to Distinguish Maize Open-Pollinated Varieties

USDA-ARS?s Scientific Manuscript database

In Africa, many smallholder farmers grow open pollinated maize varieties (OPVs), as they allow seed recycling and out-yield traditional farmer’s (unimproved) landraces. One popular OPV, ZM521 released by the International Maize and Wheat Improvement Center (CIMMYT), has been provided to farmers, o...

The Making of a Rock Festival: A Historical Creative Experience in a Group Study of Popular Music as an Instrument in Studying American Culture of the Sixties and Seventies.

ERIC Educational Resources Information Center

Chilcoat, George W.

A project in which high school students examine the social history of the United States through a popular music presentation is described. The introduction of the paper draws together a series of sources which emphasize the importance of popular music, particularly during the 1960's and 1970's. The social effects of popular music are outlined:…

Spiderman and science: How students' perceptions of scientists are shaped by popular media.

PubMed

Tan, Aik-Ling; Jocz, Jennifer Ann; Zhai, Junqing

2017-07-01

This study addresses the influence of popular media on how young children perceive science and the work of scientists. Using an adapted version of the Draw-A-Scientist Test, 15 classes of fourth graders (9-10 years old) at three different schools in Singapore were sampled ( n =  266). The students' drawings as well as their identification of three sources from which they obtained inspiration for their drawings were analyzed. Our results showed a strong relationship between students' drawings of scientists and their reported sources of inspiration. The results suggest that popular media play a large role in shaping how young children view scientists.

Neuroinformatics Database (NiDB) – A Modular, Portable Database for the Storage, Analysis, and Sharing of Neuroimaging Data

PubMed Central

Anderson, Beth M.; Stevens, Michael C.; Glahn, David C.; Assaf, Michal; Pearlson, Godfrey D.

2013-01-01

We present a modular, high performance, open-source database system that incorporates popular neuroimaging database features with novel peer-to-peer sharing, and a simple installation. An increasing number of imaging centers have created a massive amount of neuroimaging data since fMRI became popular more than 20 years ago, with much of that data unshared. The Neuroinformatics Database (NiDB) provides a stable platform to store and manipulate neuroimaging data and addresses several of the impediments to data sharing presented by the INCF Task Force on Neuroimaging Datasharing, including 1) motivation to share data, 2) technical issues, and 3) standards development. NiDB solves these problems by 1) minimizing PHI use, providing a cost effective simple locally stored platform, 2) storing and associating all data (including genome) with a subject and creating a peer-to-peer sharing model, and 3) defining a sample, normalized definition of a data storage structure that is used in NiDB. NiDB not only simplifies the local storage and analysis of neuroimaging data, but also enables simple sharing of raw data and analysis methods, which may encourage further sharing. PMID:23912507

Spatiotemporal Patterns of Urban Human Mobility

NASA Astrophysics Data System (ADS)

Hasan, Samiul; Schneider, Christian M.; Ukkusuri, Satish V.; González, Marta C.

2013-04-01

The modeling of human mobility is adopting new directions due to the increasing availability of big data sources from human activity. These sources enclose digital information about daily visited locations of a large number of individuals. Examples of these data include: mobile phone calls, credit card transactions, bank notes dispersal, check-ins in internet applications, among several others. In this study, we consider the data obtained from smart subway fare card transactions to characterize and model urban mobility patterns. We present a simple mobility model for predicting peoples' visited locations using the popularity of places in the city as an interaction parameter between different individuals. This ingredient is sufficient to reproduce several characteristics of the observed travel behavior such as: the number of trips between different locations in the city, the exploration of new places and the frequency of individual visits of a particular location. Moreover, we indicate the limitations of the proposed model and discuss open questions in the current state of the art statistical models of human mobility.

MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud.

PubMed

Expósito, Roberto R; Veiga, Jorge; González-Domínguez, Jorge; Touriño, Juan

2017-09-01

This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted MapReduce programming model to fully exploit Big Data technologies on cloud-based infrastructures. Written in Java to maximize cross-platform compatibility, MarDRe is built upon the open-source Apache Hadoop project, the most popular distributed computing framework for scalable Big Data processing. On a 16-node cluster deployed on the Amazon EC2 cloud platform, MarDRe is up to 8.52 times faster than a representative state-of-the-art tool. Source code in Java and Hadoop as well as a user's guide are freely available under the GNU GPLv3 license at http://mardre.des.udc.es . rreye@udc.es. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

A finite area scheme for shallow granular flows on three-dimensional surfaces

NASA Astrophysics Data System (ADS)

Rauter, Matthias

2017-04-01

Shallow granular flow models have become a popular tool for the estimation of natural hazards, such as landslides, debris flows and avalanches. The shallowness of the flow allows to reduce the three-dimensional governing equations to a quasi two-dimensional system. Three-dimensional flow fields are replaced by their depth-integrated two-dimensional counterparts, which yields a robust and fast method [1]. A solution for a simple shallow granular flow model, based on the so-called finite area method [3] is presented. The finite area method is an adaption of the finite volume method [4] to two-dimensional curved surfaces in three-dimensional space. This method handles the three dimensional basal topography in a simple way, making the model suitable for arbitrary (but mildly curved) topography, such as natural terrain. Furthermore, the implementation into the open source software OpenFOAM [4] is shown. OpenFOAM is a popular computational fluid dynamics application, designed so that the top-level code mimics the mathematical governing equations. This makes the code easy to read and extendable to more sophisticated models. Finally, some hints on how to get started with the code and how to extend the basic model will be given. I gratefully acknowledge the financial support by the OEAW project "beyond dense flow avalanches". Savage, S. B. & Hutter, K. 1989 The motion of a finite mass of granular material down a rough incline. Journal of Fluid Mechanics 199, 177-215. Ferziger, J. & Peric, M. 2002 Computational methods for fluid dynamics, 3rd edn. Springer. Tukovic, Z. & Jasak, H. 2012 A moving mesh finite volume interface tracking method for surface tension dominated interfacial fluid flow. Computers & fluids 55, 70-84. Weller, H. G., Tabor, G., Jasak, H. & Fureby, C. 1998 A tensorial approach to computational continuum mechanics using object-oriented techniques. Computers in physics 12(6), 620-631.

Teaching Chemistry at Indira Gandhi National Open University

ERIC Educational Resources Information Center

Fozdar, Bharat I.; Kumar, Lalita S.

2006-01-01

The Open Distance Learning (ODL) concept is fast becoming popular all over the world and it has a lot of relevance for a highly populated country like India. However, the most important aspect of this type of teaching-learning process is establishment of the credibility especially when the laboratory based science programmes are delivered from…

Education for Autonomy and Open-Mindedness in Diverse Societies

ERIC Educational Resources Information Center

Taylor, Rebecca M.

2017-01-01

In recent years, democracies across the globe have seen an increase in the popularity and power of authoritarian, nationalist politicians, groups, and policies. In this climate, the proper role of education in liberal democratic society, and in particular its role in promoting characteristics like autonomy and open-mindedness, is contested. This…

Copyright and Collaborative Spaces: Open Licensing and Wikis

ERIC Educational Resources Information Center

Botterbusch, Hope R.; Parker, Preston

2008-01-01

As recently as ten years ago, it may have seemed like science fiction to imagine collaborative spaces on the Internet. Today, collaborative websites have proliferated: (1) blogs; (2) social networking; (3) image sharing; (4) video sharing; (5) open educational resources; and (6) popularity websites. Another type is called a wiki, an online…

Imagens de Leitura na Literatura de Cordel (Images of Reading in "Cordel" Literature).

ERIC Educational Resources Information Center

Hata, Luli

1997-01-01

Shows, in "Cordel" literature (a popular manifestation found in northeastern Brazil) an expressive source for the analysis of popular culture in Brazil. Uses this literature to discuss images of reading. (PA)

Toward Global Real Time Hydrologic Modeling - An "Open" View From the Trenches

NASA Astrophysics Data System (ADS)

Nelson, J.

2015-12-01

Big Data has become a popular term to describe the exponential growth of data and related cyber infrastructure to process it so that better analysis can be performed and lead to improved decision-making. How are we doing in the hydrologic sciences? As part of a significant collaborative effort that brought together scientists from public, private, and academic organizations a new transformative hydrologic forecasting modeling infrastructure has been developed. How was it possible to go from deterministic hydrologic forecasts largely driven through manual interactions at 3600 stations to automated 15-day ensemble forecasts at 2.67 million stations? Earth observations of precipitation, temperature, moisture, and other atmospheric and land surface conditions form the foundation of global hydrologic forecasts, but this project demonstrates a critical component to harness these resources can be summed up in one word: OPEN. Whether it is open data sources, open software solutions with open standards, or just being open to collaborations and building teams across institutions, disciplines, and international boundaries, time and time again through my involvement in the development of a high-resolution real time global hydrologic forecasting model I have discovered that in every aspect the sum has always been greater than the parts. While much has been accomplished, much more remains to be done, but the most important lesson learned has been to the degree that we can remain open and work together, the greater our ability will be to use big data hydrologic modeling resources to solve the world's most vexing water related challenges. This presentation will demonstrate a transformational global real time hydrologic forecasting application based on downscaled ECMWF ensemble forecasts, RAPID routing, and Tethys Platform for cloud computing and visualization with discussions of the human and cyber infrastructure connections that make it successful and needs moving forward.

Android and ODK based data collection framework to aid in epidemiological analysis

PubMed Central

Raja, A.; Tridane, A.; Gaffar, A.; Lindquist, T.; Pribadi, K.

2014-01-01

Periodic collection of field data, analysis and interpretation of data are key to a good healthcare service. This data is used by the subsequent decision makers to recognize preventive measures, provide timely support to the affected and to help measure the effects of their interventions. While the resources required for good disease surveillance and proactive healthcare are available more readily in developed countries, the lack of these in developing countries may compromise the quality of service provided. This combined with the critical nature of some diseases makes this an essential issue to be addressed. Taking advantage of the rapid growth of cell phone usage and related infrastructure in developed as well as developing countries, several systems have been established to address the gaps in data collection. Android, being an open sourced platform, has gained considerable popularity in this aspect. Open data kit is one such tool developed to aid in data collection. The aim of this paper is to present a prototype framework built using few such existing tools and technologies to address data collection for seasonal influenza, commonly referred to as the flu. PMID:24678381

The Detection of Emerging Trends Using Wikipedia Traffic Data and Context Networks.

PubMed

Kämpf, Mirko; Tessenow, Eric; Kenett, Dror Y; Kantelhardt, Jan W

2015-01-01

Can online media predict new and emerging trends, since there is a relationship between trends in society and their representation in online systems? While several recent studies have used Google Trends as the leading online information source to answer corresponding research questions, we focus on the online encyclopedia Wikipedia often used for deeper topical reading. Wikipedia grants open access to all traffic data and provides lots of additional (semantic) information in a context network besides single keywords. Specifically, we suggest and study context-normalized and time-dependent measures for a topic's importance based on page-view time series of Wikipedia articles in different languages and articles related to them by internal links. As an example, we present a study of the recently emerging Big Data market with a focus on the Hadoop ecosystem, and compare the capabilities of Wikipedia versus Google in predicting its popularity and life cycles. To support further applications, we have developed an open web platform to share results of Wikipedia analytics, providing context-rich and language-independent relevance measures for emerging trends.

The Detection of Emerging Trends Using Wikipedia Traffic Data and Context Networks

PubMed Central

Kämpf, Mirko; Tessenow, Eric; Kenett, Dror Y.; Kantelhardt, Jan W.

2015-01-01

Can online media predict new and emerging trends, since there is a relationship between trends in society and their representation in online systems? While several recent studies have used Google Trends as the leading online information source to answer corresponding research questions, we focus on the online encyclopedia Wikipedia often used for deeper topical reading. Wikipedia grants open access to all traffic data and provides lots of additional (semantic) information in a context network besides single keywords. Specifically, we suggest and study context-normalized and time-dependent measures for a topic’s importance based on page-view time series of Wikipedia articles in different languages and articles related to them by internal links. As an example, we present a study of the recently emerging Big Data market with a focus on the Hadoop ecosystem, and compare the capabilities of Wikipedia versus Google in predicting its popularity and life cycles. To support further applications, we have developed an open web platform to share results of Wikipedia analytics, providing context-rich and language-independent relevance measures for emerging trends. PMID:26720074

From within the Belly of the Beast: Rethinking the Concept of the "Educational Marketplace" in the Popular Discourse of Education Reform

ERIC Educational Resources Information Center

Ellison, Scott

2012-01-01

The task of this article is to carry out a synthetic analysis of the concept of the "educational marketplace" as it is used in the popular discourse of education reform so as to unpack what has become a commonsensical idea in American politics. It is a conceptual framework that has opened an ever-expanding sovereign space in the American state for…

An explosively driven high-power microwave pulsed power system.

PubMed

Elsayed, M A; Neuber, A A; Dickens, J C; Walter, J W; Kristiansen, M; Altgilbers, L L

2012-02-01

The increased popularity of high power microwave systems and the various sources to drive them is the motivation behind the work to be presented. A stand-alone, self-contained explosively driven high power microwave pulsed power system has been designed, built, and tested at Texas Tech University's Center for Pulsed Power and Power Electronics. The system integrates four different sub-units that are composed of a battery driven prime power source utilizing capacitive energy storage, a dual stage helical flux compression generator as the main energy amplification device, an integrated power conditioning system with inductive energy storage including a fast opening electro-explosive switch, and a triode reflex geometry virtual cathode oscillator as the microwave radiating source. This system has displayed a measured electrical source power level of over 5 GW and peak radiated microwaves of about 200 MW. It is contained within a 15 cm diameter housing and measures 2 m in length, giving a housing volume of slightly less than 39 l. The system and its sub-components have been extensively studied, both as integrated and individual units, to further expand on components behavior and operation physics. This report will serve as a detailed design overview of each of the four subcomponents and provide detailed analysis of the overall system performance and benchmarks.

An explosively driven high-power microwave pulsed power system

NASA Astrophysics Data System (ADS)

Elsayed, M. A.; Neuber, A. A.; Dickens, J. C.; Walter, J. W.; Kristiansen, M.; Altgilbers, L. L.

2012-02-01

The increased popularity of high power microwave systems and the various sources to drive them is the motivation behind the work to be presented. A stand-alone, self-contained explosively driven high power microwave pulsed power system has been designed, built, and tested at Texas Tech University's Center for Pulsed Power and Power Electronics. The system integrates four different sub-units that are composed of a battery driven prime power source utilizing capacitive energy storage, a dual stage helical flux compression generator as the main energy amplification device, an integrated power conditioning system with inductive energy storage including a fast opening electro-explosive switch, and a triode reflex geometry virtual cathode oscillator as the microwave radiating source. This system has displayed a measured electrical source power level of over 5 GW and peak radiated microwaves of about 200 MW. It is contained within a 15 cm diameter housing and measures 2 m in length, giving a housing volume of slightly less than 39 l. The system and its sub-components have been extensively studied, both as integrated and individual units, to further expand on components behavior and operation physics. This report will serve as a detailed design overview of each of the four subcomponents and provide detailed analysis of the overall system performance and benchmarks.

"Predatory" Online Journals Lure Scholars Who Are Eager to Publish

ERIC Educational Resources Information Center

Stratford, Michael

2012-01-01

OMICS Publishing Group is an open-access publisher operating under an author-pays model. Unlike traditional journal subscriptions in which readers or institutions pay to read content, OMICS relies on its contributors for financial support. Although the author-pays model is not a new phenomenon in the realm of open access, its recent popularity has…

Effective Results of an Open Concept School

ERIC Educational Resources Information Center

Cobos, Irma; Lewallen, Joy

2009-01-01

Open concept schools were a popular architectural design in the 70s. They were built to provide large areas of flexible space for team teaching with small enclosed areas for restrooms, science labs, and special needs classrooms. Because there are no barriers and no closed doors, an attitude of inclusiveness is created merely by the building's…

Digital Learning Hubs: Theoretical and Practical Ideas for Innovating Massive Open Online Courses

ERIC Educational Resources Information Center

Kucirkova, Natalia; Littleton, Karen

2017-01-01

Massive open online courses (MOOCs) are online courses aimed at global unlimited participation, originally conceptualised to carry no fee and offer no formal accreditation to the students (McAuley et al. 2010). Although their pedagogies vary, the most popular MOOC providers (e.g., Coursera, FutureLearn and EdX) are turning towards what Rodriguez…

Exploration and Practice of Blended Teaching Model Based Flipped Classroom and SPOC in Higher University

ERIC Educational Resources Information Center

Wang, Xin-Hong; Wang, Jing-Ping; Wen, Fu-Ji; Wang, Jun; Tao, Jian-Qing

2016-01-01

SPOC is characterized by improving teaching effectiveness. Currently open teaching mode is the popular trend, which is mainly related to several aspects: how to carry out teaching practice by using MOOC proprietary, high-quality online teaching resources in open education, that is, deep integration of curriculum resources and teaching design. On…

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

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.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again.

PubMed

González-Beltrán, Alejandra; Neumann, Steffen; Maguire, Eamonn; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2014-01-01

The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests.

The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again

PubMed Central

2014-01-01

Background The ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing Investigations, Studies and Assays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment. Results The Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data. Conclusions The Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking. Software availability The Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests. PMID:24564732

40 CFR Table 3 to Subpart Wwww of... - Organic HAP Emissions Limits for Existing Open Molding Sources, New Open Molding Sources Emitting...

Code of Federal Regulations, 2010 CFR

2010-07-01

... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and... CATEGORIES National Emissions Standards for Hazardous Air Pollutants: Reinforced Plastic Composites... Existing Open Molding Sources, New Open Molding Sources Emitting Less Than 100 TPY of HAP, and New and...

YouTube Professors Scholars as Online Video Stars

ERIC Educational Resources Information Center

Young, Jeffrey R.

2008-01-01

This article takes a look at how professors are becoming the latest YouTube stars. The popularity of their appearances on YouTube and other video-sharing sites end up opening the classroom and making teaching--which once took place behind closed doors--a more public art. Web videos open a new form of public intellectualism to scholars looking to…

Choice Issue Opens Rift in Missouri: Tax-Credit Scholarships Divide Black Caucus

ERIC Educational Resources Information Center

Viadero, Debra

2006-01-01

The debate over a school choice bill in the Missouri legislature has opened a bitter rift among some of the state's top Black elected officials and reflects a larger divide among African-Americans over school choice nationwide. The bill, which is similar to programs that are growing in popularity in other states, would provide tax credits for…

The OpenMP Implementation of NAS Parallel Benchmarks and its Performance

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry

1999-01-01

As the new ccNUMA architecture became popular in recent years, parallel programming with compiler directives on these machines has evolved to accommodate new needs. In this study, we examine the effectiveness of OpenMP directives for parallelizing the NAS Parallel Benchmarks. Implementation details will be discussed and performance will be compared with the MPI implementation. We have demonstrated that OpenMP can achieve very good results for parallelization on a shared memory system, but effective use of memory and cache is very important.

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, Hannes; Dutta, Rishabh; Jónsson, Sigurjón; Mai, Martin

2017-04-01

Modern earthquake source estimation studies increasingly use non-linear optimization strategies to estimate kinematic rupture parameters, often considering geodetic and seismic data jointly. However, the optimization process is complex and consists of several steps that need to be followed in the earthquake parameter estimation procedure. These include pre-describing or modeling the fault geometry, calculating the Green's Functions (often assuming a layered elastic half-space), and estimating the distributed final slip and possibly other kinematic source parameters. Recently, Bayesian inference has become popular for estimating posterior distributions of earthquake source model parameters given measured/estimated/assumed data and model uncertainties. For instance, some research groups consider uncertainties of the layered medium and propagate these to the source parameter uncertainties. Other groups make use of informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed that efficiently explore the often high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational demands of these methods are high and estimation codes are rarely distributed along with the published results. Even if codes are made available, it is often difficult to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in earthquake source estimations, we undertook the effort of producing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package is build on top of the pyrocko seismological toolbox (www.pyrocko.org) and makes use of the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat) and we encourage and solicit contributions to the project. In this contribution, we present our strategy for developing BEAT, show application examples, and discuss future developments.

Interactive basic mathematics web using Wordpress

NASA Astrophysics Data System (ADS)

Septia, Tika; Husna; Cesaria, Anna

2017-12-01

Wordpress is a popular open source tool that can be used for developing learning media. Basic Mathematics is the difficult subject for a physics student. The students need an interactive learning to improve their knowledge. The aims of this study were to develop the interactive media using Wordpress and to know the effectiveness of web as a learning media to improve the ICT Literacy students. This study used ADDIE models. The effectiveness of interactive web can be described as the students’ equipness of ICT literacy. The population is physics students. The findings show that the interactive web is valid for the content, presentation, linguistic, and graphic aspects. The results concluded that basic mathematic interactive web is effective to equip the learners ICT literacy of categories of high, medium, and low with the observations and questionnaires are in very good criteria.

Documentation for the MODFLOW 6 framework

USGS Publications Warehouse

Hughes, Joseph D.; Langevin, Christian D.; Banta, Edward R.

2017-08-10

MODFLOW is a popular open-source groundwater flow model distributed by the U.S. Geological Survey. Growing interest in surface and groundwater interactions, local refinement with nested and unstructured grids, karst groundwater flow, solute transport, and saltwater intrusion, has led to the development of numerous MODFLOW versions. Often times, there are incompatibilities between these different MODFLOW versions. The report describes a new MODFLOW framework called MODFLOW 6 that is designed to support multiple models and multiple types of models. The framework is written in Fortran using a modular object-oriented design. The primary framework components include the simulation (or main program), Timing Module, Solutions, Models, Exchanges, and Utilities. The first version of the framework focuses on numerical solutions, numerical models, and numerical exchanges. This focus on numerical models allows multiple numerical models to be tightly coupled at the matrix level.

Avionics and Power Management for Low-Cost High-Altitude Balloon Science Platforms

NASA Technical Reports Server (NTRS)

Chin, Jeffrey; Roberts, Anthony; McNatt, Jeremiah

2016-01-01

High-altitude balloons (HABs) have become popular as educational and scientific platforms for planetary research. This document outlines key components for missions where low cost and rapid development are desired. As an alternative to ground-based vacuum and thermal testing, these systems can be flight tested at comparable costs. Communication, solar, space, and atmospheric sensing experiments often require environments where ground level testing can be challenging or impossible in certain cases. When performing HAB research the ability to monitor the status of the platform and gather data is key for both scientific and recoverability aspects of the mission. A few turnkey platform solutions are outlined that leverage rapidly evolving open-source engineering ecosystems. Rather than building custom components from scratch, these recommendations attempt to maximize simplicity and cost of HAB platforms to make launches more accessible to everyone.

All Adventurous Women Do: HPV, Narrative, and HBO's Girls.

PubMed

Rogers, Brian

2016-01-01

This study looks at media portrayals of sexual health through the popular HBO television show Girls. This rhetorical criticism of Girls delineates two emergent narrative themes. First, the show repeatedly discusses human papillomavirus (HPV) in terms of its severity, but it oscillates in terms of representing the degree of significance. Second, the show frames the source of infection as more important than other concerns related to HPV. Ultimately, this analysis demonstrates that Girls perpetuates a problematic narrative plot structure related to issues of HPV transmission; it also provides a largely scientifically accurate portrayal of HPV and promotes open and frank discussions of sexual health. It is argued that mediated narratives, such as Girls, might have the potential to transform social attitudes and actions and should thereby garner attention from health communication scholars and public health advocates.

Classical Mechanics Experiments using Wiimotes

NASA Astrophysics Data System (ADS)

Lopez, Alexander; Ochoa, Romulo

2010-02-01

The Wii, a video game console, is a very popular device. Although computationally it is not a powerful machine by today's standards, to a physics educator the controllers are its most important components. The Wiimote (or remote) controller contains a three-axis accelerometer, an infrared detector, and Bluetooth connectivity at a relatively low price. Thanks to available open source code, such as GlovePie, any PC or Laptop with Bluetooth capability can detect the information sent out by the Wiimote. We present experiments that use two or three Wiimotes simultaneously to measure the variable accelerations in two mass systems interacting via springs. Normal modes are determined from the data obtained. Masses and spring constants are varied to analyze their impact on the accelerations of the systems. We present the results of our experiments and compare them with those predicted using Lagrangian mechanics. )

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop

PubMed Central

Schumacher, André; Pireddu, Luca; Niemenmaa, Matti; Kallio, Aleksi; Korpelainen, Eija; Zanetti, Gianluigi; Heljanko, Keijo

2014-01-01

Summary: Hadoop MapReduce-based approaches have become increasingly popular due to their scalability in processing large sequencing datasets. However, as these methods typically require in-depth expertise in Hadoop and Java, they are still out of reach of many bioinformaticians. To solve this problem, we have created SeqPig, a library and a collection of tools to manipulate, analyze and query sequencing datasets in a scalable and simple manner. SeqPigscripts use the Hadoop-based distributed scripting engine Apache Pig, which automatically parallelizes and distributes data processing tasks. We demonstrate SeqPig’s scalability over many computing nodes and illustrate its use with example scripts. Availability and Implementation: Available under the open source MIT license at http://sourceforge.net/projects/seqpig/ Contact: andre.schumacher@yahoo.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24149054

The Emergence of Open-Source Software in China

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

The open-source software movement is gaining increasing momentum in China. Of the limited numbers of open-source software in China, "Red Flag Linux" stands out most strikingly, commanding 30 percent share of Chinese software market. Unlike the spontaneity of open-source movement in North America, open-source software development in…

A Study of Clinically Related Open Source Software Projects

PubMed Central

Hogarth, Michael A.; Turner, Stuart

2005-01-01

Open source software development has recently gained significant interest due to several successful mainstream open source projects. This methodology has been proposed as being similarly viable and beneficial in the clinical application domain as well. However, the clinical software development venue differs significantly from the mainstream software venue. Existing clinical open source projects have not been well characterized nor formally studied so the ‘fit’ of open source in this domain is largely unknown. In order to better understand the open source movement in the clinical application domain, we undertook a study of existing open source clinical projects. In this study we sought to characterize and classify existing clinical open source projects and to determine metrics for their viability. This study revealed several findings which we believe could guide the healthcare community in its quest for successful open source clinical software projects. PMID:16779056

Open Access, Open Source and Digital Libraries: A Current Trend in University Libraries around the World

ERIC Educational Resources Information Center

Krishnamurthy, M.

2008-01-01

Purpose: The purpose of this paper is to describe the open access and open source movement in the digital library world. Design/methodology/approach: A review of key developments in the open access and open source movement is provided. Findings: Open source software and open access to research findings are of great use to scholars in developing…

Health Information-Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease.

PubMed

Pesälä, Samuli; Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-11-06

People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician's Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs' queries, and what causes possible differences in behavior. The aim of our study was to evaluate how the general public's and HCPs' information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public's information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician's Databases, were used. We compared the general public's article openings on Lyme disease from Health Library to HCPs' article openings on Lyme disease from Physician's Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Both databases, Health Library and Physician's Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Lyme disease-related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public's article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public's access to Health Library. ©Samuli Pesälä, Mikko J Virtanen, Jussi Sane, Pekka Mustonen, Minna Kaila, Otto Helve. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.11.2017.

Health Information–Seeking Patterns of the General Public and Indications for Disease Surveillance: Register-Based Study Using Lyme Disease

PubMed Central

Virtanen, Mikko J; Sane, Jussi; Mustonen, Pekka; Kaila, Minna; Helve, Otto

2017-01-01

Background People using the Internet to find information on health issues, such as specific diseases, usually start their search from a general search engine, for example, Google. Internet searches such as these may yield results and data of questionable quality and reliability. Health Library is a free-of-charge medical portal on the Internet providing medical information for the general public. Physician’s Databases, an Internet evidence-based medicine source, provides medical information for health care professionals (HCPs) to support their clinical practice. Both databases are available throughout Finland, but the latter is used only by health professionals and pharmacies. Little is known about how the general public seeks medical information from medical sources on the Internet, how this behavior differs from HCPs’ queries, and what causes possible differences in behavior. Objective The aim of our study was to evaluate how the general public’s and HCPs’ information-seeking trends from Internet medical databases differ seasonally and temporally. In addition, we aimed to evaluate whether the general public’s information-seeking trends could be utilized for disease surveillance and whether media coverage could affect these seeking trends. Methods Lyme disease, serving as a well-defined disease model with distinct seasonal variation, was chosen as a case study. Two Internet medical databases, Health Library and Physician’s Databases, were used. We compared the general public’s article openings on Lyme disease from Health Library to HCPs’ article openings on Lyme disease from Physician’s Databases seasonally across Finland from 2011 to 2015. Additionally, media publications related to Lyme disease were searched from the largest and most popular media websites in Finland. Results Both databases, Health Library and Physician’s Databases, show visually similar patterns in temporal variations of article openings on Lyme disease in Finland from 2011 to 2015. However, Health Library openings show not only an increasing trend over time but also greater fluctuations, especially during peak opening seasons. Outside these seasons, publications in the media coincide with Health Library article openings only occasionally. Conclusions Lyme disease–related information-seeking behaviors between the general public and HCPs from Internet medical portals share similar temporal variations, which is consistent with the trend seen in epidemiological data. Therefore, the general public’s article openings could be used as a supplementary source of information for disease surveillance. The fluctuations in article openings appeared stronger among the general public, thus, suggesting that different factors such as media coverage, affect the information-seeking behaviors of the public versus professionals. However, media coverage may also have an influence on HCPs. Not every publication was associated with an increase in openings, but the higher the media coverage by some publications, the higher the general public’s access to Health Library. PMID:29109071

Toothdrawers in English popular literature prior to 1700.

PubMed

Hargreaves, A S

1993-07-01

Historical evidence about toothdrawers in England can be supplemented by references to these men in popular contemporary literature. Poetic and dramatic sources from the late medieval period to the close of the 17th century have been examined to this end, with some attempt made to distinguish satire from historical fact.

Supervised Machine Learning Algorithms Can Classify Open-Text Feedback of Doctor Performance With Human-Level Accuracy.

PubMed

Gibbons, Chris; Richards, Suzanne; Valderas, Jose Maria; Campbell, John

2017-03-15

Machine learning techniques may be an effective and efficient way to classify open-text reports on doctor's activity for the purposes of quality assurance, safety, and continuing professional development. The objective of the study was to evaluate the accuracy of machine learning algorithms trained to classify open-text reports of doctor performance and to assess the potential for classifications to identify significant differences in doctors' professional performance in the United Kingdom. We used 1636 open-text comments (34,283 words) relating to the performance of 548 doctors collected from a survey of clinicians' colleagues using the General Medical Council Colleague Questionnaire (GMC-CQ). We coded 77.75% (1272/1636) of the comments into 5 global themes (innovation, interpersonal skills, popularity, professionalism, and respect) using a qualitative framework. We trained 8 machine learning algorithms to classify comments and assessed their performance using several training samples. We evaluated doctor performance using the GMC-CQ and compared scores between doctors with different classifications using t tests. Individual algorithm performance was high (range F score=.68 to .83). Interrater agreement between the algorithms and the human coder was highest for codes relating to "popular" (recall=.97), "innovator" (recall=.98), and "respected" (recall=.87) codes and was lower for the "interpersonal" (recall=.80) and "professional" (recall=.82) codes. A 10-fold cross-validation demonstrated similar performance in each analysis. When combined together into an ensemble of multiple algorithms, mean human-computer interrater agreement was .88. Comments that were classified as "respected," "professional," and "interpersonal" related to higher doctor scores on the GMC-CQ compared with comments that were not classified (P<.05). Scores did not vary between doctors who were rated as popular or innovative and those who were not rated at all (P>.05). Machine learning algorithms can classify open-text feedback of doctor performance into multiple themes derived by human raters with high performance. Colleague open-text comments that signal respect, professionalism, and being interpersonal may be key indicators of doctor's performance. ©Chris Gibbons, Suzanne Richards, Jose Maria Valderas, John Campbell. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 15.03.2017.

New Open-Source Version of FLORIS Released | News | NREL

Science.gov Websites

New Open-Source Version of FLORIS Released New Open-Source Version of FLORIS Released January 26 , 2018 National Renewable Energy Laboratory (NREL) researchers recently released an updated open-source simplified and documented. Because of the living, open-source nature of the newly updated utility, NREL

Sources and fate of microplastics in marine and beach sediments of the Southern Baltic Sea-a preliminary study.

PubMed

Graca, Bożena; Szewc, Karolina; Zakrzewska, Danuta; Dołęga, Anna; Szczerbowska-Boruchowska, Magdalena

2017-03-01

Microplastics' (particles size ≤5 mm) sources and fate in marine bottom and beach sediments of the brackish are strongly polluted Baltic Sea have been investigated. Microplastics were extracted using sodium chloride (1.2 g cm -3 ). Their qualitative identification was conducted using micro-Fourier-transform infrared spectroscopy (μFT-IR). Concentration of microplastics varied from 25 particles kg -1 d.w. at the open sea beach to 53 particles kg -1  d.w. at beaches of strongly urbanized bay. In bottom sediments, microplastics concentration was visibly lower compared to beach sediments (0-27 particles kg -1  d.w.) and decreased from the shore to the open, deep-sea regions. The most frequent microplastics dimensions ranged from 0.1 to 2.0 mm, and transparent fibers were predominant. Polyester, which is a popular fabrics component, was the most common type of microplastic in both marine bottom (50%) and beach sediments (27%). Additionally, poly(vinyl acetate) used in shipbuilding as well as poly(ethylene-propylene) used for packaging were numerous in marine bottom (25% of all polymers) and beach sediments (18% of all polymers). Polymer density seems to be an important factor influencing microplastics circulation. Low density plastic debris probably recirculates between beach sediments and seawater in a greater extent than higher density debris. Therefore, their deposition is potentially limited and physical degradation is favored. Consequently, low density microplastics concentration may be underestimated using current methods due to too small size of the debris. This influences also the findings of qualitative research of microplastics which provide the basis for conclusions about the sources of microplastics in the marine environment.

An open pilot study of ambulatory photodynamic therapy using a wearable low-irradiance organic light-emitting diode light source in the treatment of nonmelanoma skin cancer.

PubMed

Attili, S K; Lesar, A; McNeill, A; Camacho-Lopez, M; Moseley, H; Ibbotson, S; Samuel, I D W; Ferguson, J

2009-07-01

Photodynamic therapy (PDT) is a popular treatment for nonmelanoma skin cancer with clearance rates of between 70% and 100%. Although reported to have a superior cosmetic outcome, the inconvenience of hospital visits and discomfort during therapy are considered drawbacks. To present an open pilot study of a low-irradiance, potentially disposable, lightweight, organic light-emitting diode (OLED), which is an area-emitting light source (2 cm diameter), suitable for ambulatory PDT. Twelve patients with Bowen's disease (eight) and superficial basal cell carcinoma (four) < 2 cm in diameter were recruited into the study following histological confirmation of the diagnosis. Two treatments (45-60 J cm(-2) red light, 550-750 nm, peak 620 nm, irradiance 5 mW cm(-2)) were administered 1 month apart following application of aminolaevulinic acid for 4 h. At the 12-month follow-up, seven of the 12 patients remained clear, with four of the nonresponders demonstrating peripheral margin failure. Patients were scored for pain during and immediately after treatment using the numerical rating scale (NRS; 1-10). All 12 subjects scored pain as < 2 using the NRS (median score 1). In contrast, a similar cohort of 50 consecutive patients from our routine PDT clinic (Aktilite inorganic LED source; 75 J cm(-2), irradiance 80 mW cm(-2)) scored a median of 6 on the NRS. Pain and inconvenience are practical barriers to the use of conventional PDT. This pilot study suggests that OLED-PDT is less painful than conventional PDT with the added advantage of being lightweight, and therefore has the potential for more convenient 'home PDT'. These results need to be validated in larger studies.

Creative Uses of Custom Electronics for Environmental Monitoring

NASA Astrophysics Data System (ADS)

Hicks, S.; Aufdenkampe, A. K.; Montgomery, D. S.

2012-12-01

The ability to build custom electronic devices specifically suited to a unique task has gotten easier and cheaper, thanks to the recent popularity of open source electronics platforms like Arduino. Using Arduino-based processor boards, we have been creating a variety of helpful devices to perform functions that would have been too expensive to implement with standard methods and commercial hardware. The Christina River Basin CZO is currently operating dozens of homemade dataloggers that are connected to different types of environmental sensors. Most of these Arduino loggers have been deployed for over a year, so our experiences with them and their sensors have taught us a lot about the reliability and accuracy of both the loggers and the sensors. Some loggers also have the capability for wireless radio or ethernet data transmission for reporting live data to web sites for instant graphing or archiving. Other Arduino devices have the ability to be controlled remotely through web sites or telephones, making it easy to remotely trigger sample pumps or valves. The open-source nature of Arduino means collaboration is easy because the circuit schematics and source code for programming the boards can be shared between users. And because Arduino devices are easy to use and program, we developed an interface board that allows educators to easily connect a variety of inexpensive environmental sensors to an Arduino board. Then the students can write and upload simple programs to interact with the sensors, making it a very effective tool for teaching electronics and environmental science at the same time. The flexibility and capability of electronics prototyping platforms like Arduino mean these simple boards can cheaply and effectively perform a countless number of tasks for projects in environmental science and education.

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.

Earthquake forecasting studies using radon time series data in Taiwan

NASA Astrophysics Data System (ADS)

Walia, Vivek; Kumar, Arvind; Fu, Ching-Chou; Lin, Shih-Jung; Chou, Kuang-Wu; Wen, Kuo-Liang; Chen, Cheng-Hong

2017-04-01

For few decades, growing number of studies have shown usefulness of data in the field of seismogeochemistry interpreted as geochemical precursory signals for impending earthquakes and radon is idendified to be as one of the most reliable geochemical precursor. Radon is recognized as short-term precursor and is being monitored in many countries. This study is aimed at developing an effective earthquake forecasting system by inspecting long term radon time series data. The data is obtained from a network of radon monitoring stations eastblished along different faults of Taiwan. The continuous time series radon data for earthquake studies have been recorded and some significant variations associated with strong earthquakes have been observed. The data is also examined to evaluate earthquake precursory signals against environmental factors. An automated real-time database operating system has been developed recently to improve the data processing for earthquake precursory studies. In addition, the study is aimed at the appraisal and filtrations of these environmental parameters, in order to create a real-time database that helps our earthquake precursory study. In recent years, automatic operating real-time database has been developed using R, an open source programming language, to carry out statistical computation on the data. To integrate our data with our working procedure, we use the popular and famous open source web application solution, AMP (Apache, MySQL, and PHP), creating a website that could effectively show and help us manage the real-time database.

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

PubMed Central

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

2009-01-01

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

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization.

PubMed

Bernal-Rusiel, Jorge L; Rannou, Nicolas; Gollub, Randy L; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView , a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution.

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

PubMed

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

2011-01-01

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

Agile Methods for Open Source Safety-Critical Software

PubMed Central

Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

2011-01-01

The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the right amount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion. PMID:21799545

Agile Methods for Open Source Safety-Critical Software.

PubMed

Gary, Kevin; Enquobahrie, Andinet; Ibanez, Luis; Cheng, Patrick; Yaniv, Ziv; Cleary, Kevin; Kokoori, Shylaja; Muffih, Benjamin; Heidenreich, John

2011-08-01

The introduction of software technology in a life-dependent environment requires the development team to execute a process that ensures a high level of software reliability and correctness. Despite their popularity, agile methods are generally assumed to be inappropriate as a process family in these environments due to their lack of emphasis on documentation, traceability, and other formal techniques. Agile methods, notably Scrum, favor empirical process control, or small constant adjustments in a tight feedback loop. This paper challenges the assumption that agile methods are inappropriate for safety-critical software development. Agile methods are flexible enough to encourage the rightamount of ceremony; therefore if safety-critical systems require greater emphasis on activities like formal specification and requirements management, then an agile process will include these as necessary activities. Furthermore, agile methods focus more on continuous process management and code-level quality than classic software engineering process models. We present our experiences on the image-guided surgical toolkit (IGSTK) project as a backdrop. IGSTK is an open source software project employing agile practices since 2004. We started with the assumption that a lighter process is better, focused on evolving code, and only adding process elements as the need arose. IGSTK has been adopted by teaching hospitals and research labs, and used for clinical trials. Agile methods have matured since the academic community suggested they are not suitable for safety-critical systems almost a decade ago, we present our experiences as a case study for renewing the discussion.

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

Allarakhia, Minna

2014-05-01

Increasingly, open-source-based alliances seek to provide broad access to data, research-based tools, preclinical samples and downstream compounds. The challenge is how to create value from open-source biopharmaceutical innovation. This value creation may occur via transparency and usage of data across the biopharmaceutical value chain as stakeholders move dynamically between open source and open innovation. In this article, several examples are used to trace the evolution of biopharmaceutical open-source initiatives. The article specifically discusses the technological challenges associated with the integration and standardization of big data; the human capacity development challenges associated with skill development around big data usage; and the data-material access challenge associated with data and material access and usage rights, particularly as the boundary between open source and open innovation becomes more fluid. It is the author's opinion that the assessment of when and how value creation will occur, through open-source biopharmaceutical innovation, is paramount. The key is to determine the metrics of value creation and the necessary technological, educational and legal frameworks to support the downstream outcomes of now big data-based open-source initiatives. The continued focus on the early-stage value creation is not advisable. Instead, it would be more advisable to adopt an approach where stakeholders transform open-source initiatives into open-source discovery, crowdsourcing and open product development partnerships on the same platform.

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.

Software reuse example and challenges at NSIDC

NASA Astrophysics Data System (ADS)

Billingsley, B. W.; Brodzik, M.; Collins, J. A.

2009-12-01

NSIDC has created a new data discovery and access system, Searchlight, to provide users with the data they want in the format they want. NSIDC Searchlight supports discovery and access to disparate data types with on-the-fly reprojection, regridding and reformatting. Architected to both reuse open source systems and be reused itself, Searchlight reuses GDAL and Proj4 for manipulating data and format conversions, the netCDF Java library for creating netCDF output, MapServer and OpenLayers for defining spatial criteria and the JTS Topology Suite (JTS) in conjunction with Hibernate Spatial for database interaction and rich OGC-compliant spatial objects. The application reuses popular Java and Java Script libraries including Struts 2, Spring, JPA (Hibernate), Sitemesh, JFreeChart, JQuery, DOJO and a PostGIS PostgreSQL database. Future reuse of Searchlight components is supported at varying architecture levels, ranging from the database and model components to web services. We present the tools, libraries and programs that Searchlight has reused. We describe the architecture of Searchlight and explain the strategies deployed for reusing existing software and how Searchlight is built for reuse. We will discuss NSIDC reuse of the Searchlight components to support rapid development of new data delivery systems.

2015 ESGF Progress Report

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

Williams, D. N.

2015-06-22

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration whose purpose is to develop the software infrastructure needed to facilitate and empower the study of climate change on a global scale. ESGF’s architecture employs a system of geographically distributed peer nodes that are independently administered yet united by common federation protocols and application programming interfaces. The cornerstones of its interoperability are the peer-to-peer messaging, which is continuously exchanged among all nodes in the federation; a shared architecture for search and discovery; and a security infrastructure based on industry standards. ESGF integrates popular application engines available from the open-sourcemore » community with custom components (for data publishing, searching, user interface, security, and messaging) that were developed collaboratively by the team. The full ESGF infrastructure has now been adopted by multiple Earth science projects and allows access to petabytes of geophysical data, including the Coupled Model Intercomparison Project (CMIP)—output used by the Intergovernmental Panel on Climate Change assessment reports. ESGF is a successful example of integration of disparate open-source technologies into a cohesive functional system that serves the needs of the global climate science community.« less

Popular Media Representations of Physical Activity among Mothers

ERIC Educational Resources Information Center

Sanders, Margaret P.; Dlugonski, Deirdre

2016-01-01

Purpose: Many mothers fail to meet the recommended guidelines for physical activity. Popular media magazines targeting mothers provide information about physical activity and health, but little is known about the framing and content of physical activity messages within these sources. The aim of this content analysis was to analyze the framing and…

Popular Culture: Mirror of American Life. A Courses by Newspaper Reader.

ERIC Educational Resources Information Center

White, David Manning, Ed.; Pendleton, John, Ed.

The reader is one of several supplementary materials for a 15-week newspaper course about popular culture in the United States. Four major sections contain 57 readings from sources such as monographs, novels, journal articles, and research reports. The readings present research findings, personal observations, and debate over the definition and…

Turnitoff: Identifying and Fixing a Hole in Current Plagiarism Detection Software

ERIC Educational Resources Information Center

Heather, James

2010-01-01

In recent times, "plagiarism detection software" has become popular in universities and colleges, in an attempt to stem the tide of plagiarised student coursework. Such software attempts to detect any copied material and identify its source. The most popular such software is Turnitin, a commercial system used by thousands of institutions…

Popular Culture and Academic Literacies Situated in a Pedagogical Third Space

ERIC Educational Resources Information Center

Buelow, Stephanie

2016-01-01

This critical participatory action research study sought to understand what happens when students' interest and experiences with popular culture are integrated into a standards-based sixth grade English language arts curriculum. Multiple data sources were analyzed using the theoretical concept of third space. Findings showed that (a) a democratic,…

Media Literacy Art Education: Deconstructing Lesbian and Gay Stereotypes in the Media

ERIC Educational Resources Information Center

Chung, Sheng Kuan

2007-01-01

Popular media such as films, television programmes/commercials and magazines have become the dominant source through which children learn about others and their world, develop attitudes and beliefs as manifested in media expressions, and formulate their sense of identity. Popular media have enormous influence on children who are constantly…

Open for Business

ERIC Educational Resources Information Center

Voyles, Bennett

2007-01-01

People know about the Sakai Project (open source course management system); they may even know about Kuali (open source financials). So, what is the next wave in open source software? This article discusses business intelligence (BI) systems. Though open source BI may still be only a rumor in most campus IT departments, some brave early adopters…

Open Day at SHMI.

NASA Astrophysics Data System (ADS)

Jarosova, M.

2010-09-01

During the World Meteorological Day there has been preparing "Open Day" at Slovak Hydrometeorological Institute. This event has more than 10 years traditions. "Open Day" is one of a lot of possibilities to give more information about meteorology, climatology, hydrology too to public. This "Day" is executed in whole Slovakia. People can visit the laboratories, the forecasting room....and meteo and clima measuring points. The most popular is visiting forecasting room. Visitors are interested in e.g. climatologic change in Slovakia territory, preparing weather forecasting, dangerous phenomena.... Every year we have more than 500 visitors.

Approaches in highly parameterized inversion - PEST++, a Parameter ESTimation code optimized for large environmental models

USGS Publications Warehouse

Welter, David E.; Doherty, John E.; Hunt, Randall J.; Muffels, Christopher T.; Tonkin, Matthew J.; Schreuder, Willem A.

2012-01-01

An object-oriented parameter estimation code was developed to incorporate benefits of object-oriented programming techniques for solving large parameter estimation modeling problems. The code is written in C++ and is a formulation and expansion of the algorithms included in PEST, a widely used parameter estimation code written in Fortran. The new code is called PEST++ and is designed to lower the barriers of entry for users and developers while providing efficient algorithms that can accommodate large, highly parameterized problems. This effort has focused on (1) implementing the most popular features of PEST in a fashion that is easy for novice or experienced modelers to use and (2) creating a software design that is easy to extend; that is, this effort provides a documented object-oriented framework designed from the ground up to be modular and extensible. In addition, all PEST++ source code and its associated libraries, as well as the general run manager source code, have been integrated in the Microsoft Visual Studio® 2010 integrated development environment. The PEST++ code is designed to provide a foundation for an open-source development environment capable of producing robust and efficient parameter estimation tools for the environmental modeling community into the future.

The Commercial Open Source Business Model

NASA Astrophysics Data System (ADS)

Riehle, Dirk

Commercial open source software projects are open source software projects that are owned by a single firm that derives a direct and significant revenue stream from the software. Commercial open source at first glance represents an economic paradox: How can a firm earn money if it is making its product available for free as open source? This paper presents the core properties of com mercial open source business models and discusses how they work. Using a commercial open source approach, firms can get to market faster with a superior product at lower cost than possible for traditional competitors. The paper shows how these benefits accrue from an engaged and self-supporting user community. Lacking any prior comprehensive reference, this paper is based on an analysis of public statements by practitioners of commercial open source. It forges the various anecdotes into a coherent description of revenue generation strategies and relevant business functions.

Quantarctica: A Unique, Open, Standalone GIS Package for Antarctic Research and Education

NASA Astrophysics Data System (ADS)

Roth, G.; Matsuoka, K.; Skoglund, A.; Melvaer, Y.; Tronstad, S.

2016-12-01

The Norwegian Polar Institute has developed Quantarctica, an open GIS package for use by the international Antarctic community. Quantarctica includes a wide range of cartographic basemap layers, geophysical and glaciological datasets, and satellite imagery in standardized file formats with a consistent Antarctic map projection and customized layer and labeling styles for quick, effective cartography. Quantarctica's strengths as an open science platform lie in 1) The complete, ready-to-use data package which includes full-resolution, original-quality vector and raster data, 2) A policy for freely-redistributable and modifiable data including all metadata and citations, and 3) QGIS, a free, full-featured, modular, offline-capable open-source GIS suite with a rapid and active development and support community. The Quantarctica team is actively seeking new contributions of peer-reviewed, freely distributable pan-Antarctic geospatial datasets for the next version release in 2017. As part of this ongoing development, we are investigating the best approaches for quickly and seamlessly distributing new and updated data to users, storing datasets in efficient file formats while maintaining full quality, and coexisting with numerous online data portals in a way that most actively benefits the Antarctic community. A recent survey of Quantarctica users showed broad geographical adoption among Antarctic Treaty countries, including those outside the large US and UK Antarctic programs. Maps and figures produced by Quantarctica have also appeared in open-access journals and outside of the formal scientific community on popular science and GIS blogs. Our experience with the Quantarctica project has shown the tremendous value of education and outreach, not only in promoting open software, data formats, and practices, but in empowering Antarctic science groups to more effectively use GIS and geospatial data. Open practices are making a huge impact in Antarctic GIS, where individual countries have historically maintained their own restricted Antarctic geodatabases and where a majority of the next generation of scientists are entering the field with experience in using geospatial thinking for planning, visualization, and problem solving.

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences.

PubMed

Rideout, Jai Ram; He, Yan; Navas-Molina, Jose A; Walters, William A; Ursell, Luke K; Gibbons, Sean M; Chase, John; McDonald, Daniel; Gonzalez, Antonio; Robbins-Pianka, Adam; Clemente, Jose C; Gilbert, Jack A; Huse, Susan M; Zhou, Hong-Wei; Knight, Rob; Caporaso, J Gregory

2014-01-01

We present a performance-optimized algorithm, subsampled open-reference OTU picking, for assigning marker gene (e.g., 16S rRNA) sequences generated on next-generation sequencing platforms to operational taxonomic units (OTUs) for microbial community analysis. This algorithm provides benefits over de novo OTU picking (clustering can be performed largely in parallel, reducing runtime) and closed-reference OTU picking (all reads are clustered, not only those that match a reference database sequence with high similarity). Because more of our algorithm can be run in parallel relative to "classic" open-reference OTU picking, it makes open-reference OTU picking tractable on massive amplicon sequence data sets (though on smaller data sets, "classic" open-reference OTU clustering is often faster). We illustrate that here by applying it to the first 15,000 samples sequenced for the Earth Microbiome Project (1.3 billion V4 16S rRNA amplicons). To the best of our knowledge, this is the largest OTU picking run ever performed, and we estimate that our new algorithm runs in less than 1/5 the time than would be required of "classic" open reference OTU picking. We show that subsampled open-reference OTU picking yields results that are highly correlated with those generated by "classic" open-reference OTU picking through comparisons on three well-studied datasets. An implementation of this algorithm is provided in the popular QIIME software package, which uses uclust for read clustering. All analyses were performed using QIIME's uclust wrappers, though we provide details (aided by the open-source code in our GitHub repository) that will allow implementation of subsampled open-reference OTU picking independently of QIIME (e.g., in a compiled programming language, where runtimes should be further reduced). Our analyses should generalize to other implementations of these OTU picking algorithms. Finally, we present a comparison of parameter settings in QIIME's OTU picking workflows and make recommendations on settings for these free parameters to optimize runtime without reducing the quality of the results. These optimized parameters can vastly decrease the runtime of uclust-based OTU picking in QIIME.

Developing Critical L2 Digital Literacy through the Use of Computer-Based Internet-Hosted Learning Management Systems such as Moodle

NASA Astrophysics Data System (ADS)

Meurant, Robert C.

Second Language (L2) Digital Literacy is of emerging importance within English as a Foreign Language (EFL) in Korea, and will evolve to become regarded as the most critical component of overall L2 English Literacy. Computer-based Internet-hosted Learning Management Systems (LMS), such as the popular open-source Moodle, are rapidly being adopted worldwide for distance education, and are also being applied to blended (hybrid) education. In EFL Education, they have a special potential: by setting the LMS to force English to be used exclusively throughout a course website, the meta-language can be made the target L2 language. Of necessity, students develop the ability to use English to navigate the Internet, access and contribute to online resources, and engage in computer-mediated communication. Through such pragmatic engagement with English, students significantly develop their L2 Digital Literacy.

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

PubMed Central

Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry; Gurevich, Alexey A.; Dvorkin, Mikhail; Kulikov, Alexander S.; Lesin, Valery M.; Nikolenko, Sergey I.; Pham, Son; Prjibelski, Andrey D.; Pyshkin, Alexey V.; Sirotkin, Alexander V.; Vyahhi, Nikolay; Tesler, Glenn; Pevzner, Pavel A.

2012-01-01

Abstract The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software. PMID:22506599

Body to Scalp: Evolving Trends in Body Hair Transplantation

PubMed Central

Saxena, Kuldeep; Savant, Sandeep S.

2017-01-01

Follicular unit extraction (FUE) is becoming an increasingly popular method for hair restoration. As FUE leaves behind no linear scars, it is more suitable to harvest from various body areas including beard, chest, and extremities in hirsute individuals. Body hair characteristics such as thickness, length, and hair cycle may not completely match to that of the scalp hair. The techniques of harvesting body hairs are more time consuming, requiring higher degree of skill than regular scalp FUE. Body hair transplantation can be successfully used either alone or in combination with scalp hair in advanced grades of baldness, for improving the cosmetic appearance of hairlines and in scarring alopecia when there is paucity of donor scalp hair. Harvesting of body hairs opens up a new viable donor source for hair restoration surgeons, especially in cases of advanced Norwood grades five and above of androgenetic alopecia. PMID:28584752

MixDroid: A multi-features and multi-classifiers bagging system for Android malware detection

NASA Astrophysics Data System (ADS)

Huang, Weiqing; Hou, Erhang; Zheng, Liang; Feng, Weimiao

2018-05-01

In the past decade, Android platform has rapidly taken over the mobile market for its superior convenience and open source characteristics. However, with the popularity of Android, malwares targeting on Android devices are increasing rapidly, while the conventional rule-based and expert-experienced approaches are no longer able to handle such explosive growth. In this paper, combining with the theory of natural language processing and machine learning, we not only implement the basic feature extraction of permission application features, but also propose two innovative schemes of feature extraction: Dalvik opcode features and malicious code image, and implement an automatic Android malware detection system MixDroid which is based on multi-features and multi-classifiers. According to our experiment results on 20,000 Android applications, detection accuracy of MixDroid is 98.1%, which proves our schemes' effectiveness in Android malware detection.

Pybus -- A Python Software Bus

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

Lavrijsen, Wim T.L.P.

2004-10-14

A software bus, just like its hardware equivalent, allows for the discovery, installation, configuration, loading, unloading, and run-time replacement of software components, as well as channeling of inter-component communication. Python, a popular open-source programming language, encourages a modular design on software written in it, but it offers little or no component functionality. However, the language and its interpreter provide sufficient hooks to implement a thin, integral layer of component support. This functionality can be presented to the developer in the form of a module, making it very easy to use. This paper describes a Pythonmodule, PyBus, with which the conceptmore » of a ''software bus'' can be realized in Python. It demonstrates, within the context of the ATLAS software framework Athena, how PyBus can be used for the installation and (run-time) configuration of software, not necessarily Python modules, from a Python application in a way that is transparent to the end-user.« less

Design of Xen Hybrid Multiple Police Model

NASA Astrophysics Data System (ADS)

Sun, Lei; Lin, Renhao; Zhu, Xianwei

2017-10-01

Virtualization Technology has attracted more and more attention. As a popular open-source virtualization tools, XEN is used more and more frequently. Xsm, XEN security model, has also been widespread concern. The safety status classification has not been established in the XSM, and it uses the virtual machine as a managed object to make Dom0 a unique administrative domain that does not meet the minimum privilege. According to these questions, we design a Hybrid multiple police model named SV_HMPMD that organically integrates multiple single security policy models include DTE,RBAC,BLP. It can fullfill the requirement of confidentiality and integrity for security model and use different particle size to different domain. In order to improve BLP’s practicability, the model introduce multi-level security labels. In order to divide the privilege in detail, we combine DTE with RBAC. In order to oversize privilege, we limit the privilege of domain0.

Modeling the natural UV irradiation and comparative UV measurements at Moussala BEO (BG)

NASA Astrophysics Data System (ADS)

Tyutyundzhiev, N.; Angelov, Ch; Lovchinov, K.; Nitchev, Hr; Petrov, M.; Arsov, T.

2018-03-01

Studies of and modeling the impact of natural UV irradiation on the human population are of significant importance for human activity and economics. The sharp increase of environmental problems – extraordinary temperature changes, solar irradiation abnormalities, icy rains – raises the question of developing novel means of assessing and predicting potential UV effects. In this paper, we discuss new UV irradiation modeling based on recent real-time measurements at Moussala Basic Environmental Observatory (BEO) on Moussala Peak (2925 m ASL) in Rila Mountain, Bulgaria, and highlight the development and initial validation of portable embedded devices for UV-A, UV-B monitoring using open-source software architecture, narrow bandpass UV sensors, and the popular Arduino controllers. Despite the high temporal resolution of the VIS and UV irradiation measurements, the results obtained reveal the need of new assumptions in order to minimize the discrepancy with available databases.

3D EIT image reconstruction with GREIT.

PubMed

Grychtol, Bartłomiej; Müller, Beat; Adler, Andy

2016-06-01

Most applications of thoracic EIT use a single plane of electrodes on the chest from which a transverse image 'slice' is calculated. However, interpretation of EIT images is made difficult by the large region above and below the electrode plane to which EIT is sensitive. Volumetric EIT images using two (or more) electrode planes should help compensate, but are little used currently. The Graz consensus reconstruction algorithm for EIT (GREIT) has become popular in lung EIT. One shortcoming of the original formulation of GREIT is its restriction to reconstruction onto a 2D planar image. We present an extension of the GREIT algorithm to 3D and develop open-source tools to evaluate its performance as a function of the choice of stimulation and measurement pattern. Results show 3D GREIT using two electrode layers has significantly more uniform sensitivity profiles through the chest region. Overall, the advantages of 3D EIT are compelling.

BIOLOGICAL NETWORK EXPLORATION WITH CYTOSCAPE 3

PubMed Central

Su, Gang; Morris, John H.; Demchak, Barry; Bader, Gary D.

2014-01-01

Cytoscape is one of the most popular open-source software tools for the visual exploration of biomedical networks composed of protein, gene and other types of interactions. It offers researchers a versatile and interactive visualization interface for exploring complex biological interconnections supported by diverse annotation and experimental data, thereby facilitating research tasks such as predicting gene function and pathway construction. Cytoscape provides core functionality to load, visualize, search, filter and save networks, and hundreds of Apps extend this functionality to address specific research needs. The latest generation of Cytoscape (version 3.0 and later) has substantial improvements in function, user interface and performance relative to previous versions. This protocol aims to jump-start new users with specific protocols for basic Cytoscape functions, such as installing Cytoscape and Cytoscape Apps, loading data, visualizing and navigating the network, visualizing network associated data (attributes) and identifying clusters. It also highlights new features that benefit experienced users. PMID:25199793

Introductory Physics Experiments Using the Wiimote

NASA Astrophysics Data System (ADS)

Somers, William; Rooney, Frank; Ochoa, Romulo

2009-03-01

The Wii, a video game console, is a very popular device with millions of units sold worldwide over the past two years. Although computationally it is not a powerful machine, to a physics educator its most important components can be its controllers. The Wiimote (or remote) controller contains three accelerometers, an infrared detector, and Bluetooth connectivity at a relatively low price. Thanks to available open source code, any PC with Bluetooth capability can detect the information sent out by the Wiimote. We have designed several experiments for introductory physics courses that make use of the accelerometers and Bluetooth connectivity. We have adapted the Wiimote to measure the: variable acceleration in simple harmonic motion, centripetal and tangential accelerations in circular motion, and the accelerations generated when students lift weights. We present the results of our experiments and compare them with those obtained when using motion and/or force sensors.

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

PubMed

Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

2018-06-11

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

An Overview of R in Health Decision Sciences.

PubMed

Jalal, Hawre; Pechlivanoglou, Petros; Krijkamp, Eline; Alarid-Escudero, Fernando; Enns, Eva; Hunink, M G Myriam

2017-10-01

As the complexity of health decision science applications increases, high-level programming languages are increasingly adopted for statistical analyses and numerical computations. These programming languages facilitate sophisticated modeling, model documentation, and analysis reproducibility. Among the high-level programming languages, the statistical programming framework R is gaining increased recognition. R is freely available, cross-platform compatible, and open source. A large community of users who have generated an extensive collection of well-documented packages and functions supports it. These functions facilitate applications of health decision science methodology as well as the visualization and communication of results. Although R's popularity is increasing among health decision scientists, methodological extensions of R in the field of decision analysis remain isolated. The purpose of this article is to provide an overview of existing R functionality that is applicable to the various stages of decision analysis, including model design, input parameter estimation, and analysis of model outputs.

jsPsych: a JavaScript library for creating behavioral experiments in a Web browser.

PubMed

de Leeuw, Joshua R

2015-03-01

Online experiments are growing in popularity, and the increasing sophistication of Web technology has made it possible to run complex behavioral experiments online using only a Web browser. Unlike with offline laboratory experiments, however, few tools exist to aid in the development of browser-based experiments. This makes the process of creating an experiment slow and challenging, particularly for researchers who lack a Web development background. This article introduces jsPsych, a JavaScript library for the development of Web-based experiments. jsPsych formalizes a way of describing experiments that is much simpler than writing the entire experiment from scratch. jsPsych then executes these descriptions automatically, handling the flow from one task to another. The jsPsych library is open-source and designed to be expanded by the research community. The project is available online at www.jspsych.org .

Openly Published Environmental Sensing (OPEnS) | Advancing Open-Source Research, Instrumentation, and Dissemination

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

The increasing availability and functionality of Open-Source software and hardware along with 3D printing, low-cost electronics, and proliferation of open-access resources for learning rapid prototyping are contributing to fundamental transformations and new technologies in environmental sensing. These tools invite reevaluation of time-tested methodologies and devices toward more efficient, reusable, and inexpensive alternatives. Building upon Open-Source design facilitates community engagement and invites a Do-It-Together (DIT) collaborative framework for research where solutions to complex problems may be crowd-sourced. However, barriers persist that prevent researchers from taking advantage of the capabilities afforded by open-source software, hardware, and rapid prototyping. Some of these include: requisite technical skillsets, knowledge of equipment capabilities, identifying inexpensive sources for materials, money, space, and time. A university MAKER space staffed by engineering students to assist researchers is one proposed solution to overcome many of these obstacles. This presentation investigates the unique capabilities the USDA-funded Openly Published Environmental Sensing (OPEnS) Lab affords researchers, within Oregon State and internationally, and the unique functions these types of initiatives support at the intersection of MAKER spaces, Open-Source academic research, and open-access dissemination.

Open-source software: not quite endsville.

PubMed

Stahl, Matthew T

2005-02-01

Open-source software will never achieve ubiquity. There are environments in which it simply does not flourish. By its nature, open-source development requires free exchange of ideas, community involvement, and the efforts of talented and dedicated individuals. However, pressures can come from several sources that prevent this from happening. In addition, openness and complex licensing issues invite misuse and abuse. Care must be taken to avoid the pitfalls of open-source software.

Developing an Open Source Option for NASA Software

NASA Technical Reports Server (NTRS)

Moran, Patrick J.; Parks, John W. (Technical Monitor)

2003-01-01

We present arguments in favor of developing an Open Source option for NASA software; in particular we discuss how Open Source is compatible with NASA's mission. We compare and contrast several of the leading Open Source licenses, and propose one - the Mozilla license - for use by NASA. We also address some of the related issues for NASA with respect to Open Source. In particular, we discuss some of the elements in the External Release of NASA Software document (NPG 2210.1A) that will likely have to be changed in order to make Open Source a reality withm the agency.

Mathematical detection of aortic valve opening (B point) in impedance cardiography: A comparison of three popular algorithms.

PubMed

Árbol, Javier Rodríguez; Perakakis, Pandelis; Garrido, Alba; Mata, José Luis; Fernández-Santaella, M Carmen; Vila, Jaime

2017-03-01

The preejection period (PEP) is an index of left ventricle contractility widely used in psychophysiological research. Its computation requires detecting the moment when the aortic valve opens, which coincides with the B point in the first derivative of impedance cardiogram (ICG). Although this operation has been traditionally made via visual inspection, several algorithms based on derivative calculations have been developed to enable an automatic performance of the task. However, despite their popularity, data about their empirical validation are not always available. The present study analyzes the performance in the estimation of the aortic valve opening of three popular algorithms, by comparing their performance with the visual detection of the B point made by two independent scorers. Algorithm 1 is based on the first derivative of the ICG, Algorithm 2 on the second derivative, and Algorithm 3 on the third derivative. Algorithm 3 showed the highest accuracy rate (78.77%), followed by Algorithm 1 (24.57%) and Algorithm 2 (13.82%). In the automatic computation of PEP, Algorithm 2 resulted in significantly more missed cycles (48.57%) than Algorithm 1 (6.3%) and Algorithm 3 (3.5%). Algorithm 2 also estimated a significantly lower average PEP (70 ms), compared with the values obtained by Algorithm 1 (119 ms) and Algorithm 3 (113 ms). Our findings indicate that the algorithm based on the third derivative of the ICG performs significantly better. Nevertheless, a visual inspection of the signal proves indispensable, and this article provides a novel visual guide to facilitate the manual detection of the B point. © 2016 Society for Psychophysiological Research.

Open-Source Data and the Study of Homicide.

PubMed

Parkin, William S; Gruenewald, Jeff

2015-07-20

To date, no discussion has taken place in the social sciences as to the appropriateness of using open-source data to augment, or replace, official data sources in homicide research. The purpose of this article is to examine whether open-source data have the potential to be used as a valid and reliable data source in testing theory and studying homicide. Official and open-source homicide data were collected as a case study in a single jurisdiction over a 1-year period. The data sets were compared to determine whether open-sources could recreate the population of homicides and variable responses collected in official data. Open-source data were able to replicate the population of homicides identified in the official data. Also, for every variable measured, the open-sources captured as much, or more, of the information presented in the official data. Also, variables not available in official data, but potentially useful for testing theory, were identified in open-sources. The results of the case study show that open-source data are potentially as effective as official data in identifying individual- and situational-level characteristics, provide access to variables not found in official homicide data, and offer geographic data that can be used to link macro-level characteristics to homicide events. © The Author(s) 2015.

Analysis of popular press articles concerning postpartum depression: 1998-2006.

PubMed

Schanie, Carrie L; Pinto-Foltz, Melissa D; Logsdon, M Cynthia

2008-11-01

The purpose of the study was to analyze the content of popular press magazine articles that focused on postpartum depression, published from 1998-2006. Replicating earlier research by Martinez, Johnson-Robledo, Ulsh, and Chrisler, 2000, 47 articles were identified and their content analyzed in the areas of etiology, symptoms, treatment, resources, and demographic assumptions about readers. Popular press magazines contained contradictory information about the definition, prevalence, onset, duration, symptoms, and treatment of postpartum mood disorders. Health care providers should be proactive in directing childbearing women to factual sources of information on postpartum depression.

How Is Open Source Special?

ERIC Educational Resources Information Center

Kapor, Mitchell

2005-01-01

Open source software projects involve the production of goods, but in software projects, the "goods" consist of information. The open source model is an alternative to the conventional centralized, command-and-control way in which things are usually made. In contrast, open source projects are genuinely decentralized and transparent. Transparent…

Common characteristics of open source software development and applicability for drug discovery: a systematic review.

PubMed

Ardal, Christine; Alstadsæter, Annette; Røttingen, John-Arne

2011-09-28

Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents.

Open Source Paradigm: A Synopsis of The Cathedral and the Bazaar for Health and Social Care.

PubMed

Benson, Tim

2016-07-04

Open source software (OSS) is becoming more fashionable in health and social care, although the ideas are not new. However progress has been slower than many had expected. The purpose is to summarise the Free/Libre Open Source Software (FLOSS) paradigm in terms of what it is, how it impacts users and software engineers and how it can work as a business model in health and social care sectors. Much of this paper is a synopsis of Eric Raymond's seminal book The Cathedral and the Bazaar, which was the first comprehensive description of the open source ecosystem, set out in three long essays. Direct quotes from the book are used liberally, without reference to specific passages. The first part contrasts open and closed source approaches to software development and support. The second part describes the culture and practices of the open source movement. The third part considers business models. A key benefit of open source is that users can access and collaborate on improving the software if they wish. Closed source code may be regarded as a strategic business risk that that may be unacceptable if there is an open source alternative. The sharing culture of the open source movement fits well with that of health and social care.

QUO VADIS SOURCE TRACKING? TOWARDS A STRATEGIC FRAMEWORK FOR ENVIRONMENTAL MONITORING OF FECAL POLLUTION

EPA Science Inventory

Advances in microbial source tracking (MST) have largely been driven by the need to comply with water quality standards based on traditional indicator bacteria. Recently, a number of PCR-based, culture- and library-independent methods have been gaining popularity among source tra...

Quantarctica: A Unique, Open, Standalone GIS Package for Antarctic Research and Education

NASA Astrophysics Data System (ADS)

Roth, George; Matsuoka, Kenichi; Skoglund, Anders; Melvær, Yngve; Tronstad, Stein

2017-04-01

The Norwegian Polar Institute has developed Quantarctica (http://quantarctica.npolar.no), an open GIS package for use by the international Antarctic community. Quantarctica includes a wide range of cartographic basemap layers, geophysical and glaciological datasets, and satellite imagery in standardized open file formats with a consistent Antarctic map projection and customized layer and labeling styles for quick, effective cartography. Quantarctica's strengths as an open science platform lie in 1) The complete, ready-to-use data package which includes full-resolution, original-quality vector and raster data, 2) A policy for freely-redistributable and modifiable data including all metadata and citations, and 3) QGIS, a free, full-featured, modular, offline-capable open-source GIS suite with a rapid and active development and support community. The Quantarctica team is actively incorporating more up-to-date, peer-reviewed, freely distributable pan-Antarctic geospatial datasets for the next version release in 2017. As part of this ongoing development, we are investigating the best approaches for quickly and seamlessly distributing new and updated data to users, storing datasets in efficient, open file formats while maintaining full data integrity, and coexisting with numerous online data portals in a way that most actively benefits the Antarctic community. A recent survey of Quantarctica users showed broad geographical adoption among Antarctic Treaty countries, including those outside the large US and UK Antarctic programs. Maps and figures produced by Quantarctica have also appeared in open-access journals and outside of the formal scientific community on popular science and GIS blogs. Our experience with the Quantarctica project has shown the tremendous value of education and outreach, not only in promoting open software, data formats, and practices, but in empowering Antarctic science groups to more effectively use GIS and geospatial data. Open practices are making a huge impact in Antarctic GIS, where individual countries have historically maintained their own restricted Antarctic geodatabases and where the next generation of scientists are entering the field with experience in using geospatial thinking for planning, visualization, and problem solving.

Weather forecasting with open source software

NASA Astrophysics Data System (ADS)

Rautenhaus, Marc; Dörnbrack, Andreas

2013-04-01

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

Optimization of image processing algorithms on mobile platforms

NASA Astrophysics Data System (ADS)

Poudel, Pramod; Shirvaikar, Mukul

2011-03-01

This work presents a technique to optimize popular image processing algorithms on mobile platforms such as cell phones, net-books and personal digital assistants (PDAs). The increasing demand for video applications like context-aware computing on mobile embedded systems requires the use of computationally intensive image processing algorithms. The system engineer has a mandate to optimize them so as to meet real-time deadlines. A methodology to take advantage of the asymmetric dual-core processor, which includes an ARM and a DSP core supported by shared memory, is presented with implementation details. The target platform chosen is the popular OMAP 3530 processor for embedded media systems. It has an asymmetric dual-core architecture with an ARM Cortex-A8 and a TMS320C64x Digital Signal Processor (DSP). The development platform was the BeagleBoard with 256 MB of NAND RAM and 256 MB SDRAM memory. The basic image correlation algorithm is chosen for benchmarking as it finds widespread application for various template matching tasks such as face-recognition. The basic algorithm prototypes conform to OpenCV, a popular computer vision library. OpenCV algorithms can be easily ported to the ARM core which runs a popular operating system such as Linux or Windows CE. However, the DSP is architecturally more efficient at handling DFT algorithms. The algorithms are tested on a variety of images and performance results are presented measuring the speedup obtained due to dual-core implementation. A major advantage of this approach is that it allows the ARM processor to perform important real-time tasks, while the DSP addresses performance-hungry algorithms.

Open Source Software Development

DTIC Science & Technology

2011-01-01

Software, 2002, 149(1), 3-17. 3. DiBona , C., Cooper, D., and Stone, M. (Eds.), Open Sources 2.0, 2005, O’Reilly Media, Sebastopol, CA. Also see, C... DiBona , S. Ockman, and M. Stone (Eds.). Open Sources: Vocides from the Open Source Revolution, 1999. O’Reilly Media, Sebastopol, CA. 4. Ducheneaut, N

Open-source hardware for medical devices

PubMed Central

2016-01-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device. PMID:27158528

Open-source hardware for medical devices.

PubMed

Niezen, Gerrit; Eslambolchilar, Parisa; Thimbleby, Harold

2016-04-01

Open-source hardware is hardware whose design is made publicly available so anyone can study, modify, distribute, make and sell the design or the hardware based on that design. Some open-source hardware projects can potentially be used as active medical devices. The open-source approach offers a unique combination of advantages, including reducing costs and faster innovation. This article compares 10 of open-source healthcare projects in terms of how easy it is to obtain the required components and build the device.

The case for open-source software in drug discovery.

PubMed

DeLano, Warren L

2005-02-01

Widespread adoption of open-source software for network infrastructure, web servers, code development, and operating systems leads one to ask how far it can go. Will "open source" spread broadly, or will it be restricted to niches frequented by hopeful hobbyists and midnight hackers? Here we identify reasons for the success of open-source software and predict how consumers in drug discovery will benefit from new open-source products that address their needs with increased flexibility and in ways complementary to proprietary options.

Curating and sharing structures and spectra for the environmental community

EPA Science Inventory

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resour...

Value, Cost, and Sharing: Open Issues in Constrained Clustering

NASA Technical Reports Server (NTRS)

Wagstaff, Kiri L.

2006-01-01

Clustering is an important tool for data mining, since it can identify major patterns or trends without any supervision (labeled data). Over the past five years, semi-supervised (constrained) clustering methods have become very popular. These methods began with incorporating pairwise constraints and have developed into more general methods that can learn appropriate distance metrics. However, several important open questions have arisen about which constraints are most useful, how they can be actively acquired, and when and how they should be propagated to neighboring points. This position paper describes these open questions and suggests future directions for constrained clustering research.

Choosing Open Source ERP Systems: What Reasons Are There For Doing So?

NASA Astrophysics Data System (ADS)

Johansson, Björn; Sudzina, Frantisek

Enterprise resource planning (ERP) systems attract a high attention and open source software does it as well. The question is then if, and if so, when do open source ERP systems take off. The paper describes the status of open source ERP systems. Based on literature review of ERP system selection criteria based on Web of Science articles, it discusses reported reasons for choosing open source or proprietary ERP systems. Last but not least, the article presents some conclusions that could act as input for future research. The paper aims at building up a foundation for the basic question: What are the reasons for an organization to adopt open source ERP systems.

The Ghost of "Emo:" Searching for Mental Health Themes in a Popular Music Format

ERIC Educational Resources Information Center

Baker, Timothy D.; Smith-Adcock, Sondra; Glynn, Virginia R.

2013-01-01

The concept of "Emo" has gained attention among counselors who work with teens in school settings. Emo has been associated with music and popular media has linked it to mental health concerns, but scholarly sources have not converged regarding what sort of music it is, or what it means for adolescents' wellness. The authors devise…

Antologia Del Saber Popular: A Selection from Various Genres of Mexican Folklore Across Borders. Monograph No. 2.

ERIC Educational Resources Information Center

Robe, Stanley L., Ed.

A variety of oral folk material from Mexican sources is presented in this anthology. The 114 selections are derived from the various genres available and from traditional as well as newer formations. The selections include folktales, jests and anecdotes, legends and beliefs, beliefs about popular medicine, prayers, verses, children's games and…

What's on the News? The Use of Media Texts in Exams of Clinical Biochemistry for Medical and Nutrition Students

ERIC Educational Resources Information Center

Oliveira, Julia Martins; Mesquita, Diego Martins; Hermes-Lima, Marcelo

2010-01-01

Health-related popular articles are easily found among media sources. With the increasing popularity of the internet, medical information--full of misconceptions--has become easily available to the lay people. The ability to recognize misconceptions may require good biomedical knowledge. In this sense, we decided to use articles from the internet…

Developing open-source codes for electromagnetic geophysics using industry support

NASA Astrophysics Data System (ADS)

Key, K.

2017-12-01

Funding for open-source software development in academia often takes the form of grants and fellowships awarded by government bodies and foundations where there is no conflict-of-interest between the funding entity and the free dissemination of the open-source software products. Conversely, funding for open-source projects in the geophysics industry presents challenges to conventional business models where proprietary licensing offers value that is not present in open-source software. Such proprietary constraints make it easier to convince companies to fund academic software development under exclusive software distribution agreements. A major challenge for obtaining commercial funding for open-source projects is to offer a value proposition that overcomes the criticism that such funding is a give-away to the competition. This work draws upon a decade of experience developing open-source electromagnetic geophysics software for the oil, gas and minerals exploration industry, and examines various approaches that have been effective for sustaining industry sponsorship.

Behind Linus's Law: Investigating Peer Review Processes in Open Source

ERIC Educational Resources Information Center

Wang, Jing

2013-01-01

Open source software has revolutionized the way people develop software, organize collaborative work, and innovate. The numerous open source software systems that have been created and adopted over the past decade are influential and vital in all aspects of work and daily life. The understanding of open source software development can enhance its…

Implementing Open Source Platform for Education Quality Enhancement in Primary Education: Indonesia Experience

ERIC Educational Resources Information Center

Kisworo, Marsudi Wahyu

2016-01-01

Information and Communication Technology (ICT)-supported learning using free and open source platform draws little attention as open source initiatives were focused in secondary or tertiary educations. This study investigates possibilities of ICT-supported learning using open source platform for primary educations. The data of this study is taken…

An Analysis of Open Source Security Software Products Downloads

ERIC Educational Resources Information Center

Barta, Brian J.

2014-01-01

Despite the continued demand for open source security software, a gap in the identification of success factors related to the success of open source security software persists. There are no studies that accurately assess the extent of this persistent gap, particularly with respect to the strength of the relationships of open source software…

Reusable Client-Side JavaScript Modules for Immersive Web-Based Real-Time Collaborative Neuroimage Visualization

PubMed Central

Bernal-Rusiel, Jorge L.; Rannou, Nicolas; Gollub, Randy L.; Pieper, Steve; Murphy, Shawn; Robertson, Richard; Grant, Patricia E.; Pienaar, Rudolph

2017-01-01

In this paper we present a web-based software solution to the problem of implementing real-time collaborative neuroimage visualization. In both clinical and research settings, simple and powerful access to imaging technologies across multiple devices is becoming increasingly useful. Prior technical solutions have used a server-side rendering and push-to-client model wherein only the server has the full image dataset. We propose a rich client solution in which each client has all the data and uses the Google Drive Realtime API for state synchronization. We have developed a small set of reusable client-side object-oriented JavaScript modules that make use of the XTK toolkit, a popular open-source JavaScript library also developed by our team, for the in-browser rendering and visualization of brain image volumes. Efficient realtime communication among the remote instances is achieved by using just a small JSON object, comprising a representation of the XTK image renderers' state, as the Google Drive Realtime collaborative data model. The developed open-source JavaScript modules have already been instantiated in a web-app called MedView, a distributed collaborative neuroimage visualization application that is delivered to the users over the web without requiring the installation of any extra software or browser plugin. This responsive application allows multiple physically distant physicians or researchers to cooperate in real time to reach a diagnosis or scientific conclusion. It also serves as a proof of concept for the capabilities of the presented technological solution. PMID:28507515

AIMBAT: A Python/Matplotlib Tool for Measuring Teleseismic Arrival Times

NASA Astrophysics Data System (ADS)

Lou, X.; van der Lee, S.; Lloyd, S.

2013-12-01

Python is an open-source, platform-independent, and object-oriented scripting language. It became more popular in the seismologist community since the appearance of ObsPy (Beyreuther et al. 2010, Megies et al. 2011), which provides a powerful framework for seismic data access and processing. This study introduces a new Python-based tool named AIMBAT (Automated and Interactive Measurement of Body-wave Arrival Times) for measuring teleseismic body-wave arrival times on large-scale seismic event data (Lou et al. 2013). Compared to ObsPy, AIMBAT is a lighter tool that is more focused on a particular aspect of seismic data processing. It originates from the widely used MCCC (Multi-Channel Cross-Correlation) method developed by VanDecar and Crosson (1990). On top of the original MCCC procedure, AIMBAT is automated in initial phase picking and is interactive in quality control. The core cross-correlation function is implemented in Fortran to boost up performance in addition to Python. The GUI (graphical user interface) of AIMBAT depends on Matplotlib's GUI-neutral widgets and event-handling API. A number of sorting and (de)selecting options are designed to facilitate the quality control of seismograms. By using AIMBAT, both relative and absolute teleseismic body-wave arrival times are measured. AIMBAT significantly improves efficiency and quality of the measurements. User interaction is needed only to pick the target phase arrival and to set a time window on the array stack. The package is easy to install and use, open-source, and is publicly available. Graphical user interface of AIMBAT.

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

PubMed Central

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

2011-01-01

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

Spatial occupancy models for large data sets

USGS Publications Warehouse

Johnson, Devin S.; Conn, Paul B.; Hooten, Mevin B.; Ray, Justina C.; Pond, Bruce A.

2013-01-01

Since its development, occupancy modeling has become a popular and useful tool for ecologists wishing to learn about the dynamics of species occurrence over time and space. Such models require presence–absence data to be collected at spatially indexed survey units. However, only recently have researchers recognized the need to correct for spatially induced overdisperison by explicitly accounting for spatial autocorrelation in occupancy probability. Previous efforts to incorporate such autocorrelation have largely focused on logit-normal formulations for occupancy, with spatial autocorrelation induced by a random effect within a hierarchical modeling framework. Although useful, computational time generally limits such an approach to relatively small data sets, and there are often problems with algorithm instability, yielding unsatisfactory results. Further, recent research has revealed a hidden form of multicollinearity in such applications, which may lead to parameter bias if not explicitly addressed. Combining several techniques, we present a unifying hierarchical spatial occupancy model specification that is particularly effective over large spatial extents. This approach employs a probit mixture framework for occupancy and can easily accommodate a reduced-dimensional spatial process to resolve issues with multicollinearity and spatial confounding while improving algorithm convergence. Using open-source software, we demonstrate this new model specification using a case study involving occupancy of caribou (Rangifer tarandus) over a set of 1080 survey units spanning a large contiguous region (108 000 km2) in northern Ontario, Canada. Overall, the combination of a more efficient specification and open-source software allows for a facile and stable implementation of spatial occupancy models for large data sets.

SIGNUM: A Matlab, TIN-based landscape evolution model

NASA Astrophysics Data System (ADS)

Refice, A.; Giachetta, E.; Capolongo, D.

2012-08-01

Several numerical landscape evolution models (LEMs) have been developed to date, and many are available as open source codes. Most are written in efficient programming languages such as Fortran or C, but often require additional code efforts to plug in to more user-friendly data analysis and/or visualization tools to ease interpretation and scientific insight. In this paper, we present an effort to port a common core of accepted physical principles governing landscape evolution directly into a high-level language and data analysis environment such as Matlab. SIGNUM (acronym for Simple Integrated Geomorphological Numerical Model) is an independent and self-contained Matlab, TIN-based landscape evolution model, built to simulate topography development at various space and time scales. SIGNUM is presently capable of simulating hillslope processes such as linear and nonlinear diffusion, fluvial incision into bedrock, spatially varying surface uplift which can be used to simulate changes in base level, thrust and faulting, as well as effects of climate changes. Although based on accepted and well-known processes and algorithms in its present version, it is built with a modular structure, which allows to easily modify and upgrade the simulated physical processes to suite virtually any user needs. The code is conceived as an open-source project, and is thus an ideal tool for both research and didactic purposes, thanks to the high-level nature of the Matlab environment and its popularity among the scientific community. In this paper the simulation code is presented together with some simple examples of surface evolution, and guidelines for development of new modules and algorithms are proposed.

Exploration of solar photospheric magnetic field data sets using the UCSD tomography

NASA Astrophysics Data System (ADS)

Jackson, B. V.; Yu, H.-S.; Buffington, A.; Hick, P. P.; Nishimura, N.; Nozaki, N.; Tokumaru, M.; Fujiki, K.; Hayashi, K.

2016-12-01

This article investigates the use of two different types of National Solar Observatory magnetograms and two different coronal field modeling techniques over 10 years. Both the "open-field" Current Sheet Source Surface (CSSS) and a "closed-field" technique using CSSS modeling are compared. The University of California, San Diego, tomographic modeling, using interplanetary scintillation data from Japan, provides the global velocities to extrapolate these fields outward, which are then compared with fields measured in situ near Earth. Although the open-field technique generally gives a better result for radial and tangential fields, we find that a portion of the closed extrapolated fields measured in situ near Earth comes from the direct outward mapping of these fields in the low solar corona. All three closed-field components are nonzero at 1 AU and are compared with the appropriate magnetometer values. A significant positive correlation exists between these closed-field components and the in situ measurements over the last 10 years. We determine that a small fraction of the static low-coronal component flux, which includes the Bn (north-south) component, regularly escapes from closed-field regions. The closed-field flux fraction varies by about a factor of 3 from a mean value during this period, relative to the magnitude of the field components measured in situ near Earth, and maximizes in 2014. This implies that a relatively more efficient process for closed-flux escape occurs near solar maximum. We also compare and find that the popular Potential Field Source Surface and CSSS model closed fields are nearly identical in sign and strength.

MethLAB

PubMed Central

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K

2012-01-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data. PMID:22430798

Research on OpenStack of open source cloud computing in colleges and universities’ computer room

NASA Astrophysics Data System (ADS)

Wang, Lei; Zhang, Dandan

2017-06-01

In recent years, the cloud computing technology has a rapid development, especially open source cloud computing. Open source cloud computing has attracted a large number of user groups by the advantages of open source and low cost, have now become a large-scale promotion and application. In this paper, firstly we briefly introduced the main functions and architecture of the open source cloud computing OpenStack tools, and then discussed deeply the core problems of computer labs in colleges and universities. Combining with this research, it is not that the specific application and deployment of university computer rooms with OpenStack tool. The experimental results show that the application of OpenStack tool can efficiently and conveniently deploy cloud of university computer room, and its performance is stable and the functional value is good.

Wanting to See People Like Me? Racial and Gender Diversity in Popular Adolescent Television

PubMed Central

Ellithorpe, Morgan E.; Bleakley, Amy

2016-01-01

Media are one source for adolescent identity development and social identity gratifications. Nielsen viewing data across the 2014–2015 television season for adolescents ages 14–17 was used to examine racial and gender diversity in adolescent television exposure. Compared to U.S. Census data, mainstream shows underrepresent women, but the proportion of Black characters is roughly representative. Black adolescents watch more television than non-Black adolescents and, after taking this into account, shows popular with Black adolescents are more likely than shows popular with non-Black adolescents to exhibit racial diversity. In addition, shows popular with female adolescents are more likely than shows popular with males to exhibit gender diversity. These results support the idea that adolescents seek out media messages with characters that are members of their identity groups, possibly because the characters serve as tools for identity development and social identity gratifications. PMID:26759131

Wanting to See People Like Me? Racial and Gender Diversity in Popular Adolescent Television.

PubMed

Ellithorpe, Morgan E; Bleakley, Amy

2016-07-01

Media are one source for adolescent identity development and social identity gratifications. Nielsen viewing data across the 2014-2015 television season for adolescents ages 14-17 was used to examine racial and gender diversity in adolescent television exposure. Compared to US Census data, mainstream shows under represent women, but the proportion of Black characters is roughly representative. Black adolescents watch more television than non-Black adolescents and, after taking this into account, shows popular with Black adolescents are more likely than shows popular with non-Black adolescents to exhibit racial diversity. In addition, shows popular with female adolescents are more likely than shows popular with males to exhibit gender diversity. These results support the idea that adolescents seek out media messages with characters that are members of their identity groups, possibly because the characters serve as tools for identity development and social identity gratifications.

The Water SWITCH-ON Spatial Information Platform (SIP)

NASA Astrophysics Data System (ADS)

Sala Calero, J., Sr.; Boot, G., Sr.; Dihé, P., Sr.; Arheimer, B.

2017-12-01

The amount of hydrological open data is continually growing and providing opportunities to the scientific community. Although the existing data portals (GEOSS Portal, INSPIRE community geoportal and others) enable access to open data, many users still find browsing through them difficult. Moreover, the time spent on gathering and preparing data usually is more significant than the time spent on the experiment itself. Thus, any improvement on searching, understanding, accessing or using open data is greatly beneficial. The Spatial Information Platform (SIP) has been developed to tackle these issues within the SWITCH-ON European Commission funded FP7 project. The SIP has been designed as a set of tools based on open standards that provide to the user all the necessary functionalities as described in the Publish-Find-Bind (PFB) pattern. In other words, this means that the SIP helps users to locate relevant and suitable data for their experiments analysis, to access and transform it (filtering, extraction, selection, conversion, aggregation). Moreover, the SIP can be used to provide descriptive information about the data and to publish it so others can find and use it. The SIP is based on existing open data protocols such as the OGC/CSW, OGC/WMS, OpenDAP and open-source components like PostgreSQL/PostGIS, GeoServer and pyCSW. The SIP is divided in three main user interfaces: the BYOD (Browse your open dataset) web interface, the Expert GUI tool and the Upload Data and Metadata web interface. The BYOD HTML5 client is the main entry point for users that want to browse through open data in the SIP. The BYOD has a map interface based on Leaflet JavaScript libraries so that the users can search more efficiently. The web-based Open Data Registration Tool is a user-friendly upload and metadata description interface (geographical extent, license, DOI generation). The Expert GUI is a desktop application that provides full metadata editing capabilities for the metadata moderators of the project. In conclusion, the Spatial Information Platform (SIP) provides to its community a set of tools for better understanding and ease of use of hydrological open-data. Moreover, the SIP has been based on well-known OGC standards that will allow the connection and data harvesting from popular open data portals such as the GEOSS system of systems.

Common characteristics of open source software development and applicability for drug discovery: a systematic review

PubMed Central

2011-01-01

Background Innovation through an open source model has proven to be successful for software development. This success has led many to speculate if open source can be applied to other industries with similar success. We attempt to provide an understanding of open source software development characteristics for researchers, business leaders and government officials who may be interested in utilizing open source innovation in other contexts and with an emphasis on drug discovery. Methods A systematic review was performed by searching relevant, multidisciplinary databases to extract empirical research regarding the common characteristics and barriers of initiating and maintaining an open source software development project. Results Common characteristics to open source software development pertinent to open source drug discovery were extracted. The characteristics were then grouped into the areas of participant attraction, management of volunteers, control mechanisms, legal framework and physical constraints. Lastly, their applicability to drug discovery was examined. Conclusions We believe that the open source model is viable for drug discovery, although it is unlikely that it will exactly follow the form used in software development. Hybrids will likely develop that suit the unique characteristics of drug discovery. We suggest potential motivations for organizations to join an open source drug discovery project. We also examine specific differences between software and medicines, specifically how the need for laboratories and physical goods will impact the model as well as the effect of patents. PMID:21955914

The 2017 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year’s theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest. PMID:29118973

The 2017 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Munoz-Torres, Monica; Tzovaras, Bastian Greshake; Wiencko, Heather

2017-01-01

The Bioinformatics Open Source Conference (BOSC) is a meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. The 18th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2017) took place in Prague, Czech Republic in July 2017. The conference brought together nearly 250 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, open and reproducible science, and this year's theme, open data. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community, called the OBF Codefest.

The Efficient Utilization of Open Source Information

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

Baty, Samuel R.

These are a set of slides on the efficient utilization of open source information. Open source information consists of a vast set of information from a variety of sources. Not only does the quantity of open source information pose a problem, the quality of such information can hinder efforts. To show this, two case studies are mentioned: Iran and North Korea, in order to see how open source information can be utilized. The huge breadth and depth of open source information can complicate an analysis, especially because open information has no guarantee of accuracy. Open source information can provide keymore » insights either directly or indirectly: looking at supporting factors (flow of scientists, products and waste from mines, government budgets, etc.); direct factors (statements, tests, deployments). Fundamentally, it is the independent verification of information that allows for a more complete picture to be formed. Overlapping sources allow for more precise bounds on times, weights, temperatures, yields or other issues of interest in order to determine capability. Ultimately, a "good" answer almost never comes from an individual, but rather requires the utilization of a wide range of skill sets held by a team of people.« less

Real-time detecting and tracking ball with OpenCV and Kinect

NASA Astrophysics Data System (ADS)

Osiecki, Tomasz; Jankowski, Stanislaw

2016-09-01

This paper presents a way to detect and track ball with using the OpenCV and Kinect. Object and people recognition, tracking are more and more popular topics nowadays. Described solution makes it possible to detect ball based on the range, which is set by the user and capture information about ball position in three dimensions. It can be store in the computer and use for example to display trajectory of the ball.

The Associations between Yelp Online Reviews and Vape Shops Closing or Remaining Open One Year Later.

PubMed

Kong, Grace; Unger, Jennifer; Baezconde-Garbanati, Lourdes; Sussman, Steve

2017-01-01

Vape shops are popular brick-and-mortar stores that sell e-cigarette products but are not understood well. Previous analysis of Yelp reviews of vape shops located in various ethnic neighborhoods in Los Angeles, California in 2014 identified characteristics of vape shop as delineated by consumers. In this study, we assessed the associations between these characteristics and vape shops going out of business in 2015. Content analysis of Yelp reviews of 72 vape shops in 2014 identified 1) general characteristics of the reviews/reviewers, 2) vape shop, staff, and marketing attributes, 3) physical environment, and 4) health claims. In 2015, in-person visits confirmed that 22% of these vape shops closed permanently. We analyzed whether characteristics/attributes identified in 2014 associated with stores remaining open (n = 56) or permanently closing (n = 16) in 2015. Univariate findings showed that open vape shops relative to closed shops had greater 1) number of reviews, 2) rebuilds/fixings, 3) ratings of staff attributes as "helpful/patient/respectful," and 4) report of the physical environment as "bar type." Bar type vape shops and those with rebuilding/fixing capabilities were associated with staying open, suggesting the popularity of these attributes. Yelp consumer reviews is a useful research tool to identify consumer-determined important sustaining attributes of vape shops and may be used to identify aspects of enduring shops that need regulations.

PubMed, The New York Times and The Chicago Tribune as Tools for Teaching Genetics

PubMed Central

Strauss, Bernard S.

2005-01-01

An elementary course in human heredity for students not planning to major in the sciences can be based on current scientific literature and on the popular media. Examinations are constructed from questions on recent abstracts obtained from PubMed. The course is designed to promote writing skills in the sciences, and students write two papers in the course of a quarter. In the first paper, students trace the primary source of media reports on genetics and attempt to evaluate the reporter's translation. In a second paper, students write popular articles on the basis of current primary sources. PMID:16143615

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

PubMed

Harris, Nomi L; Cock, Peter J A; Lapp, Hilmar; Chapman, Brad; Davey, Rob; Fields, Christopher; Hokamp, Karsten; Munoz-Torres, Monica

2016-02-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included "Data Science;" "Standards and Interoperability;" "Open Science and Reproducibility;" "Translational Bioinformatics;" "Visualization;" and "Bioinformatics Open Source Project Updates". In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled "Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community," that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule.

Land User and Land Cover Maps of Europe: a Webgis Platform

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Fahl, F. C.; Minghini, M.; Molinari, M. E.

2016-06-01

This paper presents the methods and implementation processes of a WebGIS platform designed to publish the available land use and land cover maps of Europe at continental scale. The system is built completely on open source infrastructure and open standards. The proposed architecture is based on a server-client model having GeoServer as the map server, Leaflet as the client-side mapping library and the Bootstrap framework at the core of the front-end user interface. The web user interface is designed to have typical features of a desktop GIS (e.g. activate/deactivate layers and order layers by drag and drop actions) and to show specific information on the activated layers (e.g. legend and simplified metadata). Users have the possibility to change the base map from a given list of map providers (e.g. OpenStreetMap and Microsoft Bing) and to control the opacity of each layer to facilitate the comparison with both other land cover layers and the underlying base map. In addition, users can add to the platform any custom layer available through a Web Map Service (WMS) and activate the visualization of photos from popular photo sharing services. This last functionality is provided in order to have a visual assessment of the available land coverages based on other user-generated contents available on the Internet. It is supposed to be a first step towards a calibration/validation service that will be made available in the future.

Gertrude Stein, opium queen: notes on a mistaken embrace.

PubMed

Solomon, Jeff

2013-01-01

Gertrude Stein was not only a fairly open lesbian but also Jewish, expatriate, and androgynous-all attributes that often retarded mass-market success. Why then was she so popular? The article offers original research highlighting how Stein was constructed as a kind of "opium queen" in the popular American press, and the ways that this decadent, bohemian celebrity persona allowed her to operate as "broadly queer" rather than "specifically gay" in the American cultural imaginary-a negotiation that accounts for the mass-market success rather than censure of The Autobiography of Alice B. Toklas despite the unparalleled visibility of its lesbian erotics.

Open Source, Openness, and Higher Education

ERIC Educational Resources Information Center

Wiley, David

2006-01-01

In this article David Wiley provides an overview of how the general expansion of open source software has affected the world of education in particular. In doing so, Wiley not only addresses the development of open source software applications for teachers and administrators, he also discusses how the fundamental philosophy of the open source…

It's Hard Saying Goodbye to an Old Flame

ERIC Educational Resources Information Center

Roy, Ken

2004-01-01

As heat sources go, the old standby for elementary and middle school science laboratories has been the centuries old alcohol lamp. Unfortunately, this inexpensive heat producer has been a continuous source of accidents--many of which are relatively serious. Hot plates are emerging as the most popular source of heat for science experiments. The…

The Emergence of Open-Source Software in North America

ERIC Educational Resources Information Center

Pan, Guohua; Bonk, Curtis J.

2007-01-01

Unlike conventional models of software development, the open source model is based on the collaborative efforts of users who are also co-developers of the software. Interest in open source software has grown exponentially in recent years. A "Google" search for the phrase open source in early 2005 returned 28.8 million webpage hits, while…

The hobbyist phenomenon in physical security.

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

Michaud, E. C.

Pro-Ams (professional amateurs) are groups of people who work on a problem as amateurs or unpaid persons in a given field at professional levels of competence. Astronomy is a good example of Pro-Am activity. At Galaxy Zoo, Pro-Ams evaluate data generated by professional observatories and are able to evaluate the millions of galaxies that have been observed but not classified, and report their findings at professional levels for fun. To allow the archiving of millions of galaxies that have been observed but not classified, the website has been engineered so that the public can view and classify galaxies even ifmore » they are not professional astronomers. In this endeavor, it has been found that amateurs can easily outperform automated vision systems. Today in the world of physical security, Pro-Ams are playing an ever-increasing role. Traditionally, locksmiths, corporations, and government organizations have been largely responsible for developing standards, uncovering vulnerabilities, and devising best security practices. Increasingly, however, nonprofit sporting organizations and clubs are doing this. They can be found all over the world, from Europe to the US and now South East Asia. Examples include TOOOL (The Open Organization of Lockpickers), the Longhorn Lockpicking Club, Sportsfreunde der Sperrtechnik - Deustcheland e.V., though there are many others. Members of these groups have been getting together weekly to discuss many elements of security, with some groups specializing in specific areas of security. When members are asked why they participate in these hobbyist groups, they usually reply (with gusto) that they do it for fun, and that they view defeating locks and other security devices as an interesting and entertaining puzzle. A lot of what happens at these clubs would not be possible if it weren't for 'Super Abundance', the ability to easily acquire (at little or no cost) the products, security tools, technologies, and intellectual resources traditionally limited to corporations, government organizations, or wealthy individuals. With this new access comes new discoveries. For example, hobbyist sport lockpicking groups discovered - and publicized - a number of new vulnerabilities between 2004 and 2009 that resulted in the majority of high-security lock manufacturers having to make changes and improvements to their products. A decade ago, amateur physical security discoveries were rare, at least those discussed publicly. In the interim, Internet sites such as lockpicking.org, lockpicking101.com and others have provided an online meeting place for people to trade tips, find friends with similar interests, and develop tools. The open, public discussion of software vulnerabilities, in contrast, has been going on for a long time. These two industries, physical security and software, have very different upgrade mechanisms. With software, a patch can typically be deployed quickly to fix a serious vulnerability, whereas a hardware fix for a physical security device or system can take upwards of months to implement in the field, especially if (as is often the case) hardware integrators are involved. Even when responding to publicly announced security vulnerabilities, manufacturers of physical security devices such as locks, intrusion detectors, or access control devices rarely view hobbyists as a positive resource. This is most unfortunate. In the field of software, it is common to speak of Open Source versus Closed Source. An Open Source software company may choose to distribute their software with a particular license, and give it away openly, with full details and all the lines of source code made available. Linux is a very popular example of this. A Close Source company, in contrast, chooses not to reveal its source code and will license its software products in a restrictive manor. Slowly, the idea of Open Source is now coming to the world of physical security. In the case of locks, it provides an alternative to the traditional Closed Source world of locksmiths. Now locks are physical objects, and can therefore be disassembled. As such, they have always been Open Source in a limited sense. Secrecy, in fact, is very difficult to maintain for a lock that is widely distributed. Having direct access to the lock design provides the hobbyist with a very open environment for finding security flaws, even if the lock manufacturer attempts to follow a Close Source model. It is clear that the field of physical security is going the digital route with companies such as Medeco, Mul-T-Lock, and Abloy manufacturing electromechanical locks. Various companies have already begun to add microcontrollers, cryptographic chip sets, solid-state sensors, and a number of other high-tech improvements to their product lineup in an effort to thwart people from defeating their security products.« less

The impact of the cigarette market opening in Taiwan

PubMed Central

Wen, C; Cheng, T; Eriksen, M; Tsai, S; Hsu, C

2005-01-01

Objective: To assess the effect of the opening of the Taiwanese cigarette market on cigarette consumption, changes in market share, and the effects on tobacco control efforts. Methods: With the use of key word "Taiwan", the Legacy Tobacco Documents Library of the University of California, San Francisco, was searched for internal documents related to smuggling activities, promotion of light cigarettes, and market share analyses in Taiwan. Age adjusted smoking rates and cigarette and betel quid consumption before and after market opening were compared. Results: By 2000, the market share of imported cigarettes increased from less than 2% in 1986 to nearly 50%, and per capita cigarette consumption increased 15% following market opening. Because of the sharp increase in smuggling, with contraband cigarettes being as popular as legal imports, and the rapid proliferation of retail outlets, such as betel quid stalls, the market penetration by foreign tobacco companies was greater in Taiwan than among the other Super 301 Asian countries. Aggressive cigarette marketing strategies were associated with a 6% increase in adult male smoking prevalence, and with a 13% increase in the youth rate, within three years after market opening. The market opening also had an incidental effect on increasing the popularity of betel quid. Betel quid chewing has since become a major public health problem in Taiwan. Conclusion: The opening of the cigarette market in 1987 had a long lasting impact on Taiwan. It increased smoking prevalence and the market has become dominated by foreign companies. The seriousness of smuggling and its associated loss of revenue by the government, the extent of increased youth smoking and its associated future health care costs, and the increased use of betel quid and the associated doubling of oral cancer mortality rates each pose significant problems to Taiwan. However, the market opening galvanised anti-smoking sentiment and forced the government to initiate and intensify a series of tobacco control efforts. PMID:15923448

The impact of the cigarette market opening in Taiwan.

PubMed

Wen, C P; Cheng, T Y; Eriksen, M P; Tsai, S P; Hsu, C C

2005-06-01

To assess the effect of the opening of the Taiwanese cigarette market on cigarette consumption, changes in market share, and the effects on tobacco control efforts. With the use of key word "Taiwan", the Legacy Tobacco Documents Library of the University of California, San Francisco, was searched for internal documents related to smuggling activities, promotion of light cigarettes, and market share analyses in Taiwan. Age adjusted smoking rates and cigarette and betel quid consumption before and after market opening were compared. By 2000, the market share of imported cigarettes increased from less than 2% in 1986 to nearly 50%, and per capita cigarette consumption increased 15% following market opening. Because of the sharp increase in smuggling, with contraband cigarettes being as popular as legal imports, and the rapid proliferation of retail outlets, such as betel quid stalls, the market penetration by foreign tobacco companies was greater in Taiwan than among the other Super 301 Asian countries. Aggressive cigarette marketing strategies were associated with a 6% increase in adult male smoking prevalence, and with a 13% increase in the youth rate, within three years after market opening. The market opening also had an incidental effect on increasing the popularity of betel quid. Betel quid chewing has since become a major public health problem in Taiwan. The opening of the cigarette market in 1987 had a long lasting impact on Taiwan. It increased smoking prevalence and the market has become dominated by foreign companies. The seriousness of smuggling and its associated loss of revenue by the government, the extent of increased youth smoking and its associated future health care costs, and the increased use of betel quid and the associated doubling of oral cancer mortality rates each pose significant problems to Taiwan. However, the market opening galvanised anti-smoking sentiment and forced the government to initiate and intensify a series of tobacco control efforts.

Open Approaches to the Anterior Skull Base in Children: Review of the Literature.

PubMed

Wasserzug, Oshri; DeRowe, Ari; Ringel, Barak; Fishman, Gadi; Fliss, Dan M

2018-02-01

Introduction  Skull base lesions in children and adolescents are rare, and comprise only 5.6% of all skull base surgery. Anterior skull base lesions dominate, averaging slightly more than 50% of the cases. Until recently, surgery of the anterior skull base was dominated by open procedures and endoscopic skull base surgery was reserved for benign pathologies. Endoscopic skull base surgery is gradually gaining popularity. In spite of that, open skull base surgery is still considered the "gold standard" for the treatment of anterior skull base lesions, and it is the preferred approach in selected cases. Objective  This article reviews current concepts and open approaches to the anterior skull base in children in the era of endoscopic surgery. Materials and Methods  Comprehensive literature review. Results  Extensive intracranial-intradural invasion, extensive orbital invasion, encasement of the optic nerve or the internal carotid artery, lateral supraorbital dural involvement and involvement of the anterior table of the frontal sinus or lateral portion of the frontal sinus precludes endoscopic surgery, and mandates open skull base surgery. The open approaches which are used most frequently for surgical resection of anterior skull base tumors are the transfacial/transmaxillary, subcranial, and subfrontal approaches. Reconstruction of anterior skull base defects is discussed in a separate article in this supplement. Discussion  Although endoscopic skull base surgery in children is gaining popularity in developed countries, in many cases open surgery is still required. In addition, in developing countries, which accounts for more than 80% of the world's population, limited access to expensive equipment precludes the use of endoscopic surgery. Several open surgical approaches are still employed to resect anterior skull base lesions in the pediatric population. With this large armamentarium of surgical approaches, tailoring the most suitable approach to a specific lesion in regard to its nature, location, and extent is of utmost importance.

Open Data, Open Source and Open Standards in chemistry: The Blue Obelisk five years on

PubMed Central

2011-01-01

Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community. PMID:21999342

Open Genetic Code: on open source in the life sciences.

PubMed

Deibel, Eric

2014-01-01

The introduction of open source in the life sciences is increasingly being suggested as an alternative to patenting. This is an alternative, however, that takes its shape at the intersection of the life sciences and informatics. Numerous examples can be identified wherein open source in the life sciences refers to access, sharing and collaboration as informatic practices. This includes open source as an experimental model and as a more sophisticated approach of genetic engineering. The first section discusses the greater flexibly in regard of patenting and the relationship to the introduction of open source in the life sciences. The main argument is that the ownership of knowledge in the life sciences should be reconsidered in the context of the centrality of DNA in informatic formats. This is illustrated by discussing a range of examples of open source models. The second part focuses on open source in synthetic biology as exemplary for the re-materialization of information into food, energy, medicine and so forth. The paper ends by raising the question whether another kind of alternative might be possible: one that looks at open source as a model for an alternative to the commodification of life that is understood as an attempt to comprehensively remove the restrictions from the usage of DNA in any of its formats.

It Must Be True -- I Read It in "Seventeen" Magazine: US Popular Culture and Sexual Messages in an Era of Abstinence-Only Education

ERIC Educational Resources Information Center

Wegmann, Jennifer

2013-01-01

As discourse in sexual education classes across the USA in 1996 began to change, media outlets became important sources of education for teenage girls. Unaffected directly by government policy, one of the most popular teenage girls' magazines, "Seventeen," provided a plethora of information on sex. Several scholars have examined…

Students' Sources of Motivation for Participating in Science Fairs: An Exploratory Study within the Canada-Wide Science Fair 2008

ERIC Educational Resources Information Center

Dionne, Liliane; Reis, Giuliano; Trudel, Louis; Guillet, Gabriel; Kleine, Leonard; Hancianu, Corina

2012-01-01

Science fairs have been for many years a popular school activity in North America. They are a venue for the popularization of science and consequently an important encouragement for the pursuit of careers in science or engineering. However, little is known about students' perceived motives for participating in local or national science fairs and…

The Open Source Teaching Project (OSTP): Research Note.

ERIC Educational Resources Information Center

Hirst, Tony

The Open Source Teaching Project (OSTP) is an attempt to apply a variant of the successful open source software approach to the development of educational materials. Open source software is software licensed in such a way as to allow anyone the right to modify and use it. From such a simple premise, a whole industry has arisen, most notably in the…

Free for All: Open Source Software

ERIC Educational Resources Information Center

Schneider, Karen

2008-01-01

Open source software has become a catchword in libraryland. Yet many remain unclear about open source's benefits--or even what it is. So what is open source software (OSS)? It's software that is free in every sense of the word: free to download, free to use, and free to view or modify. Most OSS is distributed on the Web and one doesn't need to…

Reflections on the role of open source in health information system interoperability.

PubMed

Sfakianakis, S; Chronaki, C E; Chiarugi, F; Conforti, F; Katehakis, D G

2007-01-01

This paper reflects on the role of open source in health information system interoperability. Open source is a driving force in computer science research and the development of information systems. It facilitates the sharing of information and ideas, enables evolutionary development and open collaborative testing of code, and broadens the adoption of interoperability standards. In health care, information systems have been developed largely ad hoc following proprietary specifications and customized design. However, the wide deployment of integrated services such as Electronic Health Records (EHRs) over regional health information networks (RHINs) relies on interoperability of the underlying information systems and medical devices. This reflection is built on the experiences of the PICNIC project that developed shared software infrastructure components in open source for RHINs and the OpenECG network that offers open source components to lower the implementation cost of interoperability standards such as SCP-ECG, in electrocardiography. Open source components implementing standards and a community providing feedback from real-world use are key enablers of health care information system interoperability. Investing in open source is investing in interoperability and a vital aspect of a long term strategy towards comprehensive health services and clinical research.

Open Standards, Open Source, and Open Innovation: Harnessing the Benefits of Openness

ERIC Educational Resources Information Center

Committee for Economic Development, 2006

2006-01-01

Digitization of information and the Internet have profoundly expanded the capacity for openness. This report details the benefits of openness in three areas--open standards, open-source software, and open innovation--and examines the major issues in the debate over whether openness should be encouraged or not. The report explains each of these…

SparkSeq: fast, scalable and cloud-ready tool for the interactive genomic data analysis with nucleotide precision.

PubMed

Wiewiórka, Marek S; Messina, Antonio; Pacholewska, Alicja; Maffioletti, Sergio; Gawrysiak, Piotr; Okoniewski, Michał J

2014-09-15

Many time-consuming analyses of next -: generation sequencing data can be addressed with modern cloud computing. The Apache Hadoop-based solutions have become popular in genomics BECAUSE OF: their scalability in a cloud infrastructure. So far, most of these tools have been used for batch data processing rather than interactive data querying. The SparkSeq software has been created to take advantage of a new MapReduce framework, Apache Spark, for next-generation sequencing data. SparkSeq is a general-purpose, flexible and easily extendable library for genomic cloud computing. It can be used to build genomic analysis pipelines in Scala and run them in an interactive way. SparkSeq opens up the possibility of customized ad hoc secondary analyses and iterative machine learning algorithms. This article demonstrates its scalability and overall fast performance by running the analyses of sequencing datasets. Tests of SparkSeq also prove that the use of cache and HDFS block size can be tuned for the optimal performance on multiple worker nodes. Available under open source Apache 2.0 license: https://bitbucket.org/mwiewiorka/sparkseq/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The 2015 Bioinformatics Open Source Conference (BOSC 2015)

PubMed Central

Harris, Nomi L.; Cock, Peter J. A.; Lapp, Hilmar

2016-01-01

The Bioinformatics Open Source Conference (BOSC) is organized by the Open Bioinformatics Foundation (OBF), a nonprofit group dedicated to promoting the practice and philosophy of open source software development and open science within the biological research community. Since its inception in 2000, BOSC has provided bioinformatics developers with a forum for communicating the results of their latest efforts to the wider research community. BOSC offers a focused environment for developers and users to interact and share ideas about standards; software development practices; practical techniques for solving bioinformatics problems; and approaches that promote open science and sharing of data, results, and software. BOSC is run as a two-day special interest group (SIG) before the annual Intelligent Systems in Molecular Biology (ISMB) conference. BOSC 2015 took place in Dublin, Ireland, and was attended by over 125 people, about half of whom were first-time attendees. Session topics included “Data Science;” “Standards and Interoperability;” “Open Science and Reproducibility;” “Translational Bioinformatics;” “Visualization;” and “Bioinformatics Open Source Project Updates”. In addition to two keynote talks and dozens of shorter talks chosen from submitted abstracts, BOSC 2015 included a panel, titled “Open Source, Open Door: Increasing Diversity in the Bioinformatics Open Source Community,” that provided an opportunity for open discussion about ways to increase the diversity of participants in BOSC in particular, and in open source bioinformatics in general. The complete program of BOSC 2015 is available online at http://www.open-bio.org/wiki/BOSC_2015_Schedule. PMID:26914653

A state-of-the-art review on nitrous oxide control from waste treatment and industrial sources.

PubMed

Frutos, Osvaldo D; Quijano, Guillermo; Aizpuru, Aitor; Muñoz, Raúl

This review aims at holistically analyzing the environmental problems associated with nitrous oxide (N 2 O) emissions by evaluating the most important sources of N 2 O and its environmental impacts. Emissions from wastewater treatment processes and the industrial production of nitric and adipic acid represent nowadays the most important anthropogenic point sources of N 2 O. Therefore, state-of-the-art strategies to mitigate the generation and release to the atmosphere of this greenhouse and O 3 -depleting gas in the waste treatment and industrial sectors are also reviewed. An updated review of the end-of-the-pipe technologies for N 2 O abatement, both in the waste treatment and industrial sectors, is herein presented and critically discussed for the first time. Despite the consistent efforts recently conducted in the development of cost-efficient and eco-friendly N 2 O abatement technologies, physical/chemical technologies still constitute the most popular treatments for the control of industrial N 2 O emissions at commercial scale. The recent advances achieved on biological N 2 O abatement based on heterotrophic denitrification have opened new opportunities for the development of eco-friendly alternatives for the treatment of N 2 O emissions. Finally, the main limitations and challenges faced by these novel N 2 O abatement biotechnologies are identified in order to pave the way for market implementation. Copyright © 2018 Elsevier Inc. All rights reserved.

Autochthonous Change: Self-Renewal through Open Software Design

ERIC Educational Resources Information Center

Hedbring, Charles

2005-01-01

In all likelihood, currently employed therapists and teachers grew up with computer technology. Part of their computer culture included programming computers for entertainment using popular consumer software like Microsoft Basic. Within this social-educational milieu, the "FACTS+" curriculum represents one long-term project covering the…

MOOCs

ERIC Educational Resources Information Center

Mallon, Melissa, Ed.

2013-01-01

Perhaps due to a commitment to lifelong learning, librarians are often willing participants in trying new technologies or service models that may benefit their patrons. Such an opportunity presents itself with massively open online courses, or MOOCs. This educational model, which has been gaining popularity in higher education since the first MOOC…

20180318 - Curating and sharing structures and spectra for the environmental community (ACS Spring)

EPA Science Inventory

The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resour...

A suite of R packages for web-enabled modeling and analysis of surface waters

NASA Astrophysics Data System (ADS)

Read, J. S.; Winslow, L. A.; Nüst, D.; De Cicco, L.; Walker, J. I.

2014-12-01

Researchers often create redundant methods for downloading, manipulating, and analyzing data from online resources. Moreover, the reproducibility of science can be hampered by complicated and voluminous data, lack of time for documentation and long-term maintenance of software, and fear of exposing programming skills. The combination of these factors can encourage unshared one-off programmatic solutions instead of openly provided reusable methods. Federal and academic researchers in the water resources and informatics domains have collaborated to address these issues. The result of this collaboration is a suite of modular R packages that can be used independently or as elements in reproducible analytical workflows. These documented and freely available R packages were designed to fill basic needs for the effective use of water data: the retrieval of time-series and spatial data from web resources (dataRetrieval, geoknife), performing quality assurance and quality control checks of these data with robust statistical methods (sensorQC), the creation of useful data derivatives (including physically- and biologically-relevant indices; GDopp, LakeMetabolizer), and the execution and evaluation of models (glmtools, rLakeAnalyzer). Here, we share details and recommendations for the collaborative coding process, and highlight the benefits of an open-source tool development pattern with a popular programming language in the water resources discipline (such as R). We provide examples of reproducible science driven by large volumes of web-available data using these tools, explore benefits of accessing packages as standardized web processing services (WPS) and present a working platform that allows domain experts to publish scientific algorithms in a service-oriented architecture (WPS4R). We assert that in the era of open data, tools that leverage these data should also be freely shared, transparent, and developed in an open innovation environment.

Power formula for open-channel flow resistance

USGS Publications Warehouse

Chen, Cheng-lung

1988-01-01

This paper evaluates various power formulas for flow resistance in open channels. Unlike the logarithmic resistance equation that can be theoretically derived either from Prandtl's mixing-length hypothesis or von Karman's similarity hypothesis, the power formula has long had an appearance of empiricism. Nevertheless, the simplicity in the form of the power formula has made it popular among the many possible forms of flow resistance formulas. This paper reexamines the concept and rationale of the power formulation, thereby addressing some critical issues in the modeling of flow resistance.

The 2016 Bioinformatics Open Source Conference (BOSC).

PubMed

Harris, Nomi L; Cock, Peter J A; Chapman, Brad; Fields, Christopher J; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science.

Beyond Open Source: According to Jim Hirsch, Open Technology, Not Open Source, Is the Wave of the Future

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

This article presents an interview with Jim Hirsch, an associate superintendent for technology at Piano Independent School District in Piano, Texas. Hirsch serves as a liaison for the open technologies committee of the Consortium for School Networking. In this interview, he shares his opinion on the significance of open source in K-12.

EMISSIONS OF ORGANIC AIR TOXICS FROM OPEN ...

EPA Pesticide Factsheets

A detailed literature search was performed to collect and collate available data reporting emissions of toxic organic substances into the air from open burning sources. Availability of data varied according to the source and the class of air toxics of interest. Volatile organic compound (VOC) and polycyclic aromatic hydrocarbon (PAH) data were available for many of the sources. Data on semivolatile organic compounds (SVOCs) that are not PAHs were available for several sources. Carbonyl and polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofuran (PCDD/F) data were available for only a few sources. There were several sources for which no emissions data were available at all. Several observations were made including: 1) Biomass open burning sources typically emitted less VOCs than open burning sources with anthropogenic fuels on a mass emitted per mass burned basis, particularly those where polymers were concerned; 2) Biomass open burning sources typically emitted less SVOCs and PAHs than anthropogenic sources on a mass emitted per mass burned basis. Burning pools of crude oil and diesel fuel produced significant amounts of PAHs relative to other types of open burning. PAH emissions were highest when combustion of polymers was taking place; and 3) Based on very limited data, biomass open burning sources typically produced higher levels of carbonyls than anthropogenic sources on a mass emitted per mass burned basis, probably due to oxygenated structures r

Open innovation in the European space sector: Existing practices, constraints and opportunities

NASA Astrophysics Data System (ADS)

van Burg, Elco; Giannopapa, Christina; Reymen, Isabelle M. M. J.

2017-12-01

To enhance innovative output and societal spillover of the European space sector, the open innovation approach is becoming popular. Yet, open innovation, referring to innovation practices that cross borders of individual firms, faces constraints. To explore these constraints and identify opportunities, this study performs interviews with government/agency officials and space technology entrepreneurs. The interviews highlight three topic areas with constraints and opportunities: 1) mainly one-directional knowledge flows (from outside the space sector to inside), 2) knowledge and property management, and 3) the role of small- and medium sized companies. These results bear important implications for innovation practices in the space sector.

Hua Loo-Keng's Popularization of Mathematics and the Cultural Revolution.

PubMed

Hudeček, Jiří

2017-09-01

Before 1966, Chinese mathematician Hua Loo-Keng had singled out "Two Methods" as a way to truly applied and useful mathematics. The Overall Planning Method, based on the Critical Path Method widely used in USA, mostly appealed to middle and upper management. This limited its spread during the Cultural Revolution. The Optimum Selection Method, also of US origin, was more mass-oriented and ready for popularization. Nevertheless, Hua met resistance from leftist radicals, whose ideological objections sprang from an underlying power struggle. Hua built popularization teams, mostly from talented younger people whose careers were disrupted by the Cultural Revolution, and thus opened a path for many of them to important roles in China's scientific infrastructure after 1976. Hua Loo-Keng's efforts, while interrupted during the Cultural Revolution and the subsequent political campaigns, were also helped by the populist ethos of the movement, and by the lack of other non-political endeavors at that time. In this sense, the Cultural Revolution gave Hua Loo-Keng's popularization its importance and long-term impact. Copyright © 2017 Elsevier Ltd. All rights reserved.

The sources and popularity of online drug information: an analysis of top search engine results and web page views.

PubMed

Law, Michael R; Mintzes, Barbara; Morgan, Steven G

2011-03-01

The Internet has become a popular source of health information. However, there is little information on what drug information and which Web sites are being searched. To investigate the sources of online information about prescription drugs by assessing the most common Web sites returned in online drug searches and to assess the comparative popularity of Web pages for particular drugs. This was a cross-sectional study of search results for the most commonly dispensed drugs in the US (n=278 active ingredients) on 4 popular search engines: Bing, Google (both US and Canada), and Yahoo. We determined the number of times a Web site appeared as the first result. A linked retrospective analysis counted Wikipedia page hits for each of these drugs in 2008 and 2009. About three quarters of the first result on Google USA for both brand and generic names linked to the National Library of Medicine. In contrast, Wikipedia was the first result for approximately 80% of generic name searches on the other 3 sites. On these other sites, over two thirds of brand name searches led to industry-sponsored sites. The Wikipedia pages with the highest number of hits were mainly for opiates, benzodiazepines, antibiotics, and antidepressants. Wikipedia and the National Library of Medicine rank highly in online drug searches. Further, our results suggest that patients most often seek information on drugs with the potential for dependence, for stigmatized conditions, that have received media attention, and for episodic treatments. Quality improvement efforts should focus on these drugs.

jCompoundMapper: An open source Java library and command-line tool for chemical fingerprints

PubMed Central

2011-01-01

Background The decomposition of a chemical graph is a convenient approach to encode information of the corresponding organic compound. While several commercial toolkits exist to encode molecules as so-called fingerprints, only a few open source implementations are available. The aim of this work is to introduce a library for exactly defined molecular decompositions, with a strong focus on the application of these features in machine learning and data mining. It provides several options such as search depth, distance cut-offs, atom- and pharmacophore typing. Furthermore, it provides the functionality to combine, to compare, or to export the fingerprints into several formats. Results We provide a Java 1.6 library for the decomposition of chemical graphs based on the open source Chemistry Development Kit toolkit. We reimplemented popular fingerprinting algorithms such as depth-first search fingerprints, extended connectivity fingerprints, autocorrelation fingerprints (e.g. CATS2D), radial fingerprints (e.g. Molprint2D), geometrical Molprint, atom pairs, and pharmacophore fingerprints. We also implemented custom fingerprints such as the all-shortest path fingerprint that only includes the subset of shortest paths from the full set of paths of the depth-first search fingerprint. As an application of jCompoundMapper, we provide a command-line executable binary. We measured the conversion speed and number of features for each encoding and described the composition of the features in detail. The quality of the encodings was tested using the default parametrizations in combination with a support vector machine on the Sutherland QSAR data sets. Additionally, we benchmarked the fingerprint encodings on the large-scale Ames toxicity benchmark using a large-scale linear support vector machine. The results were promising and could often compete with literature results. On the large Ames benchmark, for example, we obtained an AUC ROC performance of 0.87 with a reimplementation of the extended connectivity fingerprint. This result is comparable to the performance achieved by a non-linear support vector machine using state-of-the-art descriptors. On the Sutherland QSAR data set, the best fingerprint encodings showed a comparable or better performance on 5 of the 8 benchmarks when compared against the results of the best descriptors published in the paper of Sutherland et al. Conclusions jCompoundMapper is a library for chemical graph fingerprints with several tweaking possibilities and exporting options for open source data mining toolkits. The quality of the data mining results, the conversion speed, the LPGL software license, the command-line interface, and the exporters should be useful for many applications in cheminformatics like benchmarks against literature methods, comparison of data mining algorithms, similarity searching, and similarity-based data mining. PMID:21219648

Open-Source 3D-Printable Optics Equipment

PubMed Central

Zhang, Chenlong; Anzalone, Nicholas C.; Faria, Rodrigo P.; Pearce, Joshua M.

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods. PMID:23544104

Open-source 3D-printable optics equipment.

PubMed

Zhang, Chenlong; Anzalone, Nicholas C; Faria, Rodrigo P; Pearce, Joshua M

2013-01-01

Just as the power of the open-source design paradigm has driven down the cost of software to the point that it is accessible to most people, the rise of open-source hardware is poised to drive down the cost of doing experimental science to expand access to everyone. To assist in this aim, this paper introduces a library of open-source 3-D-printable optics components. This library operates as a flexible, low-cost public-domain tool set for developing both research and teaching optics hardware. First, the use of parametric open-source designs using an open-source computer aided design package is described to customize the optics hardware for any application. Second, details are provided on the use of open-source 3-D printers (additive layer manufacturing) to fabricate the primary mechanical components, which are then combined to construct complex optics-related devices. Third, the use of the open-source electronics prototyping platform are illustrated as control for optical experimental apparatuses. This study demonstrates an open-source optical library, which significantly reduces the costs associated with much optical equipment, while also enabling relatively easily adapted customizable designs. The cost reductions in general are over 97%, with some components representing only 1% of the current commercial investment for optical products of similar function. The results of this study make its clear that this method of scientific hardware development enables a much broader audience to participate in optical experimentation both as research and teaching platforms than previous proprietary methods.

Aerostat-Lofted Instrument Platform and Sampling Method for Determination of Emissions from Open Area Sources

EPA Science Inventory

Sampling emissions from open area sources, particularly sources of open burning, is difficult due to fast dilution of emissions and safety concerns for personnel. Representative emission samples can be difficult to obtain with flaming and explosive sources since personnel safety ...

Moral individualism and elective death.

PubMed

Prado, C G

2013-01-01

Moral individualism (Brooks, 2011; Smith, 2011) is a contemporary interpretation of morality as entirely a matter of personal choice. It is a popular rather than theory-based interpretation and has a number of social generative sources related to present-day preoccupation with individuality and personal distinctiveness. A key generative source is popularization of postmodernism, which prioritizes self-reinvention and provides moral individualism with the appearance of intellectual legitimacy. Moral individualism is a deeply flawed misconception of morality because it abolishes moral communality. My concern in this paper is that in doing so, it seriously jeopardizes productive discussion of the moral permissibility of elective death or choosing to die in despairingly and dire circumstances. Copyright © 2013 Elsevier Ltd. All rights reserved.

Desk-top publishing using IBM-compatible computers.

PubMed

Grencis, P W

1991-01-01

This paper sets out to describe one Medical Illustration Departments' experience of the introduction of computers for desk-top publishing. In this particular case, after careful consideration of all the options open, an IBM-compatible system was installed rather than the often popular choice of an Apple Macintosh.

Framing Care for Planners of Education Programs

ERIC Educational Resources Information Center

Glowacki-Dudka, Michelle; Mullett, Cathy; Griswold, Wendy; Baize-Ward, Amy; Vetor-Suits, Crissy; Londt, Susan Cole

2018-01-01

Using a framework of care to design experiences in formal or informal learning does two things. It acknowledges intentions of reflective learning through open communication and meets expectations of scholars seeking knowledge within a learning community. This proposed framework was developed from programs involving popular education, community…

Rewriting the Journal

ERIC Educational Resources Information Center

Fredette, Michelle

2012-01-01

With faculty balking at the price of academic journals, can other digital publishing options get traction? University libraries are no strangers to one of the most popular online alternatives, the open-access archive. These archives enable scholars to upload work--including drafts of articles that are published later in subscription journals--so…

Striking a Bargain?

ERIC Educational Resources Information Center

Anastasopoulos, Nicholas

2013-01-01

Massive Open Online Courses ("MOOCs") are free, online courses offered by institutions of higher education to individual users across the world, and in the vast majority of cases, without any admissions criteria. MOOCs are popular with individuals because they offer unprecedented, free access to the best institutions in the world that…

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

PubMed Central

Ackerman, Michael J.; Yoo, Terry S.

2003-01-01

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

Books and the popularization of science

USGS Publications Warehouse

Buchanan, R.

1991-01-01

This article discusses best-selling science books, the characteristics of the audience for popular science books, and the role of books within science popularization and science education. Best-selling science books have been rare, but generally readable. Regional books, also important sources of scientific information, aim at much smaller, far more price-sensitive audiences. Many successful regional, nontechnical science books are readable, heavily illustrated, and in some cases, cross-disciplinary. To increase the attentive audience for scientific information, improvement in science education is necessary, and the most efficacious role for scientific institutions may be the production of materials that can be easily incorporated into school curricula. ?? 1991 Springer.

The 2016 Bioinformatics Open Source Conference (BOSC)

PubMed Central

Harris, Nomi L.; Cock, Peter J.A.; Chapman, Brad; Fields, Christopher J.; Hokamp, Karsten; Lapp, Hilmar; Muñoz-Torres, Monica; Wiencko, Heather

2016-01-01

Message from the ISCB: The Bioinformatics Open Source Conference (BOSC) is a yearly meeting organized by the Open Bioinformatics Foundation (OBF), a non-profit group dedicated to promoting the practice and philosophy of Open Source software development and Open Science within the biological research community. BOSC has been run since 2000 as a two-day Special Interest Group (SIG) before the annual ISMB conference. The 17th annual BOSC ( http://www.open-bio.org/wiki/BOSC_2016) took place in Orlando, Florida in July 2016. As in previous years, the conference was preceded by a two-day collaborative coding event open to the bioinformatics community. The conference brought together nearly 100 bioinformatics researchers, developers and users of open source software to interact and share ideas about standards, bioinformatics software development, and open and reproducible science. PMID:27781083

WPBMB Entrez: An interface to NCBI Entrez for Wordpress.

PubMed

Gohara, David W

2018-03-01

Research-oriented websites are an important means for the timely communication of information. These websites fall under a number of categories including: research laboratories, training grant and program projects, and online service portals. Invariably there is content on a site, such as publication listings, that require frequent updating. A number of content management systems exist to aid in the task of developing and managing a website, each with their strengths and weaknesses. One popular choice is Wordpress, a free, open source and actively developed application for the creation of web content. During a recent site redesign for our department, the need arose to ensure publications were up to date for each of the research labs and department as a whole. Several plugins for Wordpress offer this type of functionality, but in many cases the plugins are either no longer maintained, are missing features that would require the use of several, possibly incompatible, plugins or lack features for layout on a webpage. WPBMB Entrez was developed to address these needs. WPBMB Entrez utilizes a subset of NCBI Entrez and RCSB databases to maintain up to date records of publications, and publication related information on Wordpress-based websites. The core functionality uses the same search query syntax as on the NCBI Entrez site, including advanced query syntaxes. The plugin is extensible allowing for rapid development and addition of new data sources as the need arises. WPBMB Entrez was designed to be easy to use, yet flexible enough to address more complex usage scenarios. Features of the plugin include: an easy to use interface, design customization, multiple templates for displaying publication results, a caching mechanism to reduce page load times, supports multiple distinct queries and retrieval modes, and the ability to aggregate multiple queries into unified lists. Additionally, developer documentation is provided to aid in customization of the plugin. WPBMB Entrez is available at no cost, is open source and works with all recent versions of Wordpress. Copyright © 2017 Elsevier B.V. All rights reserved.

Wide-Open: Accelerating public data release by automating detection of overdue datasets

PubMed Central

Poon, Hoifung; Howe, Bill

2017-01-01

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week. PMID:28594819

Wide-Open: Accelerating public data release by automating detection of overdue datasets.

PubMed

Grechkin, Maxim; Poon, Hoifung; Howe, Bill

2017-06-01

Open data is a vital pillar of open science and a key enabler for reproducibility, data reuse, and novel discoveries. Enforcement of open-data policies, however, largely relies on manual efforts, which invariably lag behind the increasingly automated generation of biological data. To address this problem, we developed a general approach to automatically identify datasets overdue for public release by applying text mining to identify dataset references in published articles and parse query results from repositories to determine if the datasets remain private. We demonstrate the effectiveness of this approach on 2 popular National Center for Biotechnology Information (NCBI) repositories: Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA). Our Wide-Open system identified a large number of overdue datasets, which spurred administrators to respond directly by releasing 400 datasets in one week.

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

Fadika, Zacharia; Dede, Elif; Govindaraju, Madhusudhan

MapReduce is increasingly becoming a popular framework, and a potent programming model. The most popular open source implementation of MapReduce, Hadoop, is based on the Hadoop Distributed File System (HDFS). However, as HDFS is not POSIX compliant, it cannot be fully leveraged by applications running on a majority of existing HPC environments such as Teragrid and NERSC. These HPC environments typicallysupport globally shared file systems such as NFS and GPFS. On such resourceful HPC infrastructures, the use of Hadoop not only creates compatibility issues, but also affects overall performance due to the added overhead of the HDFS. This paper notmore » only presents a MapReduce implementation directly suitable for HPC environments, but also exposes the design choices for better performance gains in those settings. By leveraging inherent distributed file systems' functions, and abstracting them away from its MapReduce framework, MARIANE (MApReduce Implementation Adapted for HPC Environments) not only allows for the use of the model in an expanding number of HPCenvironments, but also allows for better performance in such settings. This paper shows the applicability and high performance of the MapReduce paradigm through MARIANE, an implementation designed for clustered and shared-disk file systems and as such not dedicated to a specific MapReduce solution. The paper identifies the components and trade-offs necessary for this model, and quantifies the performance gains exhibited by our approach in distributed environments over Apache Hadoop in a data intensive setting, on the Magellan testbed at the National Energy Research Scientific Computing Center (NERSC).« less

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data processing.

PubMed

Almeida, Diogo; Skov, Ida; Lund, Jesper; Mohammadnejad, Afsaneh; Silva, Artur; Vandin, Fabio; Tan, Qihua; Baumbach, Jan; Röttger, Richard

2016-10-01

Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html.

Jllumina - A comprehensive Java-based API for statistical Illumina Infinium HumanMethylation450 and MethylationEPIC data processing.

PubMed

Almeida, Diogo; Skov, Ida; Lund, Jesper; Mohammadnejad, Afsaneh; Silva, Artur; Vandin, Fabio; Tan, Qihua; Baumbach, Jan; Röttger, Richard

2016-12-18

Measuring differential methylation of the DNA is the nowadays most common approach to linking epigenetic modifications to diseases (called epigenome-wide association studies, EWAS). For its low cost, its efficiency and easy handling, the Illumina HumanMethylation450 BeadChip and its successor, the Infinium MethylationEPIC BeadChip, is the by far most popular techniques for conduction EWAS in large patient cohorts. Despite the popularity of this chip technology, raw data processing and statistical analysis of the array data remains far from trivial and still lacks dedicated software libraries enabling high quality and statistically sound downstream analyses. As of yet, only R-based solutions are freely available for low-level processing of the Illumina chip data. However, the lack of alternative libraries poses a hurdle for the development of new bioinformatic tools, in particular when it comes to web services or applications where run time and memory consumption matter, or EWAS data analysis is an integrative part of a bigger framework or data analysis pipeline. We have therefore developed and implemented Jllumina, an open-source Java library for raw data manipulation of Illumina Infinium HumanMethylation450 and Infinium MethylationEPIC BeadChip data, supporting the developer with Java functions covering reading and preprocessing the raw data, down to statistical assessment, permutation tests, and identification of differentially methylated loci. Jllumina is fully parallelizable and publicly available at http://dimmer.compbio.sdu.dk/download.html.

Tripal: a construction toolkit for online genome databases.

PubMed

Ficklin, Stephen P; Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net.

Top of the charts: download versus citations in the International Journal of Cardiology.

PubMed

Coats, Andrew J S

2005-11-02

The medical literature is growing at an alarming rate. Research assessment exercises, research quality frameworks, league tables and the like have attempted to quantify the volume, quality and impact of research. Yet the established measures (such as citation rates) are being challenged by the sheer number of journals, variability in the "gold standard" of peer-review and the emergence of open-source or web-based journals. In the last few years, we have seen a growth in downloads to individual journal articles that now easily exceeds formal journal subscriptions. We have recorded the 10 top cited articles over a 12-month period and compared them to the 10 most popular articles being downloaded over the same time period. The citation-based listing included basic and applied, observational and interventional original research reports. For downloaded articles, which have shown a dramatic increase for the International Journal of Cardiology from 48,000 in 2002 to 120,000 in 2003 to 200,000 in 2004, the most popular articles over the same period are very different and are dominated by up-to-date reviews of either cutting-edge topics (such as the potential of stem cells) or of the management of rare or unusual conditions. There is no overlap between the two lists despite covering exactly the same 12-month period and using measures of peer esteem. Perhaps the time has come to look at the usage of articles rather than, or in addition to, their referencing.

Tripal: a construction toolkit for online genome databases

PubMed Central

Sanderson, Lacey-Anne; Cheng, Chun-Huai; Staton, Margaret E.; Lee, Taein; Cho, Il-Hyung; Jung, Sook; Bett, Kirstin E.; Main, Doreen

2011-01-01

As the availability, affordability and magnitude of genomics and genetics research increases so does the need to provide online access to resulting data and analyses. Availability of a tailored online database is the desire for many investigators or research communities; however, managing the Information Technology infrastructure needed to create such a database can be an undesired distraction from primary research or potentially cost prohibitive. Tripal provides simplified site development by merging the power of Drupal, a popular web Content Management System with that of Chado, a community-derived database schema for storage of genomic, genetic and other related biological data. Tripal provides an interface that extends the content management features of Drupal to the data housed in Chado. Furthermore, Tripal provides a web-based Chado installer, genomic data loaders, web-based editing of data for organisms, genomic features, biological libraries, controlled vocabularies and stock collections. Also available are Tripal extensions that support loading and visualizations of NCBI BLAST, InterPro, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses, as well as an extension that provides integration of Tripal with GBrowse, a popular GMOD tool. An Application Programming Interface is available to allow creation of custom extensions by site developers, and the look-and-feel of the site is completely customizable through Drupal-based PHP template files. Addition of non-biological content and user-management is afforded through Drupal. Tripal is an open source and freely available software package found at http://tripal.sourceforge.net PMID:21959868

OpenMx: An Open Source Extended Structural Equation Modeling Framework

ERIC Educational Resources Information Center

Boker, Steven; Neale, Michael; Maes, Hermine; Wilde, Michael; Spiegel, Michael; Brick, Timothy; Spies, Jeffrey; Estabrook, Ryne; Kenny, Sarah; Bates, Timothy; Mehta, Paras; Fox, John

2011-01-01

OpenMx is free, full-featured, open source, structural equation modeling (SEM) software. OpenMx runs within the "R" statistical programming environment on Windows, Mac OS-X, and Linux computers. The rationale for developing OpenMx is discussed along with the philosophy behind the user interface. The OpenMx data structures are…

a Framework for AN Open Source Geospatial Certification Model

NASA Astrophysics Data System (ADS)

Khan, T. U. R.; Davis, P.; Behr, F.-J.

2016-06-01

The geospatial industry is forecasted to have an enormous growth in the forthcoming years and an extended need for well-educated workforce. Hence ongoing education and training play an important role in the professional life. Parallel, in the geospatial and IT arena as well in the political discussion and legislation Open Source solutions, open data proliferation, and the use of open standards have an increasing significance. Based on the Memorandum of Understanding between International Cartographic Association, OSGeo Foundation, and ISPRS this development led to the implementation of the ICA-OSGeo-Lab imitative with its mission "Making geospatial education and opportunities accessible to all". Discussions in this initiative and the growth and maturity of geospatial Open Source software initiated the idea to develop a framework for a worldwide applicable Open Source certification approach. Generic and geospatial certification approaches are already offered by numerous organisations, i.e., GIS Certification Institute, GeoAcademy, ASPRS, and software vendors, i. e., Esri, Oracle, and RedHat. They focus different fields of expertise and have different levels and ways of examination which are offered for a wide range of fees. The development of the certification framework presented here is based on the analysis of diverse bodies of knowledge concepts, i.e., NCGIA Core Curriculum, URISA Body Of Knowledge, USGIF Essential Body Of Knowledge, the "Geographic Information: Need to Know", currently under development, and the Geospatial Technology Competency Model (GTCM). The latter provides a US American oriented list of the knowledge, skills, and abilities required of workers in the geospatial technology industry and influenced essentially the framework of certification. In addition to the theoretical analysis of existing resources the geospatial community was integrated twofold. An online survey about the relevance of Open Source was performed and evaluated with 105 respondents worldwide. 15 interviews (face-to-face or by telephone) with experts in different countries provided additional insights into Open Source usage and certification. The findings led to the development of a certification framework of three main categories with in total eleven sub-categories, i.e., "Certified Open Source Geospatial Data Associate / Professional", "Certified Open Source Geospatial Analyst Remote Sensing & GIS", "Certified Open Source Geospatial Cartographer", "Certified Open Source Geospatial Expert", "Certified Open Source Geospatial Associate Developer / Professional Developer", "Certified Open Source Geospatial Architect". Each certification is described by pre-conditions, scope and objectives, course content, recommended software packages, target group, expected benefits, and the methods of examination. Examinations can be flanked by proofs of professional career paths and achievements which need a peer qualification evaluation. After a couple of years a recertification is required. The concept seeks the accreditation by the OSGeo Foundation (and other bodies) and international support by a group of geospatial scientific institutions to achieve wide and international acceptance for this Open Source geospatial certification model. A business case for Open Source certification and a corresponding SWOT model is examined to support the goals of the Geo-For-All initiative of the ICA-OSGeo pact.

Ten Simple Rules for Effective Online Outreach: What a decade at Deep Sea News has taught us.

NASA Astrophysics Data System (ADS)

Martini, K. I.; McClain, C. R.; Bik, H.; Helm, R. R.; Long, D.; Warneke, A. M.; Dove, A. D.; Goldstein, M. C.; MacPherson, R.; Zelnio, K. A.

2016-12-01

Deep Sea News was established in 2005 and has become one of the most popular marine science blogs on the internet, with 7000 hits/day and over 8 million cumulative hits. Written by 6 practicing Marine Scientists with diverse interests, expertise and a deep curiosity for science, our mission statement is " Demystifying and humanizing science in an open conversation that instills passion, awe, and responsibility for the oceans." We leverage humor and popular culture to make complex science and conservation stories accessible. We will discuss what worked, what didn't, and our path forward in the changing social media landscape

The Associations between Yelp Online Reviews and Vape Shops Closing or Remaining Open One Year Later

PubMed Central

Kong, Grace; Unger, Jennifer; Baezconde-Garbanati, Lourdes; Sussman, Steve

2017-01-01

INTRODUCTION Vape shops are popular brick-and-mortar stores that sell e-cigarette products but are not understood well. Previous analysis of Yelp reviews of vape shops located in various ethnic neighborhoods in Los Angeles, California in 2014 identified characteristics of vape shop as delineated by consumers. In this study, we assessed the associations between these characteristics and vape shops going out of business in 2015. METHODS Content analysis of Yelp reviews of 72 vape shops in 2014 identified 1) general characteristics of the reviews/reviewers, 2) vape shop, staff, and marketing attributes, 3) physical environment, and 4) health claims. In 2015, in-person visits confirmed that 22% of these vape shops closed permanently. We analyzed whether characteristics/attributes identified in 2014 associated with stores remaining open (n = 56) or permanently closing (n = 16) in 2015. RESULTS Univariate findings showed that open vape shops relative to closed shops had greater 1) number of reviews, 2) rebuilds/fixings, 3) ratings of staff attributes as “helpful/patient/respectful,” and 4) report of the physical environment as “bar type.” CONCLUSIONS Bar type vape shops and those with rebuilding/fixing capabilities were associated with staying open, suggesting the popularity of these attributes. Yelp consumer reviews is a useful research tool to identify consumer-determined important sustaining attributes of vape shops and may be used to identify aspects of enduring shops that need regulations. PMID:29057379

The Case for Open Source: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

Open source has continued to evolve and in the past three years the development of a graphical user interface has made it increasingly accessible and viable for end users without special training. Open source relies to a great extent on the free software movement. In this context, the term free refers not to cost, but to the freedom users have to…

A review of the palm genus Acrocomia: Neotropical green gold

USDA-ARS?s Scientific Manuscript database

The genus Acrocomia, popularly known as macaw palm or macaúba, occurs in savanna areas and open forests of tropical America, with distribution from Central to southern South America. They are important oleaginous palm trees, due to their role in ecosystems, local economies, and their potential for b...

Exploring Geometric Sequences

ERIC Educational Resources Information Center

Reiser, Elana

2016-01-01

In this brief article Elana Reiser describes her favorite lesson that combines popular culture with mathematics in a way that motivates student thinking and participation. Exploring open-ended problems, students may feel uneasy at first, but working in small groups often leads them to experiment with a variety of solutions. Reiser explains that…

Class Analysis and the Emancipatory Potential of Education

ERIC Educational Resources Information Center

Gerrard, Jessica

2013-01-01

Recently, a range of educational theorists have explored and extended upon popular currents in political theory through articulating "open" and "unknowing" pedagogies. Such contributions represent a radical turn away from the presumed "universals" found in proclamations of justice and emancipation and, ultimately, the centering of class analysis.…

"The Italianate Englishman": The Italian Influence in Elizabethan Literature

ERIC Educational Resources Information Center

Fox, Maureen

2011-01-01

Whether it was thought of positively or negatively, Italy is a popular topic of discussion in Elizabethan literature. Some Elizabethan writers mimic Italian writers and incorporate Italian ideas into their own works, while other writers alter Italian literary conventions and openly attack Italian morals. This range of positive and negative…

Leadership in Multiplayer Online Gaming Environments

ERIC Educational Resources Information Center

Lisk, Timothy C.; Kaplancali, Ugur T.; Riggio, Ronald E.

2012-01-01

With their increased popularity, games open up possibilities for simultaneous learning on multiple levels; players may learn from contextual information embedded in the narrative of the game and through the risks, benefits, costs, outcomes, and rewards of the alternative strategies that result from fast-paced decision making. Such dynamics also…

Teaching "Trans Issues": An Intersectional and Systems-Based Approach

ERIC Educational Resources Information Center

Boucher, Michel J.

2011-01-01

Transgender people are becoming increasingly visible in popular culture, academia, and national politics. University and college administrators are struggling at every level with how to address the needs of trans-identified staff people, faculty members, and students, all of whom are increasingly becoming open, vibrant participants in university…

Reporting Subscores Using R: A Software Review

ERIC Educational Resources Information Center

Dai, Shenghai; Svetina, Dubravka; Wang, Xiaolin

2017-01-01

There is an increasing interest in reporting test subscores for diagnostic purposes. In this article, we review nine popular R packages (subscore, mirt, TAM, sirt, CDM, NPCD, lavaan, sem, and OpenMX) that are capable of implementing subscore-reporting methods within one or more frameworks including classical test theory, multidimensional item…

SolTrace | Concentrating Solar Power | NREL

Science.gov Websites

NREL packaged distribution or from source code at the SolTrace open source project website. NREL Publications Support FAQs SolTrace open source project The code uses Monte-Carlo ray-tracing methodology. The -tracing capabilities. With the release of the SolTrace open source project, the software has adopted

When Free Isn't Free: The Realities of Running Open Source in School

ERIC Educational Resources Information Center

Derringer, Pam

2009-01-01

Despite the last few years' growth in awareness of open-source software in schools and the potential savings it represents, its widespread adoption is still hampered. Randy Orwin, technology director of the Bainbridge Island School District in Washington State and a strong open-source advocate, cautions that installing an open-source…

Solvation Structure and Thermodynamic Mapping (SSTMap): An Open-Source, Flexible Package for the Analysis of Water in Molecular Dynamics Trajectories.

PubMed

Haider, Kamran; Cruz, Anthony; Ramsey, Steven; Gilson, Michael K; Kurtzman, Tom

2018-01-09

We have developed SSTMap, a software package for mapping structural and thermodynamic water properties in molecular dynamics trajectories. The package introduces automated analysis and mapping of local measures of frustration and enhancement of water structure. The thermodynamic calculations are based on Inhomogeneous Fluid Solvation Theory (IST), which is implemented using both site-based and grid-based approaches. The package also extends the applicability of solvation analysis calculations to multiple molecular dynamics (MD) simulation programs by using existing cross-platform tools for parsing MD parameter and trajectory files. SSTMap is implemented in Python and contains both command-line tools and a Python module to facilitate flexibility in setting up calculations and for automated generation of large data sets involving analysis of multiple solutes. Output is generated in formats compatible with popular Python data science packages. This tool will be used by the molecular modeling community for computational analysis of water in problems of biophysical interest such as ligand binding and protein function.

Java simulations of embedded control systems.

PubMed

Farias, Gonzalo; Cervin, Anton; Arzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

2010-01-01

This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt.

Java Simulations of Embedded Control Systems

PubMed Central

Farias, Gonzalo; Cervin, Anton; Årzén, Karl-Erik; Dormido, Sebastián; Esquembre, Francisco

2010-01-01

This paper introduces a new Open Source Java library suited for the simulation of embedded control systems. The library is based on the ideas and architecture of TrueTime, a toolbox of Matlab devoted to this topic, and allows Java programmers to simulate the performance of control processes which run in a real time environment. Such simulations can improve considerably the learning and design of multitasking real-time systems. The choice of Java increases considerably the usability of our library, because many educators program already in this language. But also because the library can be easily used by Easy Java Simulations (EJS), a popular modeling and authoring tool that is increasingly used in the field of Control Education. EJS allows instructors, students, and researchers with less programming capabilities to create advanced interactive simulations in Java. The paper describes the ideas, implementation, and sample use of the new library both for pure Java programmers and for EJS users. The JTT library and some examples are online available on http://lab.dia.uned.es/jtt. PMID:22163674

blend4php: a PHP API for galaxy

PubMed Central

Wytko, Connor; Soto, Brian; Ficklin, Stephen P.

2017-01-01

Galaxy is a popular framework for execution of complex analytical pipelines typically for large data sets, and is a commonly used for (but not limited to) genomic, genetic and related biological analysis. It provides a web front-end and integrates with high performance computing resources. Here we report the development of the blend4php library that wraps Galaxy’s RESTful API into a PHP-based library. PHP-based web applications can use blend4php to automate execution, monitoring and management of a remote Galaxy server, including its users, workflows, jobs and more. The blend4php library was specifically developed for the integration of Galaxy with Tripal, the open-source toolkit for the creation of online genomic and genetic web sites. However, it was designed as an independent library for use by any application, and is freely available under version 3 of the GNU Lesser General Public License (LPGL v3.0) at https://github.com/galaxyproject/blend4php. Database URL: https://github.com/galaxyproject/blend4php PMID:28077564

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.

The GNAT: A new tool for processing NMR data.

PubMed

Castañar, Laura; Poggetto, Guilherme Dal; Colbourne, Adam A; Morris, Gareth A; Nilsson, Mathias

2018-06-01

The GNAT (General NMR Analysis Toolbox) is a free and open-source software package for processing, visualising, and analysing NMR data. It supersedes the popular DOSY Toolbox, which has a narrower focus on diffusion NMR. Data import of most common formats from the major NMR platforms is supported, as well as a GNAT generic format. Key basic processing of NMR data (e.g., Fourier transformation, baseline correction, and phasing) is catered for within the program, as well as more advanced techniques (e.g., reference deconvolution and pure shift FID reconstruction). Analysis tools include DOSY and SCORE for diffusion data, ROSY T 1 /T 2 estimation for relaxation data, and PARAFAC for multilinear analysis. The GNAT is written for the MATLAB® language and comes with a user-friendly graphical user interface. The standard version is intended to run with a MATLAB installation, but completely free-standing compiled versions for Windows, Mac, and Linux are also freely available. © 2018 The Authors Magnetic Resonance in Chemistry Published by John Wiley & Sons Ltd.

Cross-Modal Retrieval With CNN Visual Features: A New Baseline.

PubMed

Wei, Yunchao; Zhao, Yao; Lu, Canyi; Wei, Shikui; Liu, Luoqi; Zhu, Zhenfeng; Yan, Shuicheng

2017-02-01

Recently, convolutional neural network (CNN) visual features have demonstrated their powerful ability as a universal representation for various recognition tasks. In this paper, cross-modal retrieval with CNN visual features is implemented with several classic methods. Specifically, off-the-shelf CNN visual features are extracted from the CNN model, which is pretrained on ImageNet with more than one million images from 1000 object categories, as a generic image representation to tackle cross-modal retrieval. To further enhance the representational ability of CNN visual features, based on the pretrained CNN model on ImageNet, a fine-tuning step is performed by using the open source Caffe CNN library for each target data set. Besides, we propose a deep semantic matching method to address the cross-modal retrieval problem with respect to samples which are annotated with one or multiple labels. Extensive experiments on five popular publicly available data sets well demonstrate the superiority of CNN visual features for cross-modal retrieval.

Social Medicine: Twitter in Healthcare.

PubMed

Pershad, Yash; Hangge, Patrick T; Albadawi, Hassan; Oklu, Rahmi

2018-05-28

Social media enables the public sharing of information. With the recent emphasis on transparency and the open sharing of information between doctors and patients, the intersection of social media and healthcare is of particular interest. Twitter is currently the most popular form of social media used for healthcare communication; here, we examine the use of Twitter in medicine and specifically explore in what capacity using Twitter to share information on treatments and research has the potential to improve care. The sharing of information on Twitter can create a communicative and collaborative atmosphere for patients, physicians, and researchers and even improve quality of care. However, risks involved with using Twitter for healthcare discourse include high rates of misinformation, difficulties in verifying the credibility of sources, overwhelmingly high volumes of information available on Twitter, concerns about professionalism, and the opportunity cost of using physician time. Ultimately, the use of Twitter in healthcare can allow patients, healthcare professionals, and researchers to be more informed, but specific guidelines for appropriate use are necessary.

Manipulating Environmental Time Series in Python/Numpy: the Scikits.Timeseries Package and its Applications.

NASA Astrophysics Data System (ADS)

Gerard-Marchant, P. G.

2008-12-01

Numpy is a free, open source C/Python interface designed for the fast and convenient manipulation of multidimensional numerical arrays. The base object, ndarray, can also be easily be extended to define new objects meeting specific needs. Thanks to its simplicity, efficiency and modularity, numpy and its companion library Scipy have become increasingly popular in the scientific community over the last few years, with application ranging from astronomy and engineering to finances and statistics. Its capacity to handle missing values is particularly appealing when analyzing environmental time series, where irregular data sampling might be an issue. After reviewing the main characteristics of numpy objects and the mechanism of subclassing, we will present the scikits.timeseries package, developed to manipulate single- and multi-variable arrays indexed in time. We will illustrate some typical applications of this package by introducing climpy, a set of extensions designed to help analyzing the impacts of climate variability on environmental data such as precipitations or streamflows.

MLP Tools: a PyMOL plugin for using the molecular lipophilicity potential in computer-aided drug design

NASA Astrophysics Data System (ADS)

Oberhauser, Nils; Nurisso, Alessandra; Carrupt, Pierre-Alain

2014-05-01

The molecular lipophilicity potential (MLP) is a well-established method to calculate and visualize lipophilicity on molecules. We are here introducing a new computational tool named MLP Tools, written in the programming language Python, and conceived as a free plugin for the popular open source molecular viewer PyMOL. The plugin is divided into several sub-programs which allow the visualization of the MLP on molecular surfaces, as well as in three-dimensional space in order to analyze lipophilic properties of binding pockets. The sub-program Log MLP also implements the virtual log P which allows the prediction of the octanol/water partition coefficients on multiple three-dimensional conformations of the same molecule. An implementation on the recently introduced MLP GOLD procedure, improving the GOLD docking performance in hydrophobic pockets, is also part of the plugin. In this article, all functions of the MLP Tools will be described through a few chosen examples.

The 'Geographic Emission Benchmark' model: a baseline approach to measuring emissions associated with deforestation and degradation.

PubMed

Kim, Oh Seok; Newell, Joshua P

2015-10-01

This paper proposes a new land-change model, the Geographic Emission Benchmark (GEB), as an approach to quantify land-cover changes associated with deforestation and forest degradation. The GEB is designed to determine 'baseline' activity data for reference levels. Unlike other models that forecast business-as-usual future deforestation, the GEB internally (1) characterizes 'forest' and 'deforestation' with minimal processing and ground-truthing and (2) identifies 'deforestation hotspots' using open-source spatial methods to estimate regional rates of deforestation. The GEB also characterizes forest degradation and identifies leakage belts. This paper compares the accuracy of GEB with GEOMOD, a popular land-change model used in the UN-REDD (Reducing Emissions from Deforestation and Forest Degradation) Program. Using a case study of the Chinese tropics for comparison, GEB's projection is more accurate than GEOMOD's, as measured by Figure of Merit. Thus, the GEB produces baseline activity data that are moderately accurate for the setting of reference levels.

Effective Multifocus Image Fusion Based on HVS and BP Neural Network

PubMed Central

Yang, Yong

2014-01-01

The aim of multifocus image fusion is to fuse the images taken from the same scene with different focuses to obtain a resultant image with all objects in focus. In this paper, a novel multifocus image fusion method based on human visual system (HVS) and back propagation (BP) neural network is presented. Three features which reflect the clarity of a pixel are firstly extracted and used to train a BP neural network to determine which pixel is clearer. The clearer pixels are then used to construct the initial fused image. Thirdly, the focused regions are detected by measuring the similarity between the source images and the initial fused image followed by morphological opening and closing operations. Finally, the final fused image is obtained by a fusion rule for those focused regions. Experimental results show that the proposed method can provide better performance and outperform several existing popular fusion methods in terms of both objective and subjective evaluations. PMID:24683327

Shallow water benthic imaging and substrate characterization using recreational-grade sidescan-sonar

USGS Publications Warehouse

Buscombe, Daniel D.

2017-01-01

In recent years, lightweight, inexpensive, vessel-mounted ‘recreational grade’ sonar systems have rapidly grown in popularity among aquatic scientists, for swath imaging of benthic substrates. To promote an ongoing ‘democratization’ of acoustical imaging of shallow water environments, methods to carry out geometric and radiometric correction and georectification of sonar echograms are presented, based on simplified models for sonar-target geometry and acoustic backscattering and attenuation in shallow water. Procedures are described for automated removal of the acoustic shadows, identification of bed-water interface for situations when the water is too turbid or turbulent for reliable depth echosounding, and for automated bed substrate classification based on singlebeam full-waveform analysis. These methods are encoded in an open-source and freely-available software package, which should further facilitate use of recreational-grade sidescan sonar, in a fully automated and objective manner. The sequential correction, mapping, and analysis steps are demonstrated using a data set from a shallow freshwater environment.

Simulation study of air and water cooled photovoltaic panel using ANSYS

NASA Astrophysics Data System (ADS)

Syafiqah, Z.; Amin, N. A. M.; Irwan, Y. M.; Majid, M. S. A.; Aziz, N. A.

2017-10-01

Demand for alternative energy is growing due to decrease of fossil fuels sources. One of the promising and popular renewable energy technology is a photovoltaic (PV) technology. During the actual operation of PV cells, only around 15% of solar irradiance is converted to electricity, while the rest is converted into heat. The electrical efficiency decreases with the increment in PV panel’s temperature. This electrical energy is referring to the open-circuit voltage (Voc), short-circuit current (Isc) and output power generate. This paper examines and discusses the PV panel with water and air cooling system. The air cooling system was installed at the back of PV panel while water cooling system at front surface. The analyses of both cooling systems were done by using ANSYS CFX and PSPICE software. The highest temperature of PV panel without cooling system is 66.3 °C. There is a decrement of 19.2% and 53.2% in temperature with the air and water cooling system applied to PV panel.

PLUMED 2: New feathers for an old bird

NASA Astrophysics Data System (ADS)

Tribello, Gareth A.; Bonomi, Massimiliano; Branduardi, Davide; Camilloni, Carlo; Bussi, Giovanni

2014-02-01

Enhancing sampling and analyzing simulations are central issues in molecular simulation. Recently, we introduced PLUMED, an open-source plug-in that provides some of the most popular molecular dynamics (MD) codes with implementations of a variety of different enhanced sampling algorithms and collective variables (CVs). The rapid changes in this field, in particular new directions in enhanced sampling and dimensionality reduction together with new hardware, require a code that is more flexible and more efficient. We therefore present PLUMED 2 here—a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which both extends its core capabilities and makes it far easier to add new methods and CVs. It also has a simpler interface with the MD engines and provides a single software library containing both tools and core facilities. Ultimately, the new code better serves the ever-growing community of users and contributors in coping with the new challenges arising in the field.

Open-source platforms for navigated image-guided interventions.

PubMed

Ungi, Tamas; Lasso, Andras; Fichtinger, Gabor

2016-10-01

Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application. Copyright © 2016 Elsevier B.V. All rights reserved.

Studies investigate effects of hydraulic fracturing

NASA Astrophysics Data System (ADS)

Balcerak, Ernie

2012-11-01

The use of hydraulic fracturing, also known as fracking, to enhance the retrieval of natural gas from shale has been increasing dramatically—the number of natural gas wells rose about 50% since 2000. Shale gas has been hailed as a relatively low-cost, abundant energy source that is cleaner than coal. However, fracking involves injecting large volumes of water, sand, and chemicals into deep shale gas reservoirs under high pressure to open fractures through which the gas can travel, and the process has generated much controversy. The popular press, advocacy organizations, and the documentary film Gasland by Josh Fox have helped bring this issue to a broad audience. Many have suggested that fracking has resulted in contaminated drinking water supplies, enhanced seismic activity, demands for large quantities of water that compete with other uses, and challenges in managing large volumes of resulting wastewater. As demand for expanded domestic energy production intensifies, there is potential for substantially increased use of fracking together with other recovery techniques for "unconventional gas resources," like extended horizontal drilling.

Site Protection Program and Progress Report of Ali Observatory, Tibet

NASA Astrophysics Data System (ADS)

Yao, Yongqiang; Zhou, Yunhe; Wang, Xiaohua; He, Jun; Zhou, Shu

2015-08-01

The Ali observatory, Tibet, is a promising new site identified through ten year site survey over west China, and it is of significance to establish rules of site protection during site development. The site protection program is described with five aspects: site monitoring, technical support, local government support, specific organization, and public education. The long-term sky brightness monitoring is ready with site testing instruments and basic for light pollution measurement; the monitoring also includes directions of main light sources, providing periodical reports and suggestions for coordinating meetings. The technical supports with institutes and manufacturers help to publish lighting standards and replace light fixtures; the research pays special attention to the blue-rich sources, which impact the important application of high altitude sites. An official leading group towards development and protection of astronomical resources has been established by Ali government; one of its tasks is to issue regulations against light pollution, including special restrictions of airport, mine, and winter heating, and to supervise lighting inspection and rectification. A site protection office under the official group and local astronomical society are organized by Ali observatory; the office can coordinate in government levels and promote related activities. A specific website operated by the protection office releases activity propaganda, evaluation results, and technical comparison with other observatories. Both the site protection office and Ali observatory take responsibility for public education, including popular science lectures, light pollution and energy conservation education. Ali Night Sky Park has been constructed and opens in 2014, and provides a popular place and observational experience. The establishment of Ali Observatory and Night Sky Park brings unexpected social influence, and the starry sky trip to Ali becomes a new format of culture-oriented travels in China. The related news reports and network propaganda have drawn attention of national top leadership, instructing to further investigate national support policies.

Comparison of cyclic correlation algorithm implemented in matlab and python

NASA Astrophysics Data System (ADS)

Carr, Richard; Whitney, James

Simulation is a necessary step for all engineering projects. Simulation gives the engineers an approximation of how their devices will perform under different circumstances, without hav-ing to build, or before building a physical prototype. This is especially true for space bound devices, i.e., space communication systems, where the impact of system malfunction or failure is several orders of magnitude over that of terrestrial applications. Therefore having a reliable simulation tool is key in developing these devices and systems. Math Works Matrix Laboratory (MATLAB) is a matrix based software used by scientists and engineers to solve problems and perform complex simulations. MATLAB has a number of applications in a wide variety of fields which include communications, signal processing, image processing, mathematics, eco-nomics and physics. Because of its many uses MATLAB has become the preferred software for many engineers; it is also very expensive, especially for students and startups. One alternative to MATLAB is Python. The Python is a powerful, easy to use, open source programming environment that can be used to perform many of the same functions as MATLAB. Python programming environment has been steadily gaining popularity in niche programming circles. While there are not as many function included in the software as MATLAB, there are many open source functions that have been developed that are available to be downloaded for free. This paper illustrates how Python can implement the cyclic correlation algorithm and com-pares the results to the cyclic correlation algorithm implemented in the MATLAB environment. Some of the characteristics to be compared are the accuracy and precision of the results, and the length of the programs. The paper will demonstrate that Python is capable of performing simulations of complex algorithms such cyclic correlation.

MethLAB: a graphical user interface package for the analysis of array-based DNA methylation data.

PubMed

Kilaru, Varun; Barfield, Richard T; Schroeder, James W; Smith, Alicia K; Conneely, Karen N

2012-03-01

Recent evidence suggests that DNA methylation changes may underlie numerous complex traits and diseases. The advent of commercial, array-based methods to interrogate DNA methylation has led to a profusion of epigenetic studies in the literature. Array-based methods, such as the popular Illumina GoldenGate and Infinium platforms, estimate the proportion of DNA methylated at single-base resolution for thousands of CpG sites across the genome. These arrays generate enormous amounts of data, but few software resources exist for efficient and flexible analysis of these data. We developed a software package called MethLAB (http://genetics.emory.edu/conneely/MethLAB) using R, an open source statistical language that can be edited to suit the needs of the user. MethLAB features a graphical user interface (GUI) with a menu-driven format designed to efficiently read in and manipulate array-based methylation data in a user-friendly manner. MethLAB tests for association between methylation and relevant phenotypes by fitting a separate linear model for each CpG site. These models can incorporate both continuous and categorical phenotypes and covariates, as well as fixed or random batch or chip effects. MethLAB accounts for multiple testing by controlling the false discovery rate (FDR) at a user-specified level. Standard output includes a spreadsheet-ready text file and an array of publication-quality figures. Considering the growing interest in and availability of DNA methylation data, there is a great need for user-friendly open source analytical tools. With MethLAB, we present a timely resource that will allow users with no programming experience to implement flexible and powerful analyses of DNA methylation data.

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

The U.S. Geological Survey (USGS) has a long history of developing and maintaining free, open-source software for hydrological investigations. The MODFLOW program is one of the most popular hydrologic simulation programs released by the USGS, and it is considered to be the most widely used groundwater flow simulation code. MODFLOW was written using a modular design and a procedural FORTRAN style, which resulted in code that could be understood, modified, and enhanced by many hydrologists. The code is fast, and because it uses standard FORTRAN it can be run on most operating systems. Most MODFLOW users rely on proprietary graphical user interfaces for constructing models and viewing model results. Some recent efforts, however, have focused on construction of MODFLOW models using open-source Python scripts. Customizable Python packages, such as FloPy (https://code.google.com/p/flopy), can be used to generate input files, read simulation results, and visualize results in two and three dimensions. Automating this sequence of steps leads to models that can be reproduced directly from original data and rediscretized in space and time. Python is also being used in the development and testing of new MODFLOW functionality. New packages and numerical formulations can be quickly prototyped and tested first with Python programs before implementation in MODFLOW. This is made possible by the flexible object-oriented design capabilities available in Python, the ability to call FORTRAN code from Python, and the ease with which linear systems of equations can be solved using SciPy, for example. Once new features are added to MODFLOW, Python can then be used to automate comprehensive regression testing and ensure reliability and accuracy of new versions prior to release.

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

Open Source Vision

ERIC Educational Resources Information Center

Villano, Matt

2006-01-01

Increasingly, colleges and universities are turning to open source as a way to meet their technology infrastructure and application needs. Open source has changed life for visionary CIOs and their campus communities nationwide. The author discusses what these technologists see as the benefits--and the considerations.

Optimizing Open-Ended Crowdsourcing: The Next Frontier in Crowdsourced Data Management.

PubMed

Parameswaran, Aditya; Sarma, Akash Das; Venkataraman, Vipul

2016-12-01

Crowdsourcing is the primary means to generate training data at scale, and when combined with sophisticated machine learning algorithms, crowdsourcing is an enabler for a variety of emergent automated applications impacting all spheres of our lives. This paper surveys the emerging field of formally reasoning about and optimizing open-ended crowdsourcing, a popular and crucially important, but severely understudied class of crowdsourcing-the next frontier in crowdsourced data management. The underlying challenges include distilling the right answer when none of the workers agree with each other, teasing apart the various perspectives adopted by workers when answering tasks, and effectively selecting between the many open-ended operators appropriate for a problem. We describe the approaches that we've found to be effective for open-ended crowdsourcing, drawing from our experiences in this space.

Open Reading Frame Phylogenetic Analysis on the Cloud

PubMed Central

2013-01-01

Phylogenetic analysis has become essential in researching the evolutionary relationships between viruses. These relationships are depicted on phylogenetic trees, in which viruses are grouped based on sequence similarity. Viral evolutionary relationships are identified from open reading frames rather than from complete sequences. Recently, cloud computing has become popular for developing internet-based bioinformatics tools. Biocloud is an efficient, scalable, and robust bioinformatics computing service. In this paper, we propose a cloud-based open reading frame phylogenetic analysis service. The proposed service integrates the Hadoop framework, virtualization technology, and phylogenetic analysis methods to provide a high-availability, large-scale bioservice. In a case study, we analyze the phylogenetic relationships among Norovirus. Evolutionary relationships are elucidated by aligning different open reading frame sequences. The proposed platform correctly identifies the evolutionary relationships between members of Norovirus. PMID:23671843

Undergraduates' Use of Social Media as Information Sources

ERIC Educational Resources Information Center

Kim, Kyung-Sun; Sin, Sei-Ching Joanna; Yoo-Lee, Eun Young

2014-01-01

Social media have become increasingly popular among different user groups. Although used for social purposes, some social media platforms (such as Wikipedia) have been emerging as important information sources. Focusing on undergraduate students, a survey was conducted to investigate the following: (1) which social media platforms are used as…

Amazing Race: Finding and Correctly Citing Credible Sources

ERIC Educational Resources Information Center

Field-Springer, Kimberly; Striley, Katie Margavio

2016-01-01

The "Amazing Race" activity utilizes experiential learning by encouraging students to venture outside the classroom to collect and cite sources for an upcoming assignment. In the popular TV show, "Amazing Race," teams compete to complete tasks that take them around the world. Similarly, in this classroom activity, groups…

76 FR 34634 - Federal Acquisition Regulation; Prioritizing Sources of Supplies and Services for Use by the...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-14

... contracts before commercial sources in the open market. The proposed rule amends FAR 8.002 as follows: The... requirements for supplies and services from commercial sources in the open market. The proposed FAR 8.004 would... subpart 8.6). (b) Commercial sources (including educational and non-profit institutions) in the open...

Smart Cities Intelligence System (SMACiSYS) Integrating Sensor Web with Spatial Data Infrastructures (sensdi)

NASA Astrophysics Data System (ADS)

Bhattacharya, D.; Painho, M.

2017-09-01

The paper endeavours to enhance the Sensor Web with crucial geospatial analysis capabilities through integration with Spatial Data Infrastructure. The objective is development of automated smart cities intelligence system (SMACiSYS) with sensor-web access (SENSDI) utilizing geomatics for sustainable societies. There has been a need to develop automated integrated system to categorize events and issue information that reaches users directly. At present, no web-enabled information system exists which can disseminate messages after events evaluation in real time. Research work formalizes a notion of an integrated, independent, generalized, and automated geo-event analysing system making use of geo-spatial data under popular usage platform. Integrating Sensor Web With Spatial Data Infrastructures (SENSDI) aims to extend SDIs with sensor web enablement, converging geospatial and built infrastructure, and implement test cases with sensor data and SDI. The other benefit, conversely, is the expansion of spatial data infrastructure to utilize sensor web, dynamically and in real time for smart applications that smarter cities demand nowadays. Hence, SENSDI augments existing smart cities platforms utilizing sensor web and spatial information achieved by coupling pairs of otherwise disjoint interfaces and APIs formulated by Open Geospatial Consortium (OGC) keeping entire platform open access and open source. SENSDI is based on Geonode, QGIS and Java, that bind most of the functionalities of Internet, sensor web and nowadays Internet of Things superseding Internet of Sensors as well. In a nutshell, the project delivers a generalized real-time accessible and analysable platform for sensing the environment and mapping the captured information for optimal decision-making and societal benefit.

Establishing Standards on Colors from Natural Sources.

PubMed

Simon, James E; Decker, Eric A; Ferruzzi, Mario G; Giusti, M Monica; Mejia, Carla D; Goldschmidt, Mark; Talcott, Stephen T

2017-11-01

Color additives are applied to many food, drug, and cosmetic products. With up to 85% of consumer buying decisions potentially influenced by color, appropriate application of color additives and their safety is critical. Color additives are defined by the U.S. Federal Food, Drug, and Cosmetic Act (FD&C Act) as any dye, pigment, or substance that can impart color to a food, drug, or cosmetic or to the human body. Under current U.S. Food and Drug Administration (FDA) regulations, colors fall into 2 categories as those subject to an FDA certification process and those that are exempt from certification often referred to as "natural" colors by consumers because they are sourced from plants, minerals, and animals. Certified colors have been used for decades in food and beverage products, but consumer interest in natural colors is leading market applications. However, the popularity of natural colors has also opened a door for both unintentional and intentional economic adulteration. Whereas FDA certifications for synthetic dyes and lakes involve strict quality control, natural colors are not evaluated by the FDA and often lack clear definitions and industry accepted quality and safety specifications. A significant risk of adulteration of natural colors exists, ranging from simple misbranding or misuse of the term "natural" on a product label to potentially serious cases of physical, chemical, and/or microbial contamination from raw material sources, improper processing methods, or intentional postproduction adulteration. Consistent industry-wide safety standards are needed to address the manufacturing, processing, application, and international trade of colors from natural sources to ensure quality and safety throughout the supply chain. © 2017 Institute of Food Technologists®.

A survey of authors publishing in four megajournals.

PubMed

Solomon, David J

2014-01-01

Aim. To determine the characteristics of megajournal authors, the nature of the manuscripts they are submitting to these journals, factors influencing their decision to publish in a megajournal, sources of funding for article processing charges (APCs) or other fees and their likelihood of submitting to a megajournal in the future. Methods. Web-based survey of 2,128 authors who recently published in BMJ Open, PeerJ, PLOS ONE or SAGE Open. Results. The response rate ranged from 26% for BMJ Open to 47% for SAGE Open. The authors were international, largely academics who had recently published in both subscription and Open Access (OA) journals. Across journals about 25% of the articles were preliminary findings and just under half were resubmissions of manuscripts rejected by other journals. Editors from other BMJ journals and perhaps to a lesser extent SAGE and PLOS journals appear to be encouraging authors to submit manuscripts that were rejected by the editor's journals to a megajournal published by the same publisher. Quality of the journal and speed of the review process were important factors across all four journals. Impact factor was important for PLOS ONE authors but less so for BMJ Open authors, which also has an impact factor. The review criteria and the fact the journal was OA were other significant factors particularly important for PeerJ authors. The reputation of the publisher was an important factor for SAGE Open and BMJ Open. About half of PLOS ONE and around a third of BMJ Open and PeerJ authors used grant funding for publishing charges while only about 10% of SAGE Open used grant funding for publication charges. Around 60% of SAGE Open and 32% of PeerJ authors self-funded their publication fees however the fees are modest for these journals. The majority of authors from all 4 journals were pleased with their experience and indicated they were likely to submit to the same or similar journal in the future. Conclusions. Megajournals are drawing an international group of authors who tend to be experienced academics. They are choosing to publish in megajournals for a variety of reasons but most seem to value the quality of the journal and the speed of the review/publication process. Having a broad scope was not a key factor for most authors though being OA was important for PeerJ and SAGE Open authors. Most authors appeared pleased with the experience and indicated they are likely to submit future manuscripts to the same or similar megajournal which seems to suggest these journals will continue to grow in popularity.

Biosecurity and Open-Source Biology: The Promise and Peril of Distributed Synthetic Biological Technologies.

PubMed

Evans, Nicholas G; Selgelid, Michael J

2015-08-01

In this article, we raise ethical concerns about the potential misuse of open-source biology (OSB): biological research and development that progresses through an organisational model of radical openness, deskilling, and innovation. We compare this organisational structure to that of the open-source software model, and detail salient ethical implications of this model. We demonstrate that OSB, in virtue of its commitment to openness, may be resistant to governance attempts.

Emergency pediatric anesthesia - accessibility of information.

PubMed

King, Hannah; Pipe, Georgina E M; Linford, Sarah L; Moppett, Iain K; Armstrong, James A M

2015-03-01

Emergency pediatric situations are stressful for all involved. Variation in weight, physiology, and anatomy can be substantial and errors in calculating drugs and fluids can be catastrophic. To evaluate the reliability of information resources that anesthetic trainees might use when faced with common pediatric emergencies. Anesthetic trainees from a single UK deanery were recruited and timed while they identified 18 predetermined pieces of information from three Advanced Pediatric Life Support (APLS) scenarios. The two most popular smartphone applications identified from a previous survey, PaedsED (PaedsED. iED limited, Version 1.0.8, Updated March 2011. ©2009) and Anapaed (AnaPaed. Thierry Girard, Version 1.4.2, Updated Nov 2, 2012. ©Thierry Girard), the British National Formulary for Children (cBNF) and trainee's inherent knowledge were compared with a local, check-list style, handbook of pediatric emergency algorithms - Pediatric Anesthetic Emergency Data sheets (PAEDs). Twenty anesthetic trainees were recruited. The fastest source of information was the trainees own knowledge (median 61 s, IQR 51-83 s). Second fastest was PAEDs (80, [59-110] s), followed by PaedsED (84, [65-111]). The most accurate source overall was PaedsED (100, [83-100]) although the accuracy varied between scenarios. The handbook was rated as the most popular resource by the trainees. Although fastest, trainees own knowledge is inaccurate, highlighting the need for additional, rapidly accessible, information. Of the two smartphone applications, PaedsED proved to be fast, accurate, and more popular, while Anapaed was accurate but slow to use. The PAEDs handbook, with its checklist-style format, was also fast, accurate and rated the most popular information source. © 2014 John Wiley & Sons Ltd.

Using R to implement spatial analysis in open source environment

NASA Astrophysics Data System (ADS)

Shao, Yixi; Chen, Dong; Zhao, Bo

2007-06-01

R is an open source (GPL) language and environment for spatial analysis, statistical computing and graphics which provides a wide variety of statistical and graphical techniques, and is highly extensible. In the Open Source environment it plays an important role in doing spatial analysis. So, to implement spatial analysis in the Open Source environment which we called the Open Source geocomputation is using the R data analysis language integrated with GRASS GIS and MySQL or PostgreSQL. This paper explains the architecture of the Open Source GIS environment and emphasizes the role R plays in the aspect of spatial analysis. Furthermore, one apt illustration of the functions of R is given in this paper through the project of constructing CZPGIS (Cheng Zhou Population GIS) supported by Changzhou Government, China. In this project we use R to implement the geostatistics in the Open Source GIS environment to evaluate the spatial correlation of land price and estimate it by Kriging Interpolation. We also use R integrated with MapServer and php to show how R and other Open Source software cooperate with each other in WebGIS environment, which represents the advantages of using R to implement spatial analysis in Open Source GIS environment. And in the end, we points out that the packages for spatial analysis in R is still scattered and the limited memory is still a bottleneck when large sum of clients connect at the same time. Therefore further work is to group the extensive packages in order or design normative packages and make R cooperate better with other commercial software such as ArcIMS. Also we look forward to developing packages for land price evaluation.

Design and Evaluation of a Proxy-Based Monitoring System for OpenFlow Networks.

PubMed

Taniguchi, Yoshiaki; Tsutsumi, Hiroaki; Iguchi, Nobukazu; Watanabe, Kenzi

2016-01-01

Software-Defined Networking (SDN) has attracted attention along with the popularization of cloud environment and server virtualization. In SDN, the control plane and the data plane are decoupled so that the logical topology and routing control can be configured dynamically depending on network conditions. To obtain network conditions precisely, a network monitoring mechanism is necessary. In this paper, we focus on OpenFlow which is a core technology to realize SDN. We propose, design, implement, and evaluate a network monitoring system for OpenFlow networks. Our proposed system acts as a proxy between an OpenFlow controller and OpenFlow switches. Through experimental evaluations, we confirm that our proposed system can capture packets and monitor traffic information depending on administrator's configuration. In addition, we show that our proposed system does not influence significant performance degradation to overall network performance.

Design and Evaluation of a Proxy-Based Monitoring System for OpenFlow Networks

PubMed Central

Taniguchi, Yoshiaki; Tsutsumi, Hiroaki; Iguchi, Nobukazu; Watanabe, Kenzi

2016-01-01

Software-Defined Networking (SDN) has attracted attention along with the popularization of cloud environment and server virtualization. In SDN, the control plane and the data plane are decoupled so that the logical topology and routing control can be configured dynamically depending on network conditions. To obtain network conditions precisely, a network monitoring mechanism is necessary. In this paper, we focus on OpenFlow which is a core technology to realize SDN. We propose, design, implement, and evaluate a network monitoring system for OpenFlow networks. Our proposed system acts as a proxy between an OpenFlow controller and OpenFlow switches. Through experimental evaluations, we confirm that our proposed system can capture packets and monitor traffic information depending on administrator's configuration. In addition, we show that our proposed system does not influence significant performance degradation to overall network performance. PMID:27006977

[The use of open source software in graphic anatomic reconstructions and in biomechanic simulations].

PubMed

Ciobanu, O

2009-01-01

The objective of this study was to obtain three-dimensional (3D) images and to perform biomechanical simulations starting from DICOM images obtained by computed tomography (CT). Open source software were used to prepare digitized 2D images of tissue sections and to create 3D reconstruction from the segmented structures. Finally, 3D images were used in open source software in order to perform biomechanic simulations. This study demonstrates the applicability and feasibility of open source software developed in our days for the 3D reconstruction and biomechanic simulation. The use of open source software may improve the efficiency of investments in imaging technologies and in CAD/CAM technologies for implants and prosthesis fabrication which need expensive specialized software.

A common type system for clinical natural language processing

PubMed Central

2013-01-01

Background One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings. Results We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later. Conclusions We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types. PMID:23286462

detectIR: a novel program for detecting perfect and imperfect inverted repeats using complex numbers and vector calculation.

PubMed

Ye, Congting; Ji, Guoli; Li, Lei; Liang, Chun

2014-01-01

Inverted repeats are present in abundance in both prokaryotic and eukaryotic genomes and can form DNA secondary structures--hairpins and cruciforms that are involved in many important biological processes. Bioinformatics tools for efficient and accurate detection of inverted repeats are desirable, because existing tools are often less accurate and time consuming, sometimes incapable of dealing with genome-scale input data. Here, we present a MATLAB-based program called detectIR for the perfect and imperfect inverted repeat detection that utilizes complex numbers and vector calculation and allows genome-scale data inputs. A novel algorithm is adopted in detectIR to convert the conventional sequence string comparison in inverted repeat detection into vector calculation of complex numbers, allowing non-complementary pairs (mismatches) in the pairing stem and a non-palindromic spacer (loop or gaps) in the middle of inverted repeats. Compared with existing popular tools, our program performs with significantly higher accuracy and efficiency. Using genome sequence data from HIV-1, Arabidopsis thaliana, Homo sapiens and Zea mays for comparison, detectIR can find lots of inverted repeats missed by existing tools whose outputs often contain many invalid cases. detectIR is open source and its source code is freely available at: https://sourceforge.net/projects/detectir.

STEME: A Robust, Accurate Motif Finder for Large Data Sets

PubMed Central

Reid, John E.; Wernisch, Lorenz

2014-01-01

Motif finding is a difficult problem that has been studied for over 20 years. Some older popular motif finders are not suitable for analysis of the large data sets generated by next-generation sequencing. We recently published an efficient approximation (STEME) to the EM algorithm that is at the core of many motif finders such as MEME. This approximation allows the EM algorithm to be applied to large data sets. In this work we describe several efficient extensions to STEME that are based on the MEME algorithm. Together with the original STEME EM approximation, these extensions make STEME a fully-fledged motif finder with similar properties to MEME. We discuss the difficulty of objectively comparing motif finders. We show that STEME performs comparably to existing prominent discriminative motif finders, DREME and Trawler, on 13 sets of transcription factor binding data in mouse ES cells. We demonstrate the ability of STEME to find long degenerate motifs which these discriminative motif finders do not find. As part of our method, we extend an earlier method due to Nagarajan et al. for the efficient calculation of motif E-values. STEME's source code is available under an open source license and STEME is available via a web interface. PMID:24625410

A common type system for clinical natural language processing.

PubMed

Wu, Stephen T; Kaggal, Vinod C; Dligach, Dmitriy; Masanz, James J; Chen, Pei; Becker, Lee; Chapman, Wendy W; Savova, Guergana K; Liu, Hongfang; Chute, Christopher G

2013-01-03

One challenge in reusing clinical data stored in electronic medical records is that these data are heterogenous. Clinical Natural Language Processing (NLP) plays an important role in transforming information in clinical text to a standard representation that is comparable and interoperable. Information may be processed and shared when a type system specifies the allowable data structures. Therefore, we aim to define a common type system for clinical NLP that enables interoperability between structured and unstructured data generated in different clinical settings. We describe a common type system for clinical NLP that has an end target of deep semantics based on Clinical Element Models (CEMs), thus interoperating with structured data and accommodating diverse NLP approaches. The type system has been implemented in UIMA (Unstructured Information Management Architecture) and is fully functional in a popular open-source clinical NLP system, cTAKES (clinical Text Analysis and Knowledge Extraction System) versions 2.0 and later. We have created a type system that targets deep semantics, thereby allowing for NLP systems to encapsulate knowledge from text and share it alongside heterogenous clinical data sources. Rather than surface semantics that are typically the end product of NLP algorithms, CEM-based semantics explicitly build in deep clinical semantics as the point of interoperability with more structured data types.

An architecture for genomics analysis in a clinical setting using Galaxy and Docker

PubMed Central

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A

2017-01-01

Abstract Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. PMID:29048555

An architecture for genomics analysis in a clinical setting using Galaxy and Docker.

PubMed

Digan, W; Countouris, H; Barritault, M; Baudoin, D; Laurent-Puig, P; Blons, H; Burgun, A; Rance, B

2017-11-01

Next-generation sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. We have designed an approach based on Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software. Our solution simplifies the deployment of a small-size analytical platform and simplifies the process for the clinician. From the technical point of view, the tools embedded in the platform are isolated and versioned through Docker images. Along the Galaxy platform, we also introduce the AnalysisManager, a solution that allows single-click analysis for biologists and leverages standardized bioinformatics application programming interfaces. We added a Shiny/R interactive environment to ease the visualization of the outputs. The platform relies on containers and ensures the data traceability by recording analytical actions and by associating inputs and outputs of the tools to EDAM ontology through ReGaTe. The source code is freely available on Github at https://github.com/CARPEM/GalaxyDocker. © The Author 2017. Published by Oxford University Press.

Web GIS in practice IV: publishing your health maps and connecting to remote WMS sources using the Open Source UMN MapServer and DM Solutions MapLab

PubMed Central

Boulos, Maged N Kamel; Honda, Kiyoshi

2006-01-01

Open Source Web GIS software systems have reached a stage of maturity, sophistication, robustness and stability, and usability and user friendliness rivalling that of commercial, proprietary GIS and Web GIS server products. The Open Source Web GIS community is also actively embracing OGC (Open Geospatial Consortium) standards, including WMS (Web Map Service). WMS enables the creation of Web maps that have layers coming from multiple different remote servers/sources. In this article we present one easy to implement Web GIS server solution that is based on the Open Source University of Minnesota (UMN) MapServer. By following the accompanying step-by-step tutorial instructions, interested readers running mainstream Microsoft® Windows machines and with no prior technical experience in Web GIS or Internet map servers will be able to publish their own health maps on the Web and add to those maps additional layers retrieved from remote WMS servers. The 'digital Asia' and 2004 Indian Ocean tsunami experiences in using free Open Source Web GIS software are also briefly described. PMID:16420699

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.

Cyberscience and the Knowledge-Based Economy. Open Access and Trade Publishing: From Contradiction to Compatibility with Non-Exclusive Copyright Licensing

ERIC Educational Resources Information Center

Armbruster, Chris

2008-01-01

Open source, open content and open access are set to fundamentally alter the conditions of knowledge production and distribution. Open source, open content and open access are also the most tangible result of the shift towards e-science and digital networking. Yet, widespread misperceptions exist about the impact of this shift on knowledge…

Learning from hackers: open-source clinical trials.

PubMed

Dunn, Adam G; Day, Richard O; Mandl, Kenneth D; Coiera, Enrico

2012-05-02

Open sharing of clinical trial data has been proposed as a way to address the gap between the production of clinical evidence and the decision-making of physicians. A similar gap was addressed in the software industry by their open-source software movement. Here, we examine how the social and technical principles of the movement can guide the growth of an open-source clinical trial community.

Processable Data Making in the Remote Server Sent by Android Phone as a GIS Data Collecting Tool

NASA Astrophysics Data System (ADS)

Karaagac, Abdullah; Bostancı, Bulent

2016-04-01

Mobile technologies are improving and getting cheaper everyday. Not only smart phones are improved much but also new types of mobile applications and sensors come with the smart phone together. Maps and navigation applications one of the most popular types of applications on these types. Most of these applications uses location services including GNSS, Wi Fi, cellular data and beacon services. Although these coordinate precision not very high, it is appropriate for many applications to utilize. Android is a mobile operating system based on Linux Kernel. It is compatible for varies mobile devices like smart phones, tablets, smart TV's, wearable technologies etc. Android has large capability for application development by using the open source libraries and device sensors like gyroscope, GNSS etc. Android Studio is the most popular integrated development environment (IDE) for Android devices, mainly developing by Google. It had been announced on May 16, 2013 at Google I/O conference. Android Studio is built upon Gradle architecture which is written in Java language. SQLite is a relational database operating system which has so common usage for mobile devices. It developed by using C programming library. It is mostly used via embedding into a software or application. It supports many operating systems including Android. Remote servers can be in several forms from high complexity to simplicity. For this project we will use a open source quad core board computer named Raspberry Pi 2. This device includes 900 MHz ARMv7 compatible quad core CPU, VideoCore IV GPU and 1 GB RAM. Although Raspberry Pi 2's main operating system is Raspbian, we use Debian which are both Linux based operating systems. Raspberry is compatible for many programming language, however some languages are optimized for this device. These are Python, Java, C, C++, Ruby, Perl and Squeak Smalltalk. In this paper, a mobile application will be developed to send coordinate and string data to a SQL database embedded to a remote server. The application will run on Android Operating System running mobile phone. The application will get the location information from the GNSS and cellular data. The user will enter the other information individually. These information will send by clicking a button to remote server which runs SQLite. All these informations will be convertible to any type of measure like type of coordinates could be converted from WGS 84 to ITRF.

Evaluation and selection of open-source EMR software packages based on integrated AHP and TOPSIS.

PubMed

Zaidan, A A; Zaidan, B B; Al-Haiqi, Ahmed; Kiah, M L M; Hussain, Muzammil; Abdulnabi, Mohamed

2015-02-01

Evaluating and selecting software packages that meet the requirements of an organization are difficult aspects of software engineering process. Selecting the wrong open-source EMR software package can be costly and may adversely affect business processes and functioning of the organization. This study aims to evaluate and select open-source EMR software packages based on multi-criteria decision-making. A hands-on study was performed and a set of open-source EMR software packages were implemented locally on separate virtual machines to examine the systems more closely. Several measures as evaluation basis were specified, and the systems were selected based a set of metric outcomes using Integrated Analytic Hierarchy Process (AHP) and TOPSIS. The experimental results showed that GNUmed and OpenEMR software can provide better basis on ranking score records than other open-source EMR software packages. Copyright © 2014 Elsevier Inc. All rights reserved.

Giovanni in the Cloud: Earth Science Data Exploration in Amazon Web Services

NASA Astrophysics Data System (ADS)

Hegde, M.; Petrenko, M.; Smit, C.; Zhang, H.; Pilone, P.; Zasorin, A. A.; Pham, L.

2017-12-01

Giovanni (https://giovanni.gsfc.nasa.gov/giovanni/) is a popular online data exploration tool at the NASA Goddard Earth Sciences Data Information Services Center (GES DISC), providing 22 analysis and visualization services for over 1600 Earth Science data variables. Owing to its popularity, Giovanni has experienced a consistent growth in overall demand, with periodic usage spikes attributed to trainings by education organizations, extensive data analysis in response to natural disasters, preparations for science meetings, etc. Furthermore, the new generation of spaceborne sensors and high resolution models have resulted in an exponential growth in data volume with data distributed across the traditional boundaries of datacenters. Seamless exploration of data (without users having to worry about data center boundaries) has been a key recommendation of the GES DISC User Working Group. These factors have required new strategies for delivering acceptable performance. The cloud-based Giovanni, built on Amazon Web Services (AWS), evaluates (1) AWS native solutions to provide a scalable, serverless architecture; (2) open standards for data storage in the Cloud; (3) a cost model for operations; and (4) end-user performance. Our preliminary findings indicate that the use of serverless architecture has a potential to significantly reduce development and operational cost of Giovanni. The combination of using AWS managed services, storage of data in open standards, and schema-on-read data access strategy simplifies data access and analytics, in addition to making data more accessible to the end users of Giovanni through popular programming languages.

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.

Improving Teachers' Teaching with Communication Technology

ERIC Educational Resources Information Center

Chen, Li-Ling

2012-01-01

With the growing needs to address the challenges that new teachers face and the popularity of social networking technology, this study explores how to increase the effectives of teaching through the use of such technology, and how the technology may serve to promote collaboration and open new resources of support in public education. In this…

An Exploration of Egyptian Students' Attitudes toward Online Learning

ERIC Educational Resources Information Center

El-Zayaty, Nady

2018-01-01

Open and Distance Learning (ODL) has become an increasingly popular platform for delivering education the world over. The acceptance of ODL as a viable alternative to traditional brick and mortar educational institutes has been a topic of debate however. Furthermore, many questions have been raised about the different levels of interest…

300 Junior Novel Anticipation Guides

ERIC Educational Resources Information Center

Polette, Nancy

2006-01-01

In this book, the author has created reproducible anticipation guides to 300 popular junior novels (grades 4-8) ranging from classics like Ben and Me and Cricket in Times Square to the current award winner, Kira, Kira. The book consists of 300 reproducible sets of open ended values questions to pique the interest of readers. Librarians and…

Agronomic performance of five banana cultivars under protected cultivation

USDA-ARS?s Scientific Manuscript database

Banana has been grown both in open-field and protected cultivation in Turkey. So far protected cultivation is very popular due to the high yield and quality. The objective of the study was to evaluate agronomic performance of five new banana cultivars under plastic greenhouse. ‘MA 13’, ‘Williams’, ‘...

A Dialogic Action Perspective on Open Collective Inquiry in Online Forums

ERIC Educational Resources Information Center

Jung, Yusun

2012-01-01

In today's networked environment, online forums emerge as a popular form of social structures that have greater opportunities for learning in various organizational contexts. A plethora of studies have investigated the phenomenon to identify antecedent of its success, such as individual characteristics and organizational structure. However,…

Flipping and MOOCing Your Class Or: How I Learned to Stop Worrying and Love the MOOC

ERIC Educational Resources Information Center

Hlinak, Matt

2016-01-01

Popular and scholarly discussions of higher education pedagogy focus increasingly on two ideas: the "flipped" classroom and massive open online courses (MOOCs). Both flipped classrooms and MOOCs represent substantial departures from the traditional instructional model in higher education. A MOOC is all one-way communication with no…

Public Schools in Marketized Environments: Shifting Incentives and Unintended Consequences of Competition-Based Educational Reforms

ERIC Educational Resources Information Center

Lubienski, Christopher

2005-01-01

By opening the system to competition, popular school choice reforms seek to remake public education into a more consumer-oriented endeavor. While the underlying theory holds that competitive pressures will induce change and improvement in educational processes, research indicates that organizations often respond instead by developing promotional…

Enhancing Survey Participation: Facebook Advertisements for Recruitment in Educational Research

ERIC Educational Resources Information Center

Forgasz, Helen; Tan, Hazel; Leder, Gilah; McLeod, Amber

2018-01-01

Surveys are commonly used to determine how people feel about a specific issue. The increasing availability of the internet and popularity of social networking sites have opened up new possibilities for conducting surveys and, with limited additional costs, enlarge the pool of volunteer respondents with the desired background, experience, or…

Why Study on a MOOC? The Motives of Students and Professionals

ERIC Educational Resources Information Center

Milligan, Colin; Littlejohn, Allison

2017-01-01

Massive Open Online Courses have emerged as a popular mechanism for independent learners to acquire new knowledge and skills; however, the challenge of learning online without dedicated tutor support requires learners to self-motivate. This study explores the primary motivations reported by participants in two MOOCs: "Fundamentals of Clinical…

Appropriate Uses of Modern Technology. Classroom Tips

ERIC Educational Resources Information Center

American Federation of Teachers (NJ), 2010

2010-01-01

Modern technology and the Internet have opened the door to a plethora of new opportunities to learn. It is now easier to research, communicate and study, thanks to advances in technology. There are, however, problems and dangers associated with new technology. Teachers need to remain up to date on these advances. The widespread popularity of…

NIHSeniorHealth Celebrating 10 Years of online health and wellness information! | NIH MedlinePlus the Magazine

MedlinePlus

... information Open captioned videos Easy-to-read language Research-based Content Over 60 health topics 150 health videos Over 200 quizzes Frequently asked questions Bi-weekly healthy aging tips Most Popular Health Topics Exercise and Physical Activity * Eating Well as You Get Older * Shingles * ...

Open and Distance Learning: Cultural Practices in Nepal

ERIC Educational Resources Information Center

Pangeni, Shesha Kanta

2016-01-01

Nepali education culture is dominated by face-to-face tutoring. It has a long history starting from the Gurukul culture to the present formal schooling. Emerging practices of using technology in education have been promoting online learning as a form of distance education and gaining popularity. This paper focuses on digging out the contextual…

Put Power into Your Presentations: Using Presentation Software Effectively

ERIC Educational Resources Information Center

Safransky, Robert J.; Burmeister, Marsha L.

2009-01-01

Microsoft PowerPoint, Apple Keynote, and OpenOffice Impress are relatively common tools in the classroom and in the boardroom these days. What makes presentation software so popular? As the Chinese proverb declares, a picture is worth a thousand words. People like visual presentations. Presentation software can make even a dull subject come to…

Learning Embedded Software Design in an Open 3A Multiuser Laboratory

ERIC Educational Resources Information Center

Shih, Chien-Chou; Hwang, Lain-Jinn

2011-01-01

The need for professional programmers in embedded applications has become critical for industry growth. This need has increased the popularity of embedded software design courses, which are resource-intensive and space-limited in traditional real lab-based instruction. To overcome geographic and time barriers in enhancing practical skills that…

Opening Windows

ERIC Educational Resources Information Center

Bennett, Gayle

2011-01-01

Beth Kanter is working hard to get the word out about how best to get the word out. Kanter is CEO of Zoetica, which provides word-of-mouth communication services to nonprofits and socially conscious companies; a decade-long blogger on the topic of social media and nonprofits; and a popular conference speaker and trainer. She is also co-author of…

A Phenomenology of Learning Large: The Tutorial Sphere of xMOOC Video Lectures

ERIC Educational Resources Information Center

Adams, Catherine; Yin, Yin; Vargas Madriz, Luis Francisco; Mullen, C. Scott

2014-01-01

The current discourse surrounding Massive Open Online Courses (MOOCs) is powerful. Despite their rapid and widespread deployment, research has yet to confirm or refute some of the bold claims rationalizing the popularity and efficacy of these large-scale virtual learning environments. Also, MOOCs' reputed disruptive, game-changing potential…

College Student-Athletes: What the Popular and Professional Literature Report.

ERIC Educational Resources Information Center

Whitner, Phillip A.

This research report on the academic achievements of student-athletes at the college level opens with an historical overview that provides background information on competitive sports and games. The question of amateurism and professionalism is discussed, and a synopsis is presented of the two major revenue-producing college sports, football and…

Open courses: one view of the future of online education.

PubMed

Alemi, Farrokh; Maddox, P J

2008-01-01

Open courses provide the entire course (lectures, assignments, syllabus, student's discussions, and student's projects) online without revealing student's personal information. We report on our experience in managing 8 open online courses at http://nhs.georgetown.edu/open. Open courses have several advantages over password protected courses: (1) they are available through search engines and thus reduce the program's marketing cost, (2) continuous feedback from the web enables rapid improvements to the course, (3) customer relationship tools, tied to open courses, radically reduce faculty time spent on one-on-one emails while increasing student/faculty interaction. We provide details of one course. In 15 weeks, 803 emails were received by and 1181 sent by the faculty (all within 6% of a working week and 82% savings of faculty time). We show how open courses can be accessed through search engines, how students questions are answered on the web and how student projects, in popular sites such as You Tube and Face Book, improve course marketing. The paper reports that student satisfaction with three open online courses delivered overall several semesters was high.

Has the American Public's Interest in Information Related to Relationships Beyond "The Couple" Increased Over Time?

PubMed

Moors, Amy C

2017-01-01

Finding romance, love, and sexual intimacy is a central part of our life experience. Although people engage in romance in a variety of ways, alternatives to "the couple" are largely overlooked in relationship research. Scholars and the media have recently argued that the rules of romance are changing, suggesting that interest in consensual departures from monogamy may become popular as people navigate their long-term coupling. This study utilizes Google Trends to assess Americans' interest in seeking out information related to consensual nonmonogamous relationships across a 10-year period (2006-2015). Using anonymous Web queries from hundreds of thousands of Google search engine users, results show that searches for words related to polyamory and open relationships (but not swinging) have significantly increased over time. Moreover, the magnitude of the correlation between consensual nonmonogamy Web queries and time was significantly higher than popular Web queries over the same time period, indicating this pattern of increased interest in polyamory and open relationships is unique. Future research avenues for incorporating consensual nonmonogamous relationships into relationship science are discussed.

The validity of open-source data when assessing jail suicides.

PubMed

Thomas, Amanda L; Scott, Jacqueline; Mellow, Jeff

2018-05-09

The Bureau of Justice Statistics' Deaths in Custody Reporting Program is the primary source for jail suicide research, though the data is restricted from general dissemination. This study is the first to examine whether jail suicide data obtained from publicly available sources can help inform our understanding of this serious public health problem. Of the 304 suicides that were reported through the DCRP in 2009, roughly 56 percent (N = 170) of those suicides were identified through the open-source search protocol. Each of the sources was assessed based on how much information was collected on the incident and the types of variables available. A descriptive analysis was then conducted on the variables that were present in both data sources. The four variables present in each data source were: (1) demographic characteristics of the victim, (2) the location of occurrence within the facility, (3) the location of occurrence by state, and (4) the size of the facility. Findings demonstrate that the prevalence and correlates of jail suicides are extremely similar in both open-source and official data. However, for almost every variable measured, open-source data captured as much information as official data did, if not more. Further, variables not found in official data were identified in the open-source database, thus allowing researchers to have a more nuanced understanding of the situational characteristics of the event. This research provides support for the argument in favor of including open-source data in jail suicide research as it illustrates how open-source data can be used to provide additional information not originally found in official data. In sum, this research is vital in terms of possible suicide prevention, which may be directly linked to being able to manipulate environmental factors.

Open source tools and toolkits for bioinformatics: significance, and where are we?

PubMed

Stajich, Jason E; Lapp, Hilmar

2006-09-01

This review summarizes important work in open-source bioinformatics software that has occurred over the past couple of years. The survey is intended to illustrate how programs and toolkits whose source code has been developed or released under an Open Source license have changed informatics-heavy areas of life science research. Rather than creating a comprehensive list of all tools developed over the last 2-3 years, we use a few selected projects encompassing toolkit libraries, analysis tools, data analysis environments and interoperability standards to show how freely available and modifiable open-source software can serve as the foundation for building important applications, analysis workflows and resources.

Open Source 2010: Reflections on 2007

ERIC Educational Resources Information Center

Wheeler, Brad

2007-01-01

Colleges and universities and commercial firms have demonstrated great progress in realizing the vision proffered for "Open Source 2007," and 2010 will mark even greater progress. Although much work remains in refining open source for higher education applications, the signals are now clear: the collaborative development of software can provide…

Development and Use of an Open-Source, User-Friendly Package to Simulate Voltammetry Experiments

ERIC Educational Resources Information Center

Wang, Shuo; Wang, Jing; Gao, Yanjing

2017-01-01

An open-source electrochemistry simulation package has been developed that simulates the electrode processes of four reaction mechanisms and two typical electroanalysis techniques: cyclic voltammetry and chronoamperometry. Unlike other open-source simulation software, this package balances the features with ease of learning and implementation and…

Creating Open Source Conversation

ERIC Educational Resources Information Center

Sheehan, Kate

2009-01-01

Darien Library, where the author serves as head of knowledge and learning services, launched a new website on September 1, 2008. The website is built with Drupal, an open source content management system (CMS). In this article, the author describes how she and her colleagues overhauled the library's website to provide an open source content…

Integrating an Automatic Judge into an Open Source LMS

ERIC Educational Resources Information Center

Georgouli, Katerina; Guerreiro, Pedro

2011-01-01

This paper presents the successful integration of the evaluation engine of Mooshak into the open source learning management system Claroline. Mooshak is an open source online automatic judge that has been used for international and national programming competitions. although it was originally designed for programming competitions, Mooshak has also…

76 FR 75875 - Defense Federal Acquisition Regulation Supplement; Open Source Software Public Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-05

... Regulation Supplement; Open Source Software Public Meeting AGENCY: Defense Acquisition Regulations System... initiate a dialogue with industry regarding the use of open source software in DoD contracts. DATES: Public... be held in the General Services Administration (GSA), Central Office Auditorium, 1800 F Street NW...

The open-source movement: an introduction for forestry professionals

Treesearch

Patrick Proctor; Paul C. Van Deusen; Linda S. Heath; Jeffrey H. Gove

2005-01-01

In recent years, the open-source movement has yielded a generous and powerful suite of software and utilities that rivals those developed by many commercial software companies. Open-source programs are available for many scientific needs: operating systems, databases, statistical analysis, Geographic Information System applications, and object-oriented programming....

Open Source Software Development and Lotka's Law: Bibliometric Patterns in Programming.

ERIC Educational Resources Information Center

Newby, Gregory B.; Greenberg, Jane; Jones, Paul

2003-01-01

Applies Lotka's Law to metadata on open source software development. Authoring patterns found in software development productivity are found to be comparable to prior studies of Lotka's Law for scientific and scholarly publishing, and offer promise in predicting aggregate behavior of open source developers. (Author/LRW)

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat.

PubMed

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-04-21

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation.

Conceptualization and validation of an open-source closed-loop deep brain stimulation system in rat

PubMed Central

Wu, Hemmings; Ghekiere, Hartwin; Beeckmans, Dorien; Tambuyzer, Tim; van Kuyck, Kris; Aerts, Jean-Marie; Nuttin, Bart

2015-01-01

Conventional deep brain stimulation (DBS) applies constant electrical stimulation to specific brain regions to treat neurological disorders. Closed-loop DBS with real-time feedback is gaining attention in recent years, after proved more effective than conventional DBS in terms of pathological symptom control clinically. Here we demonstrate the conceptualization and validation of a closed-loop DBS system using open-source hardware. We used hippocampal theta oscillations as system input, and electrical stimulation in the mesencephalic reticular formation (mRt) as controller output. It is well documented that hippocampal theta oscillations are highly related to locomotion, while electrical stimulation in the mRt induces freezing. We used an Arduino open-source microcontroller between input and output sources. This allowed us to use hippocampal local field potentials (LFPs) to steer electrical stimulation in the mRt. Our results showed that closed-loop DBS significantly suppressed locomotion compared to no stimulation, and required on average only 56% of the stimulation used in open-loop DBS to reach similar effects. The main advantages of open-source hardware include wide selection and availability, high customizability, and affordability. Our open-source closed-loop DBS system is effective, and warrants further research using open-source hardware for closed-loop neuromodulation. PMID:25897892

Open Source and ROI: Open Source Has Made Significant Leaps in Recent Years. What Does It Have to Offer Education?

ERIC Educational Resources Information Center

Guhlin, Miguel

2007-01-01

A switch to free open source software can minimize cost and allow funding to be diverted to equipment and other programs. For instance, the OpenOffice suite is an alternative to expensive basic application programs offered by major vendors. Many such programs on the market offer features seldom used in education but for which educators must pay.…

Characteristics, content, and significance of the popular health periodicals literature.

PubMed Central

Rees, A M

1987-01-01

An analysis of the content of sixty popular health periodicals covered in 1986 by the Consumer Health & Nutrition Index was made to identify the characteristics and concerns of popular health magazines and newsletters. The literature mirrors the health values and anxieties of the American public. While some of the literature diverges from mainstream allopathic medicine, most popular publications succeed in presenting coherent, reasoned, and documented viewpoints. Because there is no consensus on many medical problems, it is important that individuals have the freedom to read dissenting and alternative points of view and consider multiple options before making informed and reasoned health decisions. The popular literature is a valuable yet inexpensive source of reliable information on topics of current concern. The publications are not as well known as they deserve to be because they have not been adequately indexed, while they have not been indexed because they are not well known. The Consumer Health & Nutrition Index now provides expanded subject access to sixty health-related periodicals plus all health-related articles in sixteen general interest magazines. PMID:3450343

Reusable Energy and Power Sources: Rechargeable Batteries

ERIC Educational Resources Information Center

Hsiung, Steve C.; Ritz, John M.

2007-01-01

Rechargeable batteries are very popular within consumer electronics. If one uses a cell phone or portable electric tool, she/he understands the need to have a reliable product and the need to remember to use the recharging systems that follow a cycle of charge/discharge. Rechargeable batteries are being called "green" energy sources. They are a…

The LENR-CANR.ORG Website, its Past and Future

NASA Astrophysics Data System (ADS)

Rothwell, J.; Storms, E.

2005-12-01

The LENR-CANR.org web site has proven to be a popular source of information about cold fusion. This site has distributed more full text papers about LENR than any other source. In addition, it contains many features that allow easy search and insertion of the discovered references into a document.

Open source drug discovery--a new paradigm of collaborative research in tuberculosis drug development.

PubMed

Bhardwaj, Anshu; Scaria, Vinod; Raghava, Gajendra Pal Singh; Lynn, Andrew Michael; Chandra, Nagasuma; Banerjee, Sulagna; Raghunandanan, Muthukurussi V; Pandey, Vikas; Taneja, Bhupesh; Yadav, Jyoti; Dash, Debasis; Bhattacharya, Jaijit; Misra, Amit; Kumar, Anil; Ramachandran, Srinivasan; Thomas, Zakir; Brahmachari, Samir K

2011-09-01

It is being realized that the traditional closed-door and market driven approaches for drug discovery may not be the best suited model for the diseases of the developing world such as tuberculosis and malaria, because most patients suffering from these diseases have poor paying capacity. To ensure that new drugs are created for patients suffering from these diseases, it is necessary to formulate an alternate paradigm of drug discovery process. The current model constrained by limitations for collaboration and for sharing of resources with confidentiality hampers the opportunities for bringing expertise from diverse fields. These limitations hinder the possibilities of lowering the cost of drug discovery. The Open Source Drug Discovery project initiated by Council of Scientific and Industrial Research, India has adopted an open source model to power wide participation across geographical borders. Open Source Drug Discovery emphasizes integrative science through collaboration, open-sharing, taking up multi-faceted approaches and accruing benefits from advances on different fronts of new drug discovery. Because the open source model is based on community participation, it has the potential to self-sustain continuous development by generating a storehouse of alternatives towards continued pursuit for new drug discovery. Since the inventions are community generated, the new chemical entities developed by Open Source Drug Discovery will be taken up for clinical trial in a non-exclusive manner by participation of multiple companies with majority funding from Open Source Drug Discovery. This will ensure availability of drugs through a lower cost community driven drug discovery process for diseases afflicting people with poor paying capacity. Hopefully what LINUX the World Wide Web have done for the information technology, Open Source Drug Discovery will do for drug discovery. Copyright © 2011 Elsevier Ltd. All rights reserved.

Survey of practicing urologists: robotic versus open radical prostatectomy.

PubMed

Lee, Eugene K; Baack, Janet; Duchene, David A

2010-04-01

The robotic assisted radical prostatectomy (RARP) has become the most common operative choice for localized prostate cancer. At our institution, we have also seen a substantial increase in the proportion of RARP. Possible patient factors may include marketing, increased Internet usage by patients, and patient-to-patient communication. We surveyed urologists from the central United States to determine possible surgeon factors for the popularity of the RARP. We mailed a survey to all urologists in the South Central Section of the American Urological Association. After demographic information was obtained, participants were asked to choose an operation for themselves based on two prostate cancer scenarios; low risk and high risk. For the low risk prostate cancer scenario, 54.3% chose RARP while 32.9% chose a radical retropubic prostatectomy (RRP). In the high risk scenario, 32.3% chose a RARP while 58.8% chose the RRP. The top reasons for choosing robotics included decreased blood loss, better pain control, and visualization of the apex. The most popular reasons for an open operation included improved lymph node dissection, better tactile sensation, and easier operation for the surgeon. The two most important factors for choosing a particular operation were cancer control and the urologist performing the operation. Also, urologists favored the operative choice in which he or she performed. Robotic assisted radical prostatectomy has become the favored operative approach for low risk prostate cancer. However, many urologists still feel an oncologic difference may exist between open and robotic surgery as evidenced by more urologists favoring an open approach for high risk prostate cancer.

Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN

PubMed Central

Pound, Michael P.; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Leitner, Daniel; Meunier, Félicien; Pridmore, Tony P.; Schnepf, Andrea

2015-01-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. PMID:25614065

Scalable Nearest Neighbor Algorithms for High Dimensional Data.

PubMed

Muja, Marius; Lowe, David G

2014-11-01

For many computer vision and machine learning problems, large training sets are key for good performance. However, the most computationally expensive part of many computer vision and machine learning algorithms consists of finding nearest neighbor matches to high dimensional vectors that represent the training data. We propose new algorithms for approximate nearest neighbor matching and evaluate and compare them with previous algorithms. For matching high dimensional features, we find two algorithms to be the most efficient: the randomized k-d forest and a new algorithm proposed in this paper, the priority search k-means tree. We also propose a new algorithm for matching binary features by searching multiple hierarchical clustering trees and show it outperforms methods typically used in the literature. We show that the optimal nearest neighbor algorithm and its parameters depend on the data set characteristics and describe an automated configuration procedure for finding the best algorithm to search a particular data set. In order to scale to very large data sets that would otherwise not fit in the memory of a single machine, we propose a distributed nearest neighbor matching framework that can be used with any of the algorithms described in the paper. All this research has been released as an open source library called fast library for approximate nearest neighbors (FLANN), which has been incorporated into OpenCV and is now one of the most popular libraries for nearest neighbor matching.

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units.

PubMed

Zhang, Baofeng; Kilburg, Denise; Eastman, Peter; Pande, Vijay S; Gallicchio, Emilio

2017-04-15

We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion-exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii. The many-body nature of the model makes a port to GPU devices challenging. To our knowledge, this is the first reported full implementation of this model on GPU hardware. To accomplish this, we have used recursive strategies to construct the tree of overlaps and to accumulate volumes and their gradients on the tree data structures so as to minimize memory contention. The algorithm is used in the formulation of a surface area-based non-polar implicit solvent model implemented as an open source plug-in (named GaussVol) for the popular OpenMM library for molecular mechanics modeling. GaussVol is 50 to 100 times faster than our best optimized implementation for the CPUs, achieving speeds in excess of 100 ns/day with 1 fs time-step for protein-sized systems on commodity GPUs. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

State-of-the-practice and lessons learned on implementing open data and open source policies.

DOT National Transportation Integrated Search

2012-05-01

This report describes the current government, academic, and private sector practices associated with open data and open source application development. These practices are identified; and the potential uses with the ITS Programs Data Capture and M...

Your Personal Analysis Toolkit - An Open Source Solution

NASA Astrophysics Data System (ADS)

Mitchell, T.

2009-12-01

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

All-source Information Management and Integration for Improved Collective Intelligence Production

DTIC Science & Technology

2011-06-01

Intelligence (ELINT) • Open Source Intelligence ( OSINT ) • Technical Intelligence (TECHINT) These intelligence disciplines produce... intelligence , measurement and signature intelligence , signals intelligence , and open - source data, in the production of intelligence . All- source intelligence ...All- Source Information Integration and Management) R&D Project 3 All- Source Intelligence

WASS: an open-source stereo processing pipeline for sea waves 3D reconstruction

NASA Astrophysics Data System (ADS)

Bergamasco, Filippo; Benetazzo, Alvise; Torsello, Andrea; Barbariol, Francesco; Carniel, Sandro; Sclavo, Mauro

2017-04-01

Stereo 3D reconstruction of ocean waves is gaining more and more popularity in the oceanographic community. In fact, recent advances of both computer vision algorithms and CPU processing power can now allow the study of the spatio-temporal wave fields with unprecedented accuracy, especially at small scales. Even if simple in theory, multiple details are difficult to be mastered for a practitioner so that the implementation of a 3D reconstruction pipeline is in general considered a complex task. For instance, camera calibration, reliable stereo feature matching and mean sea-plane estimation are all factors for which a well designed implementation can make the difference to obtain valuable results. For this reason, we believe that the open availability of a well-tested software package that automates the steps from stereo images to a 3D point cloud would be a valuable addition for future researches in this area. We present WASS, a completely Open-Source stereo processing pipeline for sea waves 3D reconstruction, available at http://www.dais.unive.it/wass/. Our tool completely automates the recovery of dense point clouds from stereo images by providing three main functionalities. First, WASS can automatically recover the extrinsic parameters of the stereo rig (up to scale) so that no delicate calibration has to be performed on the field. Second, WASS implements a fast 3D dense stereo reconstruction procedure so that an accurate 3D point cloud can be computed from each stereo pair. We rely on the well-consolidated OpenCV library both for the image stereo rectification and disparity map recovery. Lastly, a set of 2D and 3D filtering techniques both on the disparity map and the produced point cloud are implemented to remove the vast majority of erroneous points that can naturally arise while analyzing the optically complex nature of the water surface (examples are sun-glares, large white-capped areas, fog and water areosol, etc). Developed to be as fast as possible, WASS can process roughly four 5 MPixel stereo frames per minute (on a consumer i7 CPU) to produce a sequence of outlier-free point clouds with more than 3 million points each. Finally, it comes with an easy to use user interface and designed to be scalable on multiple parallel CPUs.

Popular Berkeley Lab X-ray Data Booklet reissued

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

Robinson, Art

2001-03-02

X-ray scientists and synchrotron-radiation users who have been patiently waiting for an updated version of the popular X-Ray Data Booklet last published in 1986 by the Center for X-Ray Optics at the Lawrence Berkeley National Laboratory can breathe a sigh of relief. The venerable ''little orange book'' has now been reissued under the auspices of CXRO and the Advanced Light Source (ALS) with an April printing of 10,000 paper copies and the posting of a Web edition at http://xdb.lbl.gov.

Getting Open Source Software into Schools: Strategies and Challenges

ERIC Educational Resources Information Center

Hepburn, Gary; Buley, Jan

2006-01-01

In this article Gary Hepburn and Jan Buley outline different approaches to implementing open source software (OSS) in schools; they also address the challenges that open source advocates should anticipate as they try to convince educational leaders to adopt OSS. With regard to OSS implementation, they note that schools have a flexible range of…

Open Source Library Management Systems: A Multidimensional Evaluation

ERIC Educational Resources Information Center

Balnaves, Edmund

2008-01-01

Open source library management systems have improved steadily in the last five years. They now present a credible option for small to medium libraries and library networks. An approach to their evaluation is proposed that takes account of three additional dimensions that only open source can offer: the developer and support community, the source…

Open Source as Appropriate Technology for Global Education

ERIC Educational Resources Information Center

Carmichael, Patrick; Honour, Leslie

2002-01-01

Economic arguments for the adoption of "open source" software in business have been widely discussed. In this paper we draw on personal experience in the UK, South Africa and Southeast Asia to forward compelling reasons why open source software should be considered as an appropriate and affordable alternative to the currently prevailing…

Government Technology Acquisition Policy: The Case of Proprietary versus Open Source Software

ERIC Educational Resources Information Center

Hemphill, Thomas A.

2005-01-01

This article begins by explaining the concepts of proprietary and open source software technology, which are now competing in the marketplace. A review of recent individual and cooperative technology development and public policy advocacy efforts, by both proponents of open source software and advocates of proprietary software, subsequently…

Open Source Communities in Technical Writing: Local Exigence, Global Extensibility

ERIC Educational Resources Information Center

Conner, Trey; Gresham, Morgan; McCracken, Jill

2011-01-01

By offering open-source software (OSS)-based networks as an affordable technology alternative, we partnered with a nonprofit community organization. In this article, we narrate the client-based experiences of this partnership, highlighting the ways in which OSS and open-source culture (OSC) transformed our students' and our own expectations of…

Personal Electronic Devices and the ISR Data Explosion: The Impact of Cyber Cameras on the Intelligence Community

DTIC Science & Technology

2015-06-01

ground.aspx?p=1 Texas Tech Security Group, “Automated Open Source Intelligence ( OSINT ) Using APIs.” RaiderSec, Sunday 30 December 2012, http...Open Source Intelligence ( OSINT ) Using APIs,” RaiderSec, Sunday 30 December 2012, http://raidersec.blogspot.com/2012/12/automated-open- source

Open-Source Unionism: New Workers, New Strategies

ERIC Educational Resources Information Center

Schmid, Julie M.

2004-01-01

In "Open-Source Unionism: Beyond Exclusive Collective Bargaining," published in fall 2002 in the journal Working USA, labor scholars Richard B. Freeman and Joel Rogers use the term "open-source unionism" to describe a form of unionization that uses Web technology to organize in hard-to-unionize workplaces. Rather than depend on the traditional…

Perceptions of Open Source versus Commercial Software: Is Higher Education Still on the Fence?

ERIC Educational Resources Information Center

van Rooij, Shahron Williams

2007-01-01

This exploratory study investigated the perceptions of technology and academic decision-makers about open source benefits and risks versus commercial software applications. The study also explored reactions to a concept for outsourcing campus-wide deployment and maintenance of open source. Data collected from telephone interviews were analyzed,…

Open Source for Knowledge and Learning Management: Strategies beyond Tools

ERIC Educational Resources Information Center

Lytras, Miltiadis, Ed.; Naeve, Ambjorn, Ed.

2007-01-01

In the last years, knowledge and learning management have made a significant impact on the IT research community. "Open Source for Knowledge and Learning Management: Strategies Beyond Tools" presents learning and knowledge management from a point of view where the basic tools and applications are provided by open source technologies.…

Open-Source Learning Management Systems: A Predictive Model for Higher Education

ERIC Educational Resources Information Center

van Rooij, S. Williams

2012-01-01

The present study investigated the role of pedagogical, technical, and institutional profile factors in an institution of higher education's decision to select an open-source learning management system (LMS). Drawing on the results of previous research that measured patterns of deployment of open-source software (OSS) in US higher education and…

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…

Technology collaboration by means of an open source government

NASA Astrophysics Data System (ADS)

Berardi, Steven M.

2009-05-01

The idea of open source software originally began in the early 1980s, but it never gained widespread support until recently, largely due to the explosive growth of the Internet. Only the Internet has made this kind of concept possible, bringing together millions of software developers from around the world to pool their knowledge. The tremendous success of open source software has prompted many corporations to adopt the culture of open source and thus share information they previously held secret. The government, and specifically the Department of Defense (DoD), could also benefit from adopting an open source culture. In acquiring satellite systems, the DoD often builds walls between program offices, but installing doors between programs can promote collaboration and information sharing. This paper addresses the challenges and consequences of adopting an open source culture to facilitate technology collaboration for DoD space acquisitions. DISCLAIMER: The views presented here are the views of the author, and do not represent the views of the United States Government, United States Air Force, or the Missile Defense Agency.

Open source software integrated into data services of Japanese planetary explorations

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Embracing Open Source for NASA's Earth Science Data Systems

NASA Technical Reports Server (NTRS)

Baynes, Katie; Pilone, Dan; Boller, Ryan; Meyer, David; Murphy, Kevin

2017-01-01

The overarching purpose of NASAs Earth Science program is to develop a scientific understanding of Earth as a system. Scientific knowledge is most robust and actionable when resulting from transparent, traceable, and reproducible methods. Reproducibility includes open access to the data as well as the software used to arrive at results. Additionally, software that is custom-developed for NASA should be open to the greatest degree possible, to enable re-use across Federal agencies, reduce overall costs to the government, remove barriers to innovation, and promote consistency through the use of uniform standards. Finally, Open Source Software (OSS) practices facilitate collaboration between agencies and the private sector. To best meet these ends, NASAs Earth Science Division promotes the full and open sharing of not only all data, metadata, products, information, documentation, models, images, and research results but also the source code used to generate, manipulate and analyze them. This talk focuses on the challenges to open sourcing NASA developed software within ESD and the growing pains associated with establishing policies running the gamut of tracking issues, properly documenting build processes, engaging the open source community, maintaining internal compliance, and accepting contributions from external sources. This talk also covers the adoption of existing open source technologies and standards to enhance our custom solutions and our contributions back to the community. Finally, we will be introducing the most recent OSS contributions from NASA Earth Science program and promoting these projects for wider community review and adoption.

Open source Modeling and optimization tools for Planning

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

Peles, S.

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

StreaMorph: A Case for Synthesizing Energy-Efficient Adaptive Programs Using High-Level Abstractions

DTIC Science & Technology

2013-08-12

technique when switching from using eight cores to one core. 1. Introduction Real - time streaming of media data is growing in popularity. This includes...both capture and processing of real - time video and audio, and delivery of video and audio from servers; recent usage number shows over 800 million...source of data, when that source is a real - time source, and it is generally not necessary to get ahead of the sink. Even with real - time sources and sinks

Limitations of Phased Array Beamforming in Open Rotor Noise Source Imaging

NASA Technical Reports Server (NTRS)

Horvath, Csaba; Envia, Edmane; Podboy, Gary G.

2013-01-01

Phased array beamforming results of the F31/A31 historical baseline counter-rotating open rotor blade set were investigated for measurement data taken on the NASA Counter-Rotating Open Rotor Propulsion Rig in the 9- by 15-Foot Low-Speed Wind Tunnel of NASA Glenn Research Center as well as data produced using the LINPROP open rotor tone noise code. The planar microphone array was positioned broadside and parallel to the axis of the open rotor, roughly 2.3 rotor diameters away. The results provide insight as to why the apparent noise sources of the blade passing frequency tones and interaction tones appear at their nominal Mach radii instead of at the actual noise sources, even if those locations are not on the blades. Contour maps corresponding to the sound fields produced by the radiating sound waves, taken from the simulations, are used to illustrate how the interaction patterns of circumferential spinning modes of rotating coherent noise sources interact with the phased array, often giving misleading results, as the apparent sources do not always show where the actual noise sources are located. This suggests that a more sophisticated source model would be required to accurately locate the sources of each tone. The results of this study also have implications with regard to the shielding of open rotor sources by airframe empennages.

RSTensorFlow: GPU Enabled TensorFlow for Deep Learning on Commodity Android Devices

PubMed Central

Alzantot, Moustafa; Wang, Yingnan; Ren, Zhengshuang; Srivastava, Mani B.

2018-01-01

Mobile devices have become an essential part of our daily lives. By virtue of both their increasing computing power and the recent progress made in AI, mobile devices evolved to act as intelligent assistants in many tasks rather than a mere way of making phone calls. However, popular and commonly used tools and frameworks for machine intelligence are still lacking the ability to make proper use of the available heterogeneous computing resources on mobile devices. In this paper, we study the benefits of utilizing the heterogeneous (CPU and GPU) computing resources available on commodity android devices while running deep learning models. We leveraged the heterogeneous computing framework RenderScript to accelerate the execution of deep learning models on commodity Android devices. Our system is implemented as an extension to the popular open-source framework TensorFlow. By integrating our acceleration framework tightly into TensorFlow, machine learning engineers can now easily make benefit of the heterogeneous computing resources on mobile devices without the need of any extra tools. We evaluate our system on different android phones models to study the trade-offs of running different neural network operations on the GPU. We also compare the performance of running different models architectures such as convolutional and recurrent neural networks on CPU only vs using heterogeneous computing resources. Our result shows that although GPUs on the phones are capable of offering substantial performance gain in matrix multiplication on mobile devices. Therefore, models that involve multiplication of large matrices can run much faster (approx. 3 times faster in our experiments) due to GPU support. PMID:29629431

Twitter data analysis: temporal and term frequency analysis with real-time event

NASA Astrophysics Data System (ADS)

Yadav, Garima; Joshi, Mansi; Sasikala, R.

2017-11-01

From the past few years, World Wide Web (www) has become a prominent and huge source for user generated content and opinionative data. Among various social media, Twitter gained popularity as it offers a fast and effective way of sharing users’ perspective towards various critical and other issues in different domain. As the data is hugely generated on cloud, it has opened doors for the researchers in the field of data science and analysis. There are various domains such as ‘Political’ domain, ‘Entertainment’ domain and ‘Business’ domain. Also there are various APIs that Twitter provides for developers 1) Search API, focus on the old tweets 2) Rest API, focuses on user details and allow to collect the user profile, friends and followers 3) Streaming API, which collects details like tweets, hashtags, geo locations. In our work we are accessing Streaming API in order to fetch real-time tweets for the dynamic happening event. For this we are focusing on ‘Entertainment’ domain especially ‘Sports’ as IPL-T20 is currently the trending on-going event. We are collecting these numerous amounts of tweets and storing them in MongoDB database where the tweets are stored in JSON document format. On this document we are performing time-series analysis and term frequency analysis using different techniques such as filtering, information extraction for text-mining that fulfils our objective of finding interesting moments for temporal data in the event and finding the ranking among the players or the teams based on popularity which helps people in understanding key influencers on the social media platform.

Ubuntu Core Snaps for Science

NASA Astrophysics Data System (ADS)

Wyngaard, J.

2017-12-01

A key challenge in the burgeoning sector of IoT (Internet of Things) is ensuring device and communication security. Ubuntu Core's approach to this is the use of 'snaps'. Along side this growth, scientists are increasingly utilising the many new low cost sensors now available. This work prototypes the use of snaps as a possible avenue to reducing the barrier to entry for scientific use of these low cost sensors while also ensuring proper meta-data is captured. Snaps are contained applications that have been signed. This means that a snap application is unable to read or write to any area of the system beyond its assigned reach, thereby significantly limiting the possible impact of any break in security higher up the stack. Further, application and system updates are automatically verified as authentic before being applied. Additionally, on an embedded system running Ubuntu Core the hardware interface (Gadget), kernel, and OS (Core) are all also snaps and therefore also have acquired these same gains. The result is an architecture that enables: (1) Secure, robust, remote automatic updates of both the OS and applications. (2) A user friendly deployment mechanism.(3) A easy to maintain means of supporting multiple platforms. The above is primarily targeted at non-academic domains, however, it is proposed that the Scientific community can benefit from it too. This work therefore prototypes a snap for sensors on board a small Unmanned Aircraft System (sUAS). For demonstration purposes this snap specifically targets connecting a popular low cost CO2 meter to a Raspberry Pi3 and the popular open source sUAS autopilot Arducopter.

RSTensorFlow: GPU Enabled TensorFlow for Deep Learning on Commodity Android Devices.

PubMed

Alzantot, Moustafa; Wang, Yingnan; Ren, Zhengshuang; Srivastava, Mani B

2017-06-01

Mobile devices have become an essential part of our daily lives. By virtue of both their increasing computing power and the recent progress made in AI, mobile devices evolved to act as intelligent assistants in many tasks rather than a mere way of making phone calls. However, popular and commonly used tools and frameworks for machine intelligence are still lacking the ability to make proper use of the available heterogeneous computing resources on mobile devices. In this paper, we study the benefits of utilizing the heterogeneous (CPU and GPU) computing resources available on commodity android devices while running deep learning models. We leveraged the heterogeneous computing framework RenderScript to accelerate the execution of deep learning models on commodity Android devices. Our system is implemented as an extension to the popular open-source framework TensorFlow. By integrating our acceleration framework tightly into TensorFlow, machine learning engineers can now easily make benefit of the heterogeneous computing resources on mobile devices without the need of any extra tools. We evaluate our system on different android phones models to study the trade-offs of running different neural network operations on the GPU. We also compare the performance of running different models architectures such as convolutional and recurrent neural networks on CPU only vs using heterogeneous computing resources. Our result shows that although GPUs on the phones are capable of offering substantial performance gain in matrix multiplication on mobile devices. Therefore, models that involve multiplication of large matrices can run much faster (approx. 3 times faster in our experiments) due to GPU support.

Develop Direct Geo-referencing System Based on Open Source Software and Hardware Platform

NASA Astrophysics Data System (ADS)

Liu, H. S.; Liao, H. M.

2015-08-01

Direct geo-referencing system uses the technology of remote sensing to quickly grasp images, GPS tracks, and camera position. These data allows the construction of large volumes of images with geographic coordinates. So that users can be measured directly on the images. In order to properly calculate positioning, all the sensor signals must be synchronized. Traditional aerial photography use Position and Orientation System (POS) to integrate image, coordinates and camera position. However, it is very expensive. And users could not use the result immediately because the position information does not embed into image. To considerations of economy and efficiency, this study aims to develop a direct geo-referencing system based on open source software and hardware platform. After using Arduino microcontroller board to integrate the signals, we then can calculate positioning with open source software OpenCV. In the end, we use open source panorama browser, panini, and integrate all these to open source GIS software, Quantum GIS. A wholesome collection of data - a data processing system could be constructed.

PR-Index: Using the h-Index and PageRank for Determining True Impact.

PubMed

Gao, Chao; Wang, Zhen; Li, Xianghua; Zhang, Zili; Zeng, Wei

2016-01-01

Several technical indicators have been proposed to assess the impact of authors and institutions. Here, we combine the h-index and the PageRank algorithm to do away with some of the individual limitations of these two indices. Most importantly, we aim to take into account value differences between citations-evaluating the citation sources by defining the h-index using the PageRank score rather than with citations. The resulting PR-index is then constructed by evaluating source popularity as well as the source publication authority. Extensive tests on available collections data (i.e., Microsoft Academic Search and benchmarks on the SIGKDD innovation award) show that the PR-index provides a more balanced impact measure than many existing indices. Due to its simplicity and similarity to the popular h-index, the PR-index may thus become a welcome addition to the technical indices already in use. Moreover, growth dynamics prior to the SIGKDD innovation award indicate that the PR-index might have notable predictive power.

PR-Index: Using the h-Index and PageRank for Determining True Impact

PubMed Central

Gao, Chao; Wang, Zhen; Li, Xianghua; Zhang, Zili; Zeng, Wei

2016-01-01

Several technical indicators have been proposed to assess the impact of authors and institutions. Here, we combine the h-index and the PageRank algorithm to do away with some of the individual limitations of these two indices. Most importantly, we aim to take into account value differences between citations-evaluating the citation sources by defining the h-index using the PageRank score rather than with citations. The resulting PR-index is then constructed by evaluating source popularity as well as the source publication authority. Extensive tests on available collections data (i.e., Microsoft Academic Search and benchmarks on the SIGKDD innovation award) show that the PR-index provides a more balanced impact measure than many existing indices. Due to its simplicity and similarity to the popular h-index, the PR-index may thus become a welcome addition to the technical indices already in use. Moreover, growth dynamics prior to the SIGKDD innovation award indicate that the PR-index might have notable predictive power. PMID:27627767

What is infrasound?

PubMed

Leventhall, Geoff

2007-01-01

Definitions of infrasound and low-frequency noise are discussed and the fuzzy boundary between them described. Infrasound, in its popular definition as sound below a frequency of 20 Hz, is clearly audible, the hearing threshold having been measured down to 1.5 Hz. The popular concept that sound below 20 Hz is inaudible is not correct. Sources of infrasound are in the range from very low-frequency atmospheric fluctuations up into the lower audio frequencies. These sources include natural occurrences, industrial installations, low-speed machinery, etc. Investigations of complaints of low-frequency noise often fail to measure any significant noise. This has led some complainants to conjecture that their perception arises from non-acoustic sources, such as electromagnetic radiation. Over the past 40 years, infrasound and low-frequency noise have attracted a great deal of adverse publicity on their effects on health, based mainly on media exaggerations and misunderstandings. A result of this has been that the public takes a one-dimensional view of infrasound, concerned only by its presence, whilst ignoring its low levels.

Development of an Open Source, Air-Deployable Weather Station

NASA Astrophysics Data System (ADS)

Krejci, A.; Lopez Alcala, J. M.; Nelke, M.; Wagner, J.; Udell, C.; Higgins, C. W.; Selker, J. S.

2017-12-01

We created a packaged weather station intended to be deployed in the air on tethered systems. The device incorporates lightweight sensors and parts and runs for up to 24 hours off of lithium polymer batteries, allowing the entire package to be supported by a thin fiber. As the fiber does not provide a stable platform, additional data (pitch and roll) from typical weather parameters (e.g. temperature, pressure, humidity, wind speed, and wind direction) are determined using an embedded inertial motion unit. All designs are open sourced including electronics, CAD drawings, and descriptions of assembly and can be found on the OPEnS lab website at http://www.open-sensing.org/lowcost-weather-station/. The Openly Published Environmental Sensing Lab (OPEnS: Open-Sensing.org) expands the possibilities of scientific observation of our Earth, transforming the technology, methods, and culture by combining open-source development and cutting-edge technology. New OPEnS labs are now being established in India, France, Switzerland, the Netherlands, and Ghana.

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

Open source electronic health records and chronic disease management.

PubMed

Goldwater, Jason C; Kwon, Nancy J; Nathanson, Ashley; Muckle, Alison E; Brown, Alexa; Cornejo, Kerri

2014-02-01

To study and report on the use of open source electronic health records (EHR) to assist with chronic care management within safety net medical settings, such as community health centers (CHC). The study was conducted by NORC at the University of Chicago from April to September 2010. The NORC team undertook a comprehensive environmental scan, including a literature review, a dozen key informant interviews using a semistructured protocol, and a series of site visits to CHC that currently use an open source EHR. Two of the sites chosen by NORC were actively using an open source EHR to assist in the redesign of their care delivery system to support more effective chronic disease management. This included incorporating the chronic care model into an CHC and using the EHR to help facilitate its elements, such as care teams for patients, in addition to maintaining health records on indigent populations, such as tuberculosis status on homeless patients. The ability to modify the open-source EHR to adapt to the CHC environment and leverage the ecosystem of providers and users to assist in this process provided significant advantages in chronic care management. Improvements in diabetes management, controlled hypertension and increases in tuberculosis vaccinations were assisted through the use of these open source systems. The flexibility and adaptability of open source EHR demonstrated its utility and viability in the provision of necessary and needed chronic disease care among populations served by CHC.