OpenFLUID: an open-source software environment for modelling fluxes in landscapes

NASA Astrophysics Data System (ADS)

Fabre, Jean-Christophe; Rabotin, Michaël; Crevoisier, David; Libres, Aline; Dagès, Cécile; Moussa, Roger; Lagacherie, Philippe; Raclot, Damien; Voltz, Marc

2013-04-01

Integrative landscape functioning has become a common concept in environmental management. Landscapes are complex systems where many processes interact in time and space. In agro-ecosystems, these processes are mainly physical processes, including hydrological-processes, biological processes and human activities. Modelling such systems requires an interdisciplinary approach, coupling models coming from different disciplines, developed by different teams. In order to support collaborative works, involving many models coupled in time and space for integrative simulations, an open software modelling platform is a relevant answer. OpenFLUID is an open source software platform for modelling landscape functioning, mainly focused on spatial fluxes. It provides an advanced object-oriented architecture allowing to i) couple models developed de novo or from existing source code, and which are dynamically plugged to the platform, ii) represent landscapes as hierarchical graphs, taking into account multi-scale, spatial heterogeneities and landscape objects connectivity, iii) run and explore simulations in many ways : using the OpenFLUID software interfaces for users (command line interface, graphical user interface), or using external applications such as GNU R through the provided ROpenFLUID package. OpenFLUID is developed in C++ and relies on open source libraries only (Boost, libXML2, GLib/GTK, OGR/GDAL, …). For modelers and developers, OpenFLUID provides a dedicated environment for model development, which is based on an open source toolchain, including the Eclipse editor, the GCC compiler and the CMake build system. OpenFLUID is distributed under the GPLv3 open source license, with a special exception allowing to plug existing models licensed under any license. It is clearly in the spirit of sharing knowledge and favouring collaboration in a community of modelers. OpenFLUID has been involved in many research applications, such as modelling of hydrological network transfer, diagnosis and prediction of water quality taking into account human activities, study of the effect of spatial organization on hydrological fluxes, modelling of surface-subsurface water exchanges, … At LISAH research unit, OpenFLUID is the supporting development platform of the MHYDAS model, which is a distributed model for agrosystems (Moussa et al., 2002, Hydrological Processes, 16, 393-412). OpenFLUID web site : http://www.openfluid-project.org

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

10 CFR 39.43 - Inspection, maintenance, and opening of a source or source holder.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Inspection, maintenance, and opening of a source or source holder. 39.43 Section 39.43 Energy NUCLEAR REGULATORY COMMISSION LICENSES AND RADIATION SAFETY..., for defects before each use to ensure that the equipment is in good working condition and that...

75 FR 60341 - Licenses, Certifications, and Approvals for Material Licensees; Reopening of Comment Period

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-30

... approval processes for byproduct, source and special nuclear material licenses, and irradiators to clarify... proposed rule, which closed on September 27, 2010, is reopened and will remain open until November 29, 2010...

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.

Of Birkenstocks and Wingtips: Open Source Licenses

ERIC Educational Resources Information Center

Gandel, Paul B.; Wheeler, Brad

2005-01-01

The notion of collaborating to create open source applications for higher education is rapidly gaining momentum. From course management systems to ERP financial systems, higher education institutions are working together to explore whether they can in fact build a better mousetrap. As Lois Brooks, of Stanford University, recently observed, the…

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 clustering software.

PubMed

de Hoon, M J L; Imoto, S; Nolan, J; Miyano, S

2004-06-12

We have implemented k-means clustering, hierarchical clustering and self-organizing maps in a single multipurpose open-source library of C routines, callable from other C and C++ programs. Using this library, we have created an improved version of Michael Eisen's well-known Cluster program for Windows, Mac OS X and Linux/Unix. In addition, we generated a Python and a Perl interface to the C Clustering Library, thereby combining the flexibility of a scripting language with the speed of C. The C Clustering Library and the corresponding Python C extension module Pycluster were released under the Python License, while the Perl module Algorithm::Cluster was released under the Artistic License. The GUI code Cluster 3.0 for Windows, Macintosh and Linux/Unix, as well as the corresponding command-line program, were released under the same license as the original Cluster code. The complete source code is available at http://bonsai.ims.u-tokyo.ac.jp/mdehoon/software/cluster. Alternatively, Algorithm::Cluster can be downloaded from CPAN, while Pycluster is also available as part of the Biopython distribution.

Investigating the Acquisition of Software Systems that Rely on Open Architecture and Open Source Software

DTIC Science & Technology

2010-03-01

associated with certain software systems [Breaux and Anton 2008]. With this basis to build on, it is now possible to analyze the alignment of...Kazman, R., (2003). Software Architecture in Practice, 2nd Edition, Addison-Wesley Pro- fessional, New York.. Breaux, T.D. and Anton , A.I. (2008... calculus for license rights and obligations in license and context models. Using them, we calculate rights and obligations for specific sys- tems, identify

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

USDA-ARS?s Scientific Manuscript database

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

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.

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

PubMed

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

2015-03-01

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

[GNU Pattern: open source pattern hunter for biological sequences based on SPLASH algorithm].

PubMed

Xu, Ying; Li, Yi-xue; Kong, Xiang-yin

2005-06-01

To construct a high performance open source software engine based on IBM SPLASH algorithm for later research on pattern discovery. Gpat, which is based on SPLASH algorithm, was developed by using open source software. GNU Pattern (Gpat) software was developped, which efficiently implemented the core part of SPLASH algorithm. Full source code of Gpat was also available for other researchers to modify the program under the GNU license. Gpat is a successful implementation of SPLASH algorithm and can be used as a basic framework for later research on pattern recognition in biological sequences.

Biospark: scalable analysis of large numerical datasets from biological simulations and experiments using Hadoop and Spark.

PubMed

Klein, Max; Sharma, Rati; Bohrer, Chris H; Avelis, Cameron M; Roberts, Elijah

2017-01-15

Data-parallel programming techniques can dramatically decrease the time needed to analyze large datasets. While these methods have provided significant improvements for sequencing-based analyses, other areas of biological informatics have not yet adopted them. Here, we introduce Biospark, a new framework for performing data-parallel analysis on large numerical datasets. Biospark builds upon the open source Hadoop and Spark projects, bringing domain-specific features for biology. Source code is licensed under the Apache 2.0 open source license and is available at the project website: https://www.assembla.com/spaces/roberts-lab-public/wiki/Biospark CONTACT: eroberts@jhu.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Erratum: Erratum to: Realistic interpretation of quantum mechanics and encounter-delayed-choice experiment

NASA Astrophysics Data System (ADS)

Long, GuiLu; Qin, Wei; Yang, Zhe; Li, Jun-Lin

2018-06-01

The article Realistic interpretation of quantum mechanics and encounter-delayed-choice experiment, written by GuiLu Long, Wei Qin, Zhe Yang, and Jun-Lin Li, was originally published online without open access. After publication in volume 61, issue 3: 030311 the author decided to opt for Open Choice and to make the article an open access publication. Therefore, the copyright of the article has been changed to The Author(s) 2017 and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The original article has been corrected.

Development and Use of an Adaptive Learning Environment to Research Online Study Behaviour

ERIC Educational Resources Information Center

Jonsdottir, Anna Helga; Jakobsdottir, Audbjorg; Stefansson, Gunnar

2015-01-01

This paper describes a system for research on the behaviour of students taking online drills. The system is accessible and free to use for anyone with web access. Based on open source software, the teaching material is licensed under a Creative Commons License. The system has been used for computer-assisted education in statistics, mathematics and…

Pteros: fast and easy to use open-source C++ library for molecular analysis.

PubMed

Yesylevskyy, Semen O

2012-07-15

An open-source Pteros library for molecular modeling and analysis of molecular dynamics trajectories for C++ programming language is introduced. Pteros provides a number of routine analysis operations ranging from reading and writing trajectory files and geometry transformations to structural alignment and computation of nonbonded interaction energies. The library features asynchronous trajectory reading and parallel execution of several analysis routines, which greatly simplifies development of computationally intensive trajectory analysis algorithms. Pteros programming interface is very simple and intuitive while the source code is well documented and easily extendible. Pteros is available for free under open-source Artistic License from http://sourceforge.net/projects/pteros/. Copyright © 2012 Wiley Periodicals, Inc.

Freeing Worldview's development process: Open source everything!

NASA Astrophysics Data System (ADS)

Gunnoe, T.

2016-12-01

Freeing your code and your project are important steps for creating an inviting environment for collaboration, with the added side effect of keeping a good relationship with your users. NASA Worldview's codebase was released with the open source NOSA (NASA Open Source Agreement) license in 2014, but this is only the first step. We also have to free our ideas, empower our users by involving them in the development process, and open channels that lead to the creation of a community project. There are many highly successful examples of Free and Open Source Software (FOSS) projects of which we can take note: the Linux kernel, Debian, GNOME, etc. These projects owe much of their success to having a passionate mix of developers/users with a great community and a common goal in mind. This presentation will describe the scope of this openness and how Worldview plans to move forward with a more community-inclusive approach.

Managing multicentre clinical trials with open source.

PubMed

Raptis, Dimitri Aristotle; Mettler, Tobias; Fischer, Michael Alexander; Patak, Michael; Lesurtel, Mickael; Eshmuminov, Dilmurodjon; de Rougemont, Olivier; Graf, Rolf; Clavien, Pierre-Alain; Breitenstein, Stefan

2014-03-01

Multicentre clinical trials are challenged by high administrative burden, data management pitfalls and costs. This leads to a reduced enthusiasm and commitment of the physicians involved and thus to a reluctance in conducting multicentre clinical trials. The purpose of this study was to develop a web-based open source platform to support a multi-centre clinical trial. We developed on Drupal, an open source software distributed under the terms of the General Public License, a web-based, multi-centre clinical trial management system with the design science research approach. This system was evaluated by user-testing and well supported several completed and on-going clinical trials and is available for free download. Open source clinical trial management systems are capable in supporting multi-centre clinical trials by enhancing efficiency, quality of data management and collaboration.

Annotare--a tool for annotating high-throughput biomedical investigations and resulting data.

PubMed

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J; Ball, Catherine A

2010-10-01

Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows.

OpenStructure: a flexible software framework for computational structural biology.

PubMed

Biasini, Marco; Mariani, Valerio; Haas, Jürgen; Scheuber, Stefan; Schenk, Andreas D; Schwede, Torsten; Philippsen, Ansgar

2010-10-15

Developers of new methods in computational structural biology are often hampered in their research by incompatible software tools and non-standardized data formats. To address this problem, we have developed OpenStructure as a modular open source platform to provide a powerful, yet flexible general working environment for structural bioinformatics. OpenStructure consists primarily of a set of libraries written in C++ with a cleanly designed application programmer interface. All functionality can be accessed directly in C++ or in a Python layer, meeting both the requirements for high efficiency and ease of use. Powerful selection queries and the notion of entity views to represent these selections greatly facilitate the development and implementation of algorithms on structural data. The modular integration of computational core methods with powerful visualization tools makes OpenStructure an ideal working and development environment. Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms. Source code licensed under the GNU lesser general public license and binaries for MacOS X, Linux and Windows are available for download at http://www.openstructure.org. torsten.schwede@unibas.ch Supplementary data are available at Bioinformatics online.

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches.

PubMed

Vaudel, Marc; Barsnes, Harald; Berven, Frode S; Sickmann, Albert; Martens, Lennart

2011-03-01

The identification of proteins by mass spectrometry is a standard technique in the field of proteomics, relying on search engines to perform the identifications of the acquired spectra. Here, we present a user-friendly, lightweight and open-source graphical user interface called SearchGUI (http://searchgui.googlecode.com), for configuring and running the freely available OMSSA (open mass spectrometry search algorithm) and X!Tandem search engines simultaneously. Freely available under the permissible Apache2 license, SearchGUI is supported on Windows, Linux and OSX. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

OpenChrom: a cross-platform open source software for the mass spectrometric analysis of chromatographic data.

PubMed

Wenig, Philip; Odermatt, Juergen

2010-07-30

Today, data evaluation has become a bottleneck in chromatographic science. Analytical instruments equipped with automated samplers yield large amounts of measurement data, which needs to be verified and analyzed. Since nearly every GC/MS instrument vendor offers its own data format and software tools, the consequences are problems with data exchange and a lack of comparability between the analytical results. To challenge this situation a number of either commercial or non-profit software applications have been developed. These applications provide functionalities to import and analyze several data formats but have shortcomings in terms of the transparency of the implemented analytical algorithms and/or are restricted to a specific computer platform. This work describes a native approach to handle chromatographic data files. The approach can be extended in its functionality such as facilities to detect baselines, to detect, integrate and identify peaks and to compare mass spectra, as well as the ability to internationalize the application. Additionally, filters can be applied on the chromatographic data to enhance its quality, for example to remove background and noise. Extended operations like do, undo and redo are supported. OpenChrom is a software application to edit and analyze mass spectrometric chromatographic data. It is extensible in many different ways, depending on the demands of the users or the analytical procedures and algorithms. It offers a customizable graphical user interface. The software is independent of the operating system, due to the fact that the Rich Client Platform is written in Java. OpenChrom is released under the Eclipse Public License 1.0 (EPL). There are no license constraints regarding extensions. They can be published using open source as well as proprietary licenses. OpenChrom is available free of charge at http://www.openchrom.net.

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

Gearhart, Jared Lee; Adair, Kristin Lynn; Durfee, Justin David.

When developing linear programming models, issues such as budget limitations, customer requirements, or licensing may preclude the use of commercial linear programming solvers. In such cases, one option is to use an open-source linear programming solver. A survey of linear programming tools was conducted to identify potential open-source solvers. From this survey, four open-source solvers were tested using a collection of linear programming test problems and the results were compared to IBM ILOG CPLEX Optimizer (CPLEX) [1], an industry standard. The solvers considered were: COIN-OR Linear Programming (CLP) [2], [3], GNU Linear Programming Kit (GLPK) [4], lp_solve [5] and Modularmore » In-core Nonlinear Optimization System (MINOS) [6]. As no open-source solver outperforms CPLEX, this study demonstrates the power of commercial linear programming software. CLP was found to be the top performing open-source solver considered in terms of capability and speed. GLPK also performed well but cannot match the speed of CLP or CPLEX. lp_solve and MINOS were considerably slower and encountered issues when solving several test problems.« less

Annotare—a tool for annotating high-throughput biomedical investigations and resulting data

PubMed Central

Shankar, Ravi; Parkinson, Helen; Burdett, Tony; Hastings, Emma; Liu, Junmin; Miller, Michael; Srinivasa, Rashmi; White, Joseph; Brazma, Alvis; Sherlock, Gavin; Stoeckert, Christian J.; Ball, Catherine A.

2010-01-01

Summary: Computational methods in molecular biology will increasingly depend on standards-based annotations that describe biological experiments in an unambiguous manner. Annotare is a software tool that enables biologists to easily annotate their high-throughput experiments, biomaterials and data in a standards-compliant way that facilitates meaningful search and analysis. Availability and Implementation: Annotare is available from http://code.google.com/p/annotare/ under the terms of the open-source MIT License (http://www.opensource.org/licenses/mit-license.php). It has been tested on both Mac and Windows. Contact: rshankar@stanford.edu PMID:20733062

Software licensing policy for the Open Source Application Development Portal (OSADP).

DOT National Transportation Integrated Search

1998-07-01

The purpose of the Commercial Vehicle Information Systems and Networks Model Deployment Initiative (CVISN MDI) is to demonstrate the technical and institutional feasibility, costs, and benefits of the primary Intelligent Transportation Systems (ITS) ...

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-07-01

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

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 Rights Reversed: A Study of Copyleft, Open-Source, and Open-Content Licensing

ERIC Educational Resources Information Center

Frantsvog, Dean A.

2012-01-01

In the United States and much of the world, the current framework of intellectual property laws revolves around protecting others from tampering with an author's work. The copyright holder decides who can use it, who can change it, and who can share. There is a growing school of thought, though, that holds that intellectual creations should be…

Correction to: Association of adiposity with hemoglobin levels in patients with chronic kidney disease not on dialysis.

PubMed

Honda, Hirokazu; Ono, Kota; Akizawa, Tadao; Nitta, Kosaku; Hishida, Akira

2018-02-06

The article Association of adiposity with hemoglobin levels in patients with chronic kidney disease not on dialysis, written by Hirokazu Honda, Kota Ono, Tadao Akizawa, Kosaku Nitta and Akira Hishida, was originally published electronically on the publisher's internet portal (currently springerlink) on November 4, 2017 without open access. With the author(s)' decision to opt for Open Choice, the copyright of the article changed on February 6, 2018 to © The Author(s) [2017] and the article is forthwith distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/ ), which permits use, duplication, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. The original article was corrected.

Numerical Analysis of the Cavity Flow subjected to Passive Controls Techniques

NASA Astrophysics Data System (ADS)

Melih Guleren, Kursad; Turk, Seyfettin; Mirza Demircan, Osman; Demir, Oguzhan

2018-03-01

Open-source flow solvers are getting more and more popular for the analysis of challenging flow problems in aeronautical and mechanical engineering applications. They are offered under the GNU General Public License and can be run, examined, shared and modified according to user’s requirements. SU2 and OpenFOAM are the two most popular open-source solvers in Computational Fluid Dynamics (CFD) community. In the present study, some passive control methods on the high-speed cavity flows are numerically simulated using these open-source flow solvers along with one commercial flow solver called ANSYS/Fluent. The results are compared with the available experimental data. The solver SU2 are seen to predict satisfactory the mean streamline velocity but not turbulent kinetic energy and overall averaged sound pressure level (OASPL). Whereas OpenFOAM predicts all these parameters nearly as the same levels of ANSYS/Fluent.

General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

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

Evaluating Intellectual Property and Data Rights in Competition Source Selections - Leveraging the Assertions Process to a New Level to Foster Open Systems Architecture

DTIC Science & Technology

2015-04-30

itself. This is the traditional methodology (combined with attaching commercial software licenses to the contract and citing patent royalty ... Royalties It helps to visualize the Intellectual Property Volume approach so the following notional tables with example deliverable technical data...attorney’s fees  Automatic renewal provisions that violate the Anti-Deficiency Act  Provisions that prohibit disclosure of license terms/conditions

Opendf - An Implementation of the Dual Fermion Method for Strongly Correlated Systems

NASA Astrophysics Data System (ADS)

Antipov, Andrey E.; LeBlanc, James P. F.; Gull, Emanuel

The dual fermion method is a multiscale approach for solving lattice problems of interacting strongly correlated systems. In this paper, we present the opendfcode, an open-source implementation of the dual fermion method applicable to fermionic single- orbital lattice models in dimensions D = 1, 2, 3 and 4. The method is built on a dynamical mean field starting point, which neglects all local correlations, and perturbatively adds spatial correlations. Our code is distributed as an open-source package under the GNU public license version 2.

scikit-image: image processing in Python.

PubMed

van der Walt, Stéfan; Schönberger, Johannes L; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

Development of an open-source web-based intervention for Brazilian smokers - Viva sem Tabaco.

PubMed

Gomide, H P; Bernardino, H S; Richter, K; Martins, L F; Ronzani, T M

2016-08-02

Web-based interventions for smoking cessation available in Portuguese do not adhere to evidence-based treatment guidelines. Besides, all existing web-based interventions are built on proprietary platforms that developing countries often cannot afford. We aimed to describe the development of "Viva sem Tabaco", an open-source web-based intervention. The development of the intervention included the selection of content from evidence-based guidelines for smoking cessation, the design of the first layout, conduction of 2 focus groups to identify potential features, refinement of the layout based on focus groups and correction of content based on feedback provided by specialists on smoking cessation. At the end, we released the source-code and intervention on the Internet and translated it into Spanish and English. The intervention developed fills gaps in the information available in Portuguese and the lack of open-source interventions for smoking cessation. The open-source licensing format and its translation system may help researchers from different countries deploying evidence-based interventions for smoking cessation.

High Resolution Topography of Polar Regions from Commercial Satellite Imagery, Petascale Computing and Open Source Software

NASA Astrophysics Data System (ADS)

Morin, Paul; Porter, Claire; Cloutier, Michael; Howat, Ian; Noh, Myoung-Jong; Willis, Michael; Kramer, WIlliam; Bauer, Greg; Bates, Brian; Williamson, Cathleen

2017-04-01

Surface topography is among the most fundamental data sets for geosciences, essential for disciplines ranging from glaciology to geodynamics. Two new projects are using sub-meter, commercial imagery licensed by the National Geospatial-Intelligence Agency and open source photogrammetry software to produce a time-tagged 2m posting elevation model of the Arctic and an 8m posting reference elevation model for the Antarctic. When complete, this publically available data will be at higher resolution than any elevation models that cover the entirety of the Western United States. These two polar projects are made possible due to three equally important factors: 1) open-source photogrammetry software, 2) petascale computing, and 3) sub-meter imagery licensed to the United States Government. Our talk will detail the technical challenges of using automated photogrammetry software; the rapid workflow evolution to allow DEM production; the task of deploying the workflow on one of the world's largest supercomputers; the trials of moving massive amounts of data, and the management strategies the team needed to solve in order to meet deadlines. Finally, we will discuss the implications of this type of collaboration for future multi-team use of leadership-class systems such as Blue Waters, and for further elevation mapping.

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.

Open source system OpenVPN in a function of Virtual Private Network

NASA Astrophysics Data System (ADS)

Skendzic, A.; Kovacic, B.

2017-05-01

Using of Virtual Private Networks (VPN) can establish high security level in network communication. VPN technology enables high security networking using distributed or public network infrastructure. VPN uses different security and managing rules inside networks. It can be set up using different communication channels like Internet or separate ISP communication infrastructure. VPN private network makes security communication channel over public network between two endpoints (computers). OpenVPN is an open source software product under GNU General Public License (GPL) that can be used to establish VPN communication between two computers inside business local network over public communication infrastructure. It uses special security protocols and 256-bit Encryption and it is capable of traversing network address translators (NATs) and firewalls. It allows computers to authenticate each other using a pre-shared secret key, certificates or username and password. This work gives review of VPN technology with a special accent on OpenVPN. This paper will also give comparison and financial benefits of using open source VPN software in business environment.

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

PubMed

Wójcikowski, Maciej; Zielenkiewicz, Piotr; Siedlecki, Pawel

2015-01-01

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

Open source tools for ATR development and performance evaluation

NASA Astrophysics Data System (ADS)

Baumann, James M.; Dilsavor, Ronald L.; Stubbles, James; Mossing, John C.

2002-07-01

Early in almost every engineering project, a decision must be made about tools; should I buy off-the-shelf tools or should I develop my own. Either choice can involve significant cost and risk. Off-the-shelf tools may be readily available, but they can be expensive to purchase and to maintain licenses, and may not be flexible enough to satisfy all project requirements. On the other hand, developing new tools permits great flexibility, but it can be time- (and budget-) consuming, and the end product still may not work as intended. Open source software has the advantages of both approaches without many of the pitfalls. This paper examines the concept of open source software, including its history, unique culture, and informal yet closely followed conventions. These characteristics influence the quality and quantity of software available, and ultimately its suitability for serious ATR development work. We give an example where Python, an open source scripting language, and OpenEV, a viewing and analysis tool for geospatial data, have been incorporated into ATR performance evaluation projects. While this case highlights the successful use of open source tools, we also offer important insight into risks associated with this approach.

Resource sharing of online teaching materials: The lon-capa project

NASA Astrophysics Data System (ADS)

Bauer, Wolfgang

2004-03-01

The use of information technology resources in conventional lecture-based courses, in distance-learning offerings, as well as hybrid courses, is increasing. But this may put additional burden on faculty, who are now asked to deliver this new content. Additionally, it may require the installation of commercial courseware systems, putting the colleges and universities in new financial licensing dependencies. To address exactly these two problems, the lon-capa system was invented to provide an open-source, gnu public license based, courseware system that allows for sharing of educational resources across institutional and disciplinary boundaries. This presentation will focus on both aspects of the system, the courseware capabilities that allow for customized environments for individual students, and the educational resources library that enables teachers to take full advantages of the work of their colleagues. Research results on learning effectiveness, resource and system usage patterns, and customization for different learning styles will be shown. Institutional perceptions of and responses to open source courseware systems will be discussed.

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.

scikit-image: image processing in Python

PubMed Central

Schönberger, Johannes L.; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D.; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org. PMID:25024921

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 .

Open Source Software Compliance within the Government

DTIC Science & Technology

2016-12-01

The exception to this rule is the various General Public License (GPLs), which consider all distributions to contractors as outside distribution...is developed by a contractor at the government’s expense or for the government’s exclusive use. The third condition that must be met is that ERDC...executables and source code can only be offered by an authorized delivering entity to an authorized receiving entity. This means that contractors , with

No Strings Attached: Open Source Solutions

ERIC Educational Resources Information Center

Fredricks, Kathy

2009-01-01

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

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information

PubMed Central

Hagedorn, Gregor; Mietchen, Daniel; Morris, Robert A.; Agosti, Donat; Penev, Lyubomir; Berendsohn, Walter G.; Hobern, Donald

2011-01-01

Abstract The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a “non-commercial” (NC) condition. Although many people identify “non-commercial” with “non-profit”, detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works. PMID:22207810

Creative Commons licenses and the non-commercial condition: Implications for the re-use of biodiversity information.

PubMed

Hagedorn, Gregor; Mietchen, Daniel; Morris, Robert A; Agosti, Donat; Penev, Lyubomir; Berendsohn, Walter G; Hobern, Donald

2011-01-01

The Creative Commons (CC) licenses are a suite of copyright-based licenses defining terms for the distribution and re-use of creative works. CC provides licenses for different use cases and includes open content licenses such as the Attribution license (CC BY, used by many Open Access scientific publishers) and the Attribution Share Alike license (CC BY-SA, used by Wikipedia, for example). However, the license suite also contains non-free and non-open licenses like those containing a "non-commercial" (NC) condition. Although many people identify "non-commercial" with "non-profit", detailed analysis reveals that significant differences exist and that the license may impose some unexpected re-use limitations on works thus licensed. After providing background information on the concepts of Creative Commons licenses in general, this contribution focuses on the NC condition, its advantages, disadvantages and appropriate scope. Specifically, it contributes material towards a risk analysis for potential re-users of NC-licensed works.

The openEHR Java reference implementation project.

PubMed

Chen, Rong; Klein, Gunnar

2007-01-01

The openEHR foundation has developed an innovative design for interoperable and future-proof Electronic Health Record (EHR) systems based on a dual model approach with a stable reference information model complemented by archetypes for specific clinical purposes.A team from Sweden has implemented all the stable specifications in the Java programming language and donated the source code to the openEHR foundation. It was adopted as the openEHR Java Reference Implementation in March 2005 and released under open source licenses. This encourages early EHR implementation projects around the world and a number of groups have already started to use this code. The early Java implementation experience has also led to the publication of the openEHR Java Implementation Technology Specification. A number of design changes to the specifications and important minor corrections have been directly initiated by the implementation project over the last two years. The Java Implementation has been important for the validation and improvement of the openEHR design specifications and provides building blocks for future EHR systems.

Finding Resolution for the Responsible Transparency of Economic Models in Health and Medicine.

PubMed

Padula, William V; McQueen, Robert Brett; Pronovost, Peter J

2017-11-01

The Second Panel on Cost-Effectiveness in Health and Medicine recommendations for conduct, methodological practices, and reporting of cost-effectiveness analyses has a number of questions unanswered with respect to the implementation of transparent, open source code interface for economic models. The possibility of making economic model source code could be positive and progressive for the field; however, several unintended consequences of this system should be first considered before complete implementation of this model. First, there is the concern regarding intellectual property rights that modelers have to their analyses. Second, the open source code could make analyses more accessible to inexperienced modelers, leading to inaccurate or misinterpreted results. We propose several resolutions to these concerns. The field should establish a licensing system of open source code such that the model originators maintain control of the code use and grant permissions to other investigators who wish to use it. The field should also be more forthcoming towards the teaching of cost-effectiveness analysis in medical and health services education so that providers and other professionals are familiar with economic modeling and able to conduct analyses with open source code. These types of unintended consequences need to be fully considered before the field's preparedness to move forward into an era of model transparency with open source code.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

eMZed: an open source framework in Python for rapid and interactive development of LC/MS data analysis workflows.

PubMed

Kiefer, Patrick; Schmitt, Uwe; Vorholt, Julia A

2013-04-01

The Python-based, open-source eMZed framework was developed for mass spectrometry (MS) users to create tailored workflows for liquid chromatography (LC)/MS data analysis. The goal was to establish a unique framework with comprehensive basic functionalities that are easy to apply and allow for the extension and modification of the framework in a straightforward manner. eMZed supports the iterative development and prototyping of individual evaluation strategies by providing a computing environment and tools for inspecting and modifying underlying LC/MS data. The framework specifically addresses non-expert programmers, as it requires only basic knowledge of Python and relies largely on existing successful open-source software, e.g. OpenMS. The framework eMZed and its documentation are freely available at http://emzed.biol.ethz.ch/. eMZed is published under the GPL 3.0 license, and an online discussion group is available at https://groups.google.com/group/emzed-users. Supplementary data are available at Bioinformatics online.

Adopting Open Source Software to Address Software Risks during the Scientific Data Life Cycle

NASA Astrophysics Data System (ADS)

Vinay, S.; Downs, R. R.

2012-12-01

Software enables the creation, management, storage, distribution, discovery, and use of scientific data throughout the data lifecycle. However, the capabilities offered by software also present risks for the stewardship of scientific data, since future access to digital data is dependent on the use of software. From operating systems to applications for analyzing data, the dependence of data on software presents challenges for the stewardship of scientific data. Adopting open source software provides opportunities to address some of the proprietary risks of data dependence on software. For example, in some cases, open source software can be deployed to avoid licensing restrictions for using, modifying, and transferring proprietary software. The availability of the source code of open source software also enables the inclusion of modifications, which may be contributed by various community members who are addressing similar issues. Likewise, an active community that is maintaining open source software can be a valuable source of help, providing an opportunity to collaborate to address common issues facing adopters. As part of the effort to meet the challenges of software dependence for scientific data stewardship, risks from software dependence have been identified that exist during various times of the data lifecycle. The identification of these risks should enable the development of plans for mitigating software dependencies, where applicable, using open source software, and to improve understanding of software dependency risks for scientific data and how they can be reduced during the data life cycle.

CosmoQuest Transient Tracker: Opensource Photometry & Astrometry software

NASA Astrophysics Data System (ADS)

Myers, Joseph L.; Lehan, Cory; Gay, Pamela; Richardson, Matthew; CosmoQuest Team

2018-01-01

CosmoQuest is moving from online citizen science, to observational astronomy with the creation of Transient Trackers. This open source software is designed to identify asteroids and other transient/variable objects in image sets. Transient Tracker’s features in final form will include: astrometric and photometric solutions, identification of moving/transient objects, identification of variable objects, and lightcurve analysis. In this poster we present our initial, v0.1 release and seek community input.This software builds on the existing NIH funded ImageJ libraries. Creation of this suite of opensource image manipulation routines is lead by Wayne Rasband and is released primarily under the MIT license. In this release, we are building on these libraries to add source identification for point / point-like sources, and to do astrometry. Our materials released under the Apache 2.0 license on github (http://github.com/CosmoQuestTeam) and documentation can be found at http://cosmoquest.org/TransientTracker.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

The state and profile of open source software projects in health and medical informatics.

PubMed

Janamanchi, Balaji; Katsamakas, Evangelos; Raghupathi, Wullianallur; Gao, Wei

2009-07-01

Little has been published about the application profiles and development patterns of open source software (OSS) in health and medical informatics. This study explores these issues with an analysis of health and medical informatics related OSS projects on SourceForge, a large repository of open source projects. A search was conducted on the SourceForge website during the period from May 1 to 15, 2007, to identify health and medical informatics OSS projects. This search resulted in a sample of 174 projects. A Java-based parser was written to extract data for several of the key variables of each project. Several visually descriptive statistics were generated to analyze the profiles of the OSS projects. Many of the projects have sponsors, implying a growing interest in OSS among organizations. Sponsorship, we discovered, has a significant impact on project success metrics. Nearly two-thirds of the projects have a restrictive license type. Restrictive licensing may indicate tighter control over the development process. Our sample includes a wide range of projects that are at various stages of development (status). Projects targeted towards the advanced end user are primarily focused on bio-informatics, data formats, database and medical science applications. We conclude that there exists an active and thriving OSS development community that is focusing on health and medical informatics. A wide range of OSS applications are in development, from bio-informatics to hospital information systems. A profile of OSS in health and medical informatics emerges that is distinct and unique to the health care field. Future research can focus on OSS acceptance and diffusion and impact on cost, efficiency and quality of health care.

Free Software and Free Textbooks

ERIC Educational Resources Information Center

Takhteyev, Yuri

2012-01-01

Some of the world's best and most sophisticated software is distributed today under "free" or "open source" licenses, which allow the recipients of such software to use, modify, and share it without paying royalties or asking for permissions. If this works for software, could it also work for educational resources, such as books? The economics of…

It's Time to Consider Open Source Software

ERIC Educational Resources Information Center

Pfaffman, Jay

2007-01-01

In 1985 Richard Stallman, a computer programmer, released "The GNU Manifesto" in which he proclaimed a golden rule: One must share computer programs. Software vendors required him to agree to license agreements that forbade sharing programs with others, but he refused to "break solidarity" with other computer users whom he assumed also wanted to…

Graph-based word sense disambiguation of biomedical documents.

PubMed

Agirre, Eneko; Soroa, Aitor; Stevenson, Mark

2010-11-15

Word Sense Disambiguation (WSD), automatically identifying the meaning of ambiguous words in context, is an important stage of text processing. This article presents a graph-based approach to WSD in the biomedical domain. The method is unsupervised and does not require any labeled training data. It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph. A state-of-the-art algorithm, Personalized PageRank, is used to perform WSD. When evaluated on the NLM-WSD dataset, the algorithm outperforms other methods that rely on the UMLS Metathesaurus alone. The WSD system is open source licensed and available from http://ixa2.si.ehu.es/ukb/. The UMLS, MetaMap program and NLM-WSD corpus are available from the National Library of Medicine https://www.nlm.nih.gov/research/umls/, http://mmtx.nlm.nih.gov and http://wsd.nlm.nih.gov. Software to convert the NLM-WSD corpus into a format that can be used by our WSD system is available from http://www.dcs.shef.ac.uk/∼marks/biomedical_wsd under open source license.

The Impact of Open Licensing on the Early Reader Ecosystem

ERIC Educational Resources Information Center

Butcher, Neil; Hoosen, Sarah; Levey, Lisbeth; Moore, Derek

2016-01-01

The Impact of Open Licensing on the Early Reader Ecosystem examines how to use open licensing to promote quality learning resources for young children that are relevant and interesting. Research in early reading tends to focus on traditional publishing value and supply chains, without taking much consideration of new approaches and solutions…

SmartR: an open-source platform for interactive visual analytics for translational research data

PubMed Central

Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

2017-01-01

Abstract Summary: In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR, a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. Availability and Implementation: The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR. Contact: reinhard.schneider@uni.lu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28334291

SmartR: an open-source platform for interactive visual analytics for translational research data.

PubMed

Herzinger, Sascha; Gu, Wei; Satagopam, Venkata; Eifes, Serge; Rege, Kavita; Barbosa-Silva, Adriano; Schneider, Reinhard

2017-07-15

In translational research, efficient knowledge exchange between the different fields of expertise is crucial. An open platform that is capable of storing a multitude of data types such as clinical, pre-clinical or OMICS data combined with strong visual analytical capabilities will significantly accelerate the scientific progress by making data more accessible and hypothesis generation easier. The open data warehouse tranSMART is capable of storing a variety of data types and has a growing user community including both academic institutions and pharmaceutical companies. tranSMART, however, currently lacks interactive and dynamic visual analytics and does not permit any post-processing interaction or exploration. For this reason, we developed SmartR , a plugin for tranSMART, that equips the platform not only with several dynamic visual analytical workflows, but also provides its own framework for the addition of new custom workflows. Modern web technologies such as D3.js or AngularJS were used to build a set of standard visualizations that were heavily improved with dynamic elements. The source code is licensed under the Apache 2.0 License and is freely available on GitHub: https://github.com/transmart/SmartR . reinhard.schneider@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.

PubMed

Barker, Michael S; Dlugosch, Katrina M; Reddy, A Chaitanya C; Amyotte, Sarah N; Rieseberg, Loren H

2009-02-15

Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences. SCARF is freely available at http://msbarker.com/software.htm, and is released under the open source GPLv3 license (http://www.opensource.org/licenses/gpl-3.0.html.

Building CHAOS: An Operating System for Livermore Linux Clusters

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

Garlick, J E; Dunlap, C M

2003-02-21

The Livermore Computing (LC) Linux Integration and Development Project (the Linux Project) produces and supports the Clustered High Availability Operating System (CHAOS), a cluster operating environment based on Red Hat Linux. Each CHAOS release begins with a set of requirements and ends with a formally tested, packaged, and documented release suitable for use on LC's production Linux clusters. One characteristic of CHAOS is that component software packages come from different sources under varying degrees of project control. Some are developed by the Linux Project, some are developed by other LC projects, some are external open source projects, and some aremore » commercial software packages. A challenge to the Linux Project is to adhere to release schedules and testing disciplines in a diverse, highly decentralized development environment. Communication channels are maintained for externally developed packages in order to obtain support, influence development decisions, and coordinate/understand release schedules. The Linux Project embraces open source by releasing locally developed packages under open source license, by collaborating with open source projects where mutually beneficial, and by preferring open source over proprietary software. Project members generally use open source development tools. The Linux Project requires system administrators and developers to work together to resolve problems that arise in production. This tight coupling of production and development is a key strategy for making a product that directly addresses LC's production requirements. It is another challenge to balance support and development activities in such a way that one does not overwhelm the other.« less

Unipro UGENE: a unified bioinformatics toolkit.

PubMed

Okonechnikov, Konstantin; Golosova, Olga; Fursov, Mikhail

2012-04-15

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

mdFoam+: Advanced molecular dynamics in OpenFOAM

NASA Astrophysics Data System (ADS)

Longshaw, S. M.; Borg, M. K.; Ramisetti, S. B.; Zhang, J.; Lockerby, D. A.; Emerson, D. R.; Reese, J. M.

2018-03-01

This paper introduces mdFoam+, which is an MPI parallelised molecular dynamics (MD) solver implemented entirely within the OpenFOAM software framework. It is open-source and released under the same GNU General Public License (GPL) as OpenFOAM. The source code is released as a publicly open software repository that includes detailed documentation and tutorial cases. Since mdFoam+ is designed entirely within the OpenFOAM C++ object-oriented framework, it inherits a number of key features. The code is designed for extensibility and flexibility, so it is aimed first and foremost as an MD research tool, in which new models and test cases can be developed and tested rapidly. Implementing mdFoam+ in OpenFOAM also enables easier development of hybrid methods that couple MD with continuum-based solvers. Setting up MD cases follows the standard OpenFOAM format, as mdFoam+ also relies upon the OpenFOAM dictionary-based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of an MD simulation is not typical of most OpenFOAM applications. Results show that mdFoam+ compares well to another well-known MD code (e.g. LAMMPS) in terms of benchmark problems, although it also has additional functionality that does not exist in other open-source MD codes.

Performing Quantitative Imaging Acquisition, Analysis and Visualization Using the Best of Open Source and Commercial Software Solutions.

PubMed

Shenoy, Shailesh M

2016-07-01

A challenge in any imaging laboratory, especially one that uses modern techniques, is to achieve a sustainable and productive balance between using open source and commercial software to perform quantitative image acquisition, analysis and visualization. In addition to considering the expense of software licensing, one must consider factors such as the quality and usefulness of the software's support, training and documentation. Also, one must consider the reproducibility with which multiple people generate results using the same software to perform the same analysis, how one may distribute their methods to the community using the software and the potential for achieving automation to improve productivity.

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets.

PubMed

Maguire, Eamonn; González-Beltrán, Alejandra; Whetzel, Patricia L; Sansone, Susanna-Assunta; Rocca-Serra, Philippe

2013-02-15

Data collection in spreadsheets is ubiquitous, but current solutions lack support for collaborative semantic annotation that would promote shared and interdisciplinary annotation practices, supporting geographically distributed players. OntoMaton is an open source solution that brings ontology lookup and tagging capabilities into a cloud-based collaborative editing environment, harnessing Google Spreadsheets and the NCBO Web services. It is a general purpose, format-agnostic tool that may serve as a component of the ISA software suite. OntoMaton can also be used to assist the ontology development process. OntoMaton is freely available from Google widgets under the CPAL open source license; documentation and examples at: https://github.com/ISA-tools/OntoMaton.

The Bioperl Toolkit: Perl Modules for the Life Sciences

PubMed Central

Stajich, Jason E.; Block, David; Boulez, Kris; Brenner, Steven E.; Chervitz, Stephen A.; Dagdigian, Chris; Fuellen, Georg; Gilbert, James G.R.; Korf, Ian; Lapp, Hilmar; Lehväslaiho, Heikki; Matsalla, Chad; Mungall, Chris J.; Osborne, Brian I.; Pocock, Matthew R.; Schattner, Peter; Senger, Martin; Stein, Lincoln D.; Stupka, Elia; Wilkinson, Mark D.; Birney, Ewan

2002-01-01

The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort. [Supplemental material is available online at www.genome.org. Bioperl is available as open-source software free of charge and is licensed under the Perl Artistic License (http://www.perl.com/pub/a/language/misc/Artistic.html). It is available for download at http://www.bioperl.org. Support inquiries should be addressed to bioperl-l@bioperl.org.] PMID:12368254

Global health equity in United Kingdom university research: a landscape of current policies and practices.

PubMed

Gotham, Dzintars; Meldrum, Jonathan; Nageshwaran, Vaitehi; Counts, Christopher; Kumari, Nina; Martin, Manuel; Beattie, Ben; Post, Nathan

2016-10-10

Universities are significant contributors to research and technologies in health; however, the health needs of the world's poor are historically neglected in research. Medical discoveries are frequently licensed exclusively to one producer, allowing a monopoly and inequitable pricing. Similarly, research is often published in ways that make it inaccessible. Universities can adopt policies and practices to overcome neglect and ensure equitable access to research and its products. For 25 United Kingdom universities, data on health research funding were extracted from the top five United Kingdom funders' databases and coded as research on neglected diseases (NDs) and/or health in low- and lower-middle-income countries (hLLMIC). Data on intellectual property licensing policies and practices and open-access policies were obtained from publicly available sources and by direct contact with universities. Proportions of research articles published as open-access were extracted from PubMed and PubMed Central. Across United Kingdom universities, the median proportion of 2011-2014 health research funds attributable to ND research was 2.6% and for hLLMIC it was 1.7%. Overall, 79% of all ND funding and 74% of hLLMIC funding were granted to the top four institutions within each category. Seven institutions had policies to ensure that technologies developed from their research are affordable globally. Mostly, universities licensed their inventions to third parties in a way that confers monopoly rights. Fifteen institutions had an institutional open-access publishing policy; three had an institutional open-access publishing fund. The proportion of health-related articles with full-text versions freely available online ranged from 58% to 100% across universities (2012-2013); 23% of articles also had a creative commons CC-BY license. There is wide variation in the amount of global health research undertaken by United Kingdom universities, with a large proportion of total research funding awarded to a few institutions. To meet a level of research commitment in line with the global burden of disease, most universities should seek to expand their research activity. Most universities do not license their intellectual property in a way that is likely to encourage access in resource-poor settings, and lack policies to do so. The majority of recent research publications are published open-access, but not as gold standard (CC-BY) open-access.

QuTiP: An open-source Python framework for the dynamics of open quantum systems

NASA Astrophysics Data System (ADS)

Johansson, J. R.; Nation, P. D.; Nori, Franco

2012-08-01

We present an object-oriented open-source framework for solving the dynamics of open quantum systems written in Python. Arbitrary Hamiltonians, including time-dependent systems, may be built up from operators and states defined by a quantum object class, and then passed on to a choice of master equation or Monte Carlo solvers. We give an overview of the basic structure for the framework before detailing the numerical simulation of open system dynamics. Several examples are given to illustrate the build up to a complete calculation. Finally, we measure the performance of our library against that of current implementations. The framework described here is particularly well suited to the fields of quantum optics, superconducting circuit devices, nanomechanics, and trapped ions, while also being ideal for use in classroom instruction. Catalogue identifier: AEMB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEMB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 16 482 No. of bytes in distributed program, including test data, etc.: 213 438 Distribution format: tar.gz Programming language: Python Computer: i386, x86-64 Operating system: Linux, Mac OSX, Windows RAM: 2+ Gigabytes Classification: 7 External routines: NumPy (http://numpy.scipy.org/), SciPy (http://www.scipy.org/), Matplotlib (http://matplotlib.sourceforge.net/) Nature of problem: Dynamics of open quantum systems. Solution method: Numerical solutions to Lindblad master equation or Monte Carlo wave function method. Restrictions: Problems must meet the criteria for using the master equation in Lindblad form. Running time: A few seconds up to several tens of minutes, depending on size of underlying Hilbert space.

Effects of Taxi Regulatory Revision in Seattle, Washington

DOT National Transportation Integrated Search

1983-05-01

In May 1979 the City of Seattle enacted license code revisions affecting taxicabs. Entry is opened to both fleets and independents and there is no limit on total licenses or the number of licenses a single operator may obtain. Open rate setting repla...

#GoOpen District Launch Packet

ERIC Educational Resources Information Center

Office of Educational Technology, US Department of Education, 2016

2016-01-01

Across the country, districts are choosing to #GoOpen and transitioning to the use of openly licensed educational resources to improve student learning in their schools. Openly licensed educational resources enable districts to reallocate significant funds currently spent on inflexible, static learning materials to resources and activities that…

Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action.

PubMed

Wallner, Jürgen; Hochegger, Kerstin; Chen, Xiaojun; Mischak, Irene; Reinbacher, Knut; Pau, Mauro; Zrnc, Tomislav; Schwenzer-Zimmerer, Katja; Zemann, Wolfgang; Schmalstieg, Dieter; Egger, Jan

2018-01-01

Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However-due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score and the Hausdorff distance. Overall semi-automatic GrowCut segmentation times were about one minute. Mean Dice Score values of over 85% and Hausdorff Distances below 33.5 voxel could be achieved between the algorithmic GrowCut-based segmentations and the manual generated ground truth schemes. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the two groups. Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Due to an open-source basis the used method could be further developed by other groups or specialists. Systematic comparisons to other segmentation approaches or with a greater data amount are areas of future works.

CellAnimation: an open source MATLAB framework for microscopy assays.

PubMed

Georgescu, Walter; Wikswo, John P; Quaranta, Vito

2012-01-01

Advances in microscopy technology have led to the creation of high-throughput microscopes that are capable of generating several hundred gigabytes of images in a few days. Analyzing such wealth of data manually is nearly impossible and requires an automated approach. There are at present a number of open-source and commercial software packages that allow the user to apply algorithms of different degrees of sophistication to the images and extract desired metrics. However, the types of metrics that can be extracted are severely limited by the specific image processing algorithms that the application implements, and by the expertise of the user. In most commercial software, code unavailability prevents implementation by the end user of newly developed algorithms better suited for a particular type of imaging assay. While it is possible to implement new algorithms in open-source software, rewiring an image processing application requires a high degree of expertise. To obviate these limitations, we have developed an open-source high-throughput application that allows implementation of different biological assays such as cell tracking or ancestry recording, through the use of small, relatively simple image processing modules connected into sophisticated imaging pipelines. By connecting modules, non-expert users can apply the particular combination of well-established and novel algorithms developed by us and others that are best suited for each individual assay type. In addition, our data exploration and visualization modules make it easy to discover or select specific cell phenotypes from a heterogeneous population. CellAnimation is distributed under the Creative Commons Attribution-NonCommercial 3.0 Unported license (http://creativecommons.org/licenses/by-nc/3.0/). CellAnimationsource code and documentation may be downloaded from www.vanderbilt.edu/viibre/software/documents/CellAnimation.zip. Sample data are available at www.vanderbilt.edu/viibre/software/documents/movies.zip. walter.georgescu@vanderbilt.edu Supplementary data available at Bioinformatics online.

Taxi Regulatory Revision in Seattle, Washington : Background and Implementation

DOT National Transportation Integrated Search

1980-01-01

In May 1979 the City of Seattle enacted license code revisions affecting taxicabs. Entry is opened to both fleets and independents and there is no limit on total licenses or the number of licenses a single operator may obtain. Open rate setting repla...

openPSTD: The open source pseudospectral time-domain method for acoustic propagation

NASA Astrophysics Data System (ADS)

Hornikx, Maarten; Krijnen, Thomas; van Harten, Louis

2016-06-01

An open source implementation of the Fourier pseudospectral time-domain (PSTD) method for computing the propagation of sound is presented, which is geared towards applications in the built environment. Being a wave-based method, PSTD captures phenomena like diffraction, but maintains efficiency in processing time and memory usage as it allows to spatially sample close to the Nyquist criterion, thus keeping both the required spatial and temporal resolution coarse. In the implementation it has been opted to model the physical geometry as a composition of rectangular two-dimensional subdomains, hence initially restricting the implementation to orthogonal and two-dimensional situations. The strategy of using subdomains divides the problem domain into local subsets, which enables the simulation software to be built according to Object-Oriented Programming best practices and allows room for further computational parallelization. The software is built using the open source components, Blender, Numpy and Python, and has been published under an open source license itself as well. For accelerating the software, an option has been included to accelerate the calculations by a partial implementation of the code on the Graphical Processing Unit (GPU), which increases the throughput by up to fifteen times. The details of the implementation are reported, as well as the accuracy of the code.

SimVascular: An Open Source Pipeline for Cardiovascular Simulation.

PubMed

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

2017-03-01

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

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

pyAudioAnalysis: An Open-Source Python Library for Audio Signal Analysis.

PubMed

Giannakopoulos, Theodoros

2015-01-01

Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal analysis (e.g. audio-visual analysis of online videos for content-based recommendation), etc. This paper presents pyAudioAnalysis, an open-source Python library that provides a wide range of audio analysis procedures including: feature extraction, classification of audio signals, supervised and unsupervised segmentation and content visualization. pyAudioAnalysis is licensed under the Apache License and is available at GitHub (https://github.com/tyiannak/pyAudioAnalysis/). Here we present the theoretical background behind the wide range of the implemented methodologies, along with evaluation metrics for some of the methods. pyAudioAnalysis has been already used in several audio analysis research applications: smart-home functionalities through audio event detection, speech emotion recognition, depression classification based on audio-visual features, music segmentation, multimodal content-based movie recommendation and health applications (e.g. monitoring eating habits). The feedback provided from all these particular audio applications has led to practical enhancement of the library.

pyAudioAnalysis: An Open-Source Python Library for Audio Signal Analysis

PubMed Central

Giannakopoulos, Theodoros

2015-01-01

Audio information plays a rather important role in the increasing digital content that is available today, resulting in a need for methodologies that automatically analyze such content: audio event recognition for home automations and surveillance systems, speech recognition, music information retrieval, multimodal analysis (e.g. audio-visual analysis of online videos for content-based recommendation), etc. This paper presents pyAudioAnalysis, an open-source Python library that provides a wide range of audio analysis procedures including: feature extraction, classification of audio signals, supervised and unsupervised segmentation and content visualization. pyAudioAnalysis is licensed under the Apache License and is available at GitHub (https://github.com/tyiannak/pyAudioAnalysis/). Here we present the theoretical background behind the wide range of the implemented methodologies, along with evaluation metrics for some of the methods. pyAudioAnalysis has been already used in several audio analysis research applications: smart-home functionalities through audio event detection, speech emotion recognition, depression classification based on audio-visual features, music segmentation, multimodal content-based movie recommendation and health applications (e.g. monitoring eating habits). The feedback provided from all these particular audio applications has led to practical enhancement of the library. PMID:26656189

Swan: A tool for porting CUDA programs to OpenCL

NASA Astrophysics Data System (ADS)

Harvey, M. J.; De Fabritiis, G.

2011-04-01

The use of modern, high-performance graphical processing units (GPUs) for acceleration of scientific computation has been widely reported. The majority of this work has used the CUDA programming model supported exclusively by GPUs manufactured by NVIDIA. An industry standardisation effort has recently produced the OpenCL specification for GPU programming. This offers the benefits of hardware-independence and reduced dependence on proprietary tool-chains. Here we describe a source-to-source translation tool, "Swan" for facilitating the conversion of an existing CUDA code to use the OpenCL model, as a means to aid programmers experienced with CUDA in evaluating OpenCL and alternative hardware. While the performance of equivalent OpenCL and CUDA code on fixed hardware should be comparable, we find that a real-world CUDA application ported to OpenCL exhibits an overall 50% increase in runtime, a reduction in performance attributable to the immaturity of contemporary compilers. The ported application is shown to have platform independence, running on both NVIDIA and AMD GPUs without modification. We conclude that OpenCL is a viable platform for developing portable GPU applications but that the more mature CUDA tools continue to provide best performance. Program summaryProgram title: Swan Catalogue identifier: AEIH_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIH_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU Public License version 2 No. of lines in distributed program, including test data, etc.: 17 736 No. of bytes in distributed program, including test data, etc.: 131 177 Distribution format: tar.gz Programming language: C Computer: PC Operating system: Linux RAM: 256 Mbytes Classification: 6.5 External routines: NVIDIA CUDA, OpenCL Nature of problem: Graphical Processing Units (GPUs) from NVIDIA are preferentially programed with the proprietary CUDA programming toolkit. An alternative programming model promoted as an industry standard, OpenCL, provides similar capabilities to CUDA and is also supported on non-NVIDIA hardware (including multicore ×86 CPUs, AMD GPUs and IBM Cell processors). The adaptation of a program from CUDA to OpenCL is relatively straightforward but laborious. The Swan tool facilitates this conversion. Solution method:Swan performs a translation of CUDA kernel source code into an OpenCL equivalent. It also generates the C source code for entry point functions, simplifying kernel invocation from the host program. A concise host-side API abstracts the CUDA and OpenCL APIs. A program adapted to use Swan has no dependency on the CUDA compiler for the host-side program. The converted program may be built for either CUDA or OpenCL, with the selection made at compile time. Restrictions: No support for CUDA C++ features Running time: Nominal

10 CFR 40.21 - General license to receive title to source or byproduct material.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license to receive title to source or byproduct material. 40.21 Section 40.21 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.21 General license to receive title to source or byproduct material. A general...

jTraML: an open source Java API for TraML, the PSI standard for sharing SRM transitions.

PubMed

Helsens, Kenny; Brusniak, Mi-Youn; Deutsch, Eric; Moritz, Robert L; Martens, Lennart

2011-11-04

We here present jTraML, a Java API for the Proteomics Standards Initiative TraML data standard. The library provides fully functional classes for all elements specified in the TraML XSD document, as well as convenient methods to construct controlled vocabulary-based instances required to define SRM transitions. The use of jTraML is demonstrated via a two-way conversion tool between TraML documents and vendor specific files, facilitating the adoption process of this new community standard. The library is released as open source under the permissive Apache2 license and can be downloaded from http://jtraml.googlecode.com . TraML files can also be converted online at http://iomics.ugent.be/jtraml .

Tatool: a Java-based open-source programming framework for psychological studies.

PubMed

von Bastian, Claudia C; Locher, André; Ruflin, Michael

2013-03-01

Tatool (Training and Testing Tool) was developed to assist researchers with programming training software, experiments, and questionnaires. Tatool is Java-based, and thus is a platform-independent and object-oriented framework. The architecture was designed to meet the requirements of experimental designs and provides a large number of predefined functions that are useful in psychological studies. Tatool comprises features crucial for training studies (e.g., configurable training schedules, adaptive training algorithms, and individual training statistics) and allows for running studies online via Java Web Start. The accompanying "Tatool Online" platform provides the possibility to manage studies and participants' data easily with a Web-based interface. Tatool is published open source under the GNU Lesser General Public License, and is available at www.tatool.ch.

pyNS: an open-source framework for 0D haemodynamic modelling.

PubMed

Manini, Simone; Antiga, Luca; Botti, Lorenzo; Remuzzi, Andrea

2015-06-01

A number of computational approaches have been proposed for the simulation of haemodynamics and vascular wall dynamics in complex vascular networks. Among them, 0D pulse wave propagation methods allow to efficiently model flow and pressure distributions and wall displacements throughout vascular networks at low computational costs. Although several techniques are documented in literature, the availability of open-source computational tools is still limited. We here present python Network Solver, a modular solver framework for 0D problems released under a BSD license as part of the archToolkit ( http://archtk.github.com ). As an application, we describe patient-specific models of the systemic circulation and detailed upper extremity for use in the prediction of maturation after surgical creation of vascular access for haemodialysis.

LSST communications middleware implementation

NASA Astrophysics Data System (ADS)

Mills, Dave; Schumacher, German; Lotz, Paul

2016-07-01

The LSST communications middleware is based on a set of software abstractions; which provide standard interfaces for common communications services. The observatory requires communication between diverse subsystems, implemented by different contractors, and comprehensive archiving of subsystem status data. The Service Abstraction Layer (SAL) is implemented using open source packages that implement open standards of DDS (Data Distribution Service1) for data communication, and SQL (Standard Query Language) for database access. For every subsystem, abstractions for each of the Telemetry datastreams, along with Command/Response and Events, have been agreed with the appropriate component vendor (such as Dome, TMA, Hexapod), and captured in ICD's (Interface Control Documents).The OpenSplice (Prismtech) Community Edition of DDS provides an LGPL licensed distribution which may be freely redistributed. The availability of the full source code provides assurances that the project will be able to maintain it over the full 10 year survey, independent of the fortunes of the original providers.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

PubMed

Cock, Peter J A; Antao, Tiago; Chang, Jeffrey T; Chapman, Brad A; Cox, Cymon J; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J L

2009-06-01

The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Biopython is freely available, with documentation and source code at (www.biopython.org) under the Biopython license.

10 CFR 40.20 - Types of licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Types of licenses. 40.20 Section 40.20 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.20 Types of licenses. (a) Licenses for source material and byproduct material are of two types: general and specific. Licenses for...

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

NASA Astrophysics Data System (ADS)

Ames, D. P.

2013-12-01

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

Journal of Open Source Software (JOSS): design and first-year review

NASA Astrophysics Data System (ADS)

Smith, Arfon M.

2018-01-01

JOSS is a free and open-access journal that publishes articles describing research software across all disciplines. It has the dual goals of improving the quality of the software submitted and providing a mechanism for research software developers to receive credit. While designed to work within the current merit system of science, JOSS addresses the dearth of rewards for key contributions to science made in the form of software. JOSS publishes articles that encapsulate scholarship contained in the software itself, and its rigorous peer review targets the software components: functionality, documentation, tests, continuous integration, and the license. A JOSS article contains an abstract describing the purpose and functionality of the software, references, and a link to the software archive. JOSS published more than 100 articles in its first year, many from the scientific python ecosystem (including a number of articles related to astronomy and astrophysics). JOSS is a sponsored project of the nonprofit organization NumFOCUS and is an affiliate of the Open Source Initiative.In this presentation, I'll describes the motivation, design, and progress of the Journal of Open Source Software (JOSS) and how it compares to other avenues for publishing research software in astronomy.

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

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

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states frommore » PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of changes subsurface electrical conductivity, in both the saturated and unsaturated zones, arising from water table changes and from river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev .« less

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

NASA Astrophysics Data System (ADS)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

2017-02-01

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev.

Unipept web services for metaproteomics analysis.

PubMed

Mesuere, Bart; Willems, Toon; Van der Jeugt, Felix; Devreese, Bart; Vandamme, Peter; Dawyndt, Peter

2016-06-01

Unipept is an open source web application that is designed for metaproteomics analysis with a focus on interactive datavisualization. It is underpinned by a fast index built from UniProtKB and the NCBI taxonomy that enables quick retrieval of all UniProt entries in which a given tryptic peptide occurs. Unipept version 2.4 introduced web services that provide programmatic access to the metaproteomics analysis features. This enables integration of Unipept functionality in custom applications and data processing pipelines. The web services are freely available at http://api.unipept.ugent.be and are open sourced under the MIT license. Unipept@ugent.be Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Drekar v.2.0

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

Seefeldt, Ben; Sondak, David; Hensinger, David M.

Drekar is an application code that solves partial differential equations for fluids that can be optionally coupled to electromagnetics. Drekar solves low-mach compressible and incompressible computational fluid dynamics (CFD), compressible and incompressible resistive magnetohydrodynamics (MHD), and multiple species plasmas interacting with electromagnetic fields. Drekar discretization technology includes continuous and discontinuous finite element formulations, stabilized finite element formulations, mixed integration finite element bases (nodal, edge, face, volume) and an initial arbitrary Lagrangian Eulerian (ALE) capability. Drekar contains the implementation of the discretized physics and leverages the open source Trilinos project for both parallel solver capabilities and general finite element discretization tools.more » The code will be released open source under a BSD license. The code is used for fundamental research for simulation of fluids and plasmas on high performance computing environments.« less

10 CFR 40.31 - Application for specific licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Application for specific licenses. 40.31 Section 40.31 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL License Applications § 40.31... application for a source material license, other than a license exempted from part 170 of this chapter, shall...

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials.

PubMed

Giannozzi, Paolo; Baroni, Stefano; Bonini, Nicola; Calandra, Matteo; Car, Roberto; Cavazzoni, Carlo; Ceresoli, Davide; Chiarotti, Guido L; Cococcioni, Matteo; Dabo, Ismaila; Dal Corso, Andrea; de Gironcoli, Stefano; Fabris, Stefano; Fratesi, Guido; Gebauer, Ralph; Gerstmann, Uwe; Gougoussis, Christos; Kokalj, Anton; Lazzeri, Michele; Martin-Samos, Layla; Marzari, Nicola; Mauri, Francesco; Mazzarello, Riccardo; Paolini, Stefano; Pasquarello, Alfredo; Paulatto, Lorenzo; Sbraccia, Carlo; Scandolo, Sandro; Sclauzero, Gabriele; Seitsonen, Ari P; Smogunov, Alexander; Umari, Paolo; Wentzcovitch, Renata M

2009-09-30

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Design and implementation of an open source indexing solution for a large set of radiological reports and images.

PubMed

Voet, T; Devolder, P; Pynoo, B; Vercruysse, J; Duyck, P

2007-11-01

This paper hopes to share the insights we experienced during designing, building, and running an indexing solution for a large set of radiological reports and images in a production environment for more than 3 years. Several technical challenges were encountered and solved in the course of this project. One hundred four million words in 1.8 million radiological reports from 1989 to the present were indexed and became instantaneously searchable in a user-friendly fashion; the median query duration is only 31 ms. Currently, our highly tuned index holds 332,088 unique words in four languages. The indexing system is feature-rich and language-independent and allows for making complex queries. For research and training purposes it certainly is a valuable and convenient addition to our radiology informatics toolbox. Extended use of open-source technology dramatically reduced both implementation time and cost. All software we developed related to the indexing project has been made available to the open-source community covered by an unrestricted Berkeley Software Distribution-style license.

PAL: A Positional Astronomy Library

NASA Astrophysics Data System (ADS)

Jenness, T.; Berry, D. S.

2013-10-01

PAL is a new positional astronomy library written in C that attempts to retain the SLALIB API but is distributed with an open source GPL license. The library depends on the IAU SOFA library wherever a SOFA routine exists and uses the most recent nutation and precession models. Currently about 100 of the 200 SLALIB routines are available. Interfaces are also available from Perl and Python. PAL is freely available via github.

World Wind Tools Reveal Environmental Change

NASA Technical Reports Server (NTRS)

2012-01-01

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

Clinical evaluation of semi-automatic open-source algorithmic software segmentation of the mandibular bone: Practical feasibility and assessment of a new course of action

PubMed Central

Wallner, Jürgen; Hochegger, Kerstin; Chen, Xiaojun; Mischak, Irene; Reinbacher, Knut; Pau, Mauro; Zrnc, Tomislav; Schwenzer-Zimmerer, Katja; Zemann, Wolfgang; Schmalstieg, Dieter

2018-01-01

Introduction Computer assisted technologies based on algorithmic software segmentation are an increasing topic of interest in complex surgical cases. However—due to functional instability, time consuming software processes, personnel resources or licensed-based financial costs many segmentation processes are often outsourced from clinical centers to third parties and the industry. Therefore, the aim of this trial was to assess the practical feasibility of an easy available, functional stable and licensed-free segmentation approach to be used in the clinical practice. Material and methods In this retrospective, randomized, controlled trail the accuracy and accordance of the open-source based segmentation algorithm GrowCut was assessed through the comparison to the manually generated ground truth of the same anatomy using 10 CT lower jaw data-sets from the clinical routine. Assessment parameters were the segmentation time, the volume, the voxel number, the Dice Score and the Hausdorff distance. Results Overall semi-automatic GrowCut segmentation times were about one minute. Mean Dice Score values of over 85% and Hausdorff Distances below 33.5 voxel could be achieved between the algorithmic GrowCut-based segmentations and the manual generated ground truth schemes. Statistical differences between the assessment parameters were not significant (p<0.05) and correlation coefficients were close to the value one (r > 0.94) for any of the comparison made between the two groups. Discussion Complete functional stable and time saving segmentations with high accuracy and high positive correlation could be performed by the presented interactive open-source based approach. In the cranio-maxillofacial complex the used method could represent an algorithmic alternative for image-based segmentation in the clinical practice for e.g. surgical treatment planning or visualization of postoperative results and offers several advantages. Due to an open-source basis the used method could be further developed by other groups or specialists. Systematic comparisons to other segmentation approaches or with a greater data amount are areas of future works. PMID:29746490

Toward a legal framework that promotes and protects sex workers' health and human rights.

PubMed

Overs, Cheryl; Loff, Bebe

2013-06-14

Complex combinations of law, policy, and enforcement practices determine sex workers vulnerability to HIV and rights abuses. We identify "lack of recognition as a person before the law" as an important but undocumented barrier to accessing services and conclude that multi-faceted, setting-specific reform is needed-rather than a singular focus on decriminalization-if the health and human rights of sex workers are to be realized. Copyright © 2013 Overs and Loff. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Pharmer: efficient and exact pharmacophore search.

PubMed

Koes, David Ryan; Camacho, Carlos J

2011-06-27

Pharmacophore search is a key component of many drug discovery efforts. Pharmer is a new computational approach to pharmacophore search that scales with the breadth and complexity of the query, not the size of the compound library being screened. Two novel methods for organizing pharmacophore data, the Pharmer KDB-tree and Bloom fingerprints, enable Pharmer to perform an exact pharmacophore search of almost two million structures in less than a minute. In general, Pharmer is more than an order of magnitude faster than existing technologies. The complete source code is available under an open-source license at http://pharmer.sourceforge.net .

3Dmol.js: molecular visualization with WebGL.

PubMed

Rego, Nicholas; Koes, David

2015-04-15

3Dmol.js is a modern, object-oriented JavaScript library that uses the latest web technologies to provide interactive, hardware-accelerated three-dimensional representations of molecular data without the need to install browser plugins or Java. 3Dmol.js provides a full featured API for developers as well as a straightforward declarative interface that lets users easily share and embed molecular data in websites. 3Dmol.js is distributed under the permissive BSD open source license. Source code and documentation can be found at http://3Dmol.csb.pitt.edu dkoes@pitt.edu. © The Author 2014. Published by Oxford University Press.

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

PubMed

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

2004-09-24

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

Virtual Observer Controller (VOC) for Small Unit Infantry Laser Simulation Training

DTIC Science & Technology

2007-04-01

per-seat license when deployed. As a result, ViaVoice was abandoned early in development. Next, the SPHINX engine from Carnegie Mellon University was...examined. Sphinx is Java-based software, providing cross-platform functionality, and it is also free, open-source software. Software developers at...IST had experience using SPHINX , so it was initially selected it to be the VOC speech engine. After implementing a small portion of the VOC grammar

ReSEARCH: A Requirements Search Engine: Progress Report 2

DTIC Science & Technology

2008-09-01

and provides a convenient user interface for the search process. Ideally, the web application would be based on Tomcat, a free Java Servlet and JSP...Implementation issues Lucene Java is an Open Source project, available under the Apache License, which provides an accessible API for the development of...from the Apache Lucene website (Lucene- java Wiki , 2008). A search application developed with Lucene consists of the same two major com- ponents

Gaining Leverage Over Vendor Lock to Improve Acquisition Performance and Cost Efficiencies

DTIC Science & Technology

2014-04-30

Virginia Wydler, MITRE Corporation Open Systems Architecture License Rights: A New Era for the Public– Private Market -Place Nickolas Guertin, DASN RDT...if only one vendor can replace or upgrade those key components, that de facto monopolist may be able to exert excess negotiating leverage over...instead of sole source subcontractor procurement. The Program Office should have the prime vendor to provide a full market research data in accordance

FORM version 4.0

NASA Astrophysics Data System (ADS)

Kuipers, J.; Ueda, T.; Vermaseren, J. A. M.; Vollinga, J.

2013-05-01

We present version 4.0 of the symbolic manipulation system FORM. The most important new features are manipulation of rational polynomials and the factorization of expressions. Many other new functions and commands are also added; some of them are very general, while others are designed for building specific high level packages, such as one for Gröbner bases. New is also the checkpoint facility, that allows for periodic backups during long calculations. Finally, FORM 4.0 has become available as open source under the GNU General Public License version 3. Program summaryProgram title: FORM. Catalogue identifier: AEOT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOT_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 151599 No. of bytes in distributed program, including test data, etc.: 1 078 748 Distribution format: tar.gz Programming language: The FORM language. FORM itself is programmed in a mixture of C and C++. Computer: All. Operating system: UNIX, LINUX, Mac OS, Windows. Classification: 5. Nature of problem: FORM defines a symbolic manipulation language in which the emphasis lies on fast processing of very large formulas. It has been used successfully for many calculations in Quantum Field Theory and mathematics. In speed and size of formulas that can be handled it outperforms other systems typically by an order of magnitude. Special in this version: The version 4.0 contains many new features. Most important are factorization and rational arithmetic. The program has also become open source under the GPL. The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes. Solution method: See "Nature of Problem", above. Additional comments: NOTE: The code in CPC is for reference. You are encouraged to upload the most recent sources from www.nikhef.nl/form/formcvs.php because of frequent bug fixes.

Fast and accurate resonance assignment of small-to-large proteins by combining automated and manual approaches.

PubMed

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available.

Fast and Accurate Resonance Assignment of Small-to-Large Proteins by Combining Automated and Manual Approaches

PubMed Central

Niklasson, Markus; Ahlner, Alexandra; Andresen, Cecilia; Marsh, Joseph A.; Lundström, Patrik

2015-01-01

The process of resonance assignment is fundamental to most NMR studies of protein structure and dynamics. Unfortunately, the manual assignment of residues is tedious and time-consuming, and can represent a significant bottleneck for further characterization. Furthermore, while automated approaches have been developed, they are often limited in their accuracy, particularly for larger proteins. Here, we address this by introducing the software COMPASS, which, by combining automated resonance assignment with manual intervention, is able to achieve accuracy approaching that from manual assignments at greatly accelerated speeds. Moreover, by including the option to compensate for isotope shift effects in deuterated proteins, COMPASS is far more accurate for larger proteins than existing automated methods. COMPASS is an open-source project licensed under GNU General Public License and is available for download from http://www.liu.se/forskning/foass/tidigare-foass/patrik-lundstrom/software?l=en. Source code and binaries for Linux, Mac OS X and Microsoft Windows are available. PMID:25569628

Cluster-lensing: A Python Package for Galaxy Clusters and Miscentering

NASA Astrophysics Data System (ADS)

Ford, Jes; VanderPlas, Jake

2016-12-01

We describe a new open source package for calculating properties of galaxy clusters, including Navarro, Frenk, and White halo profiles with and without the effects of cluster miscentering. This pure-Python package, cluster-lensing, provides well-documented and easy-to-use classes and functions for calculating cluster scaling relations, including mass-richness and mass-concentration relations from the literature, as well as the surface mass density {{Σ }}(R) and differential surface mass density {{Δ }}{{Σ }}(R) profiles, probed by weak lensing magnification and shear. Galaxy cluster miscentering is especially a concern for stacked weak lensing shear studies of galaxy clusters, where offsets between the assumed and the true underlying matter distribution can lead to a significant bias in the mass estimates if not accounted for. This software has been developed and released in a public GitHub repository, and is licensed under the permissive MIT license. The cluster-lensing package is archived on Zenodo. Full documentation, source code, and installation instructions are available at http://jesford.github.io/cluster-lensing/.

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

PubMed

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

2015-06-01

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

Open-Source Assisted Laboratory Automation through Graphical User Interfaces and 3D Printers: Application to Equipment Hyphenation for Higher-Order Data Generation.

PubMed

Siano, Gabriel G; Montemurro, Milagros; Alcaráz, Mirta R; Goicoechea, Héctor C

2017-10-17

Higher-order data generation implies some automation challenges, which are mainly related to the hidden programming languages and electronic details of the equipment. When techniques and/or equipment hyphenation are the key to obtaining higher-order data, the required simultaneous control of them demands funds for new hardware, software, and licenses, in addition to very skilled operators. In this work, we present Design of Inputs-Outputs with Sikuli (DIOS), a free and open-source code program that provides a general framework for the design of automated experimental procedures without prior knowledge of programming or electronics. Basically, instruments and devices are considered as nodes in a network, and every node is associated both with physical and virtual inputs and outputs. Virtual components, such as graphical user interfaces (GUIs) of equipment, are handled by means of image recognition tools provided by Sikuli scripting language, while handling of their physical counterparts is achieved using an adapted open-source three-dimensional (3D) printer. Two previously reported experiments of our research group, related to fluorescence matrices derived from kinetics and high-performance liquid chromatography, were adapted to be carried out in a more automated fashion. Satisfactory results, in terms of analytical performance, were obtained. Similarly, advantages derived from open-source tools assistance could be appreciated, mainly in terms of lesser intervention of operators and cost savings.

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

NASA Astrophysics Data System (ADS)

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

2014-03-01

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

10 CFR 40.22 - Small quantities of source material.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Small quantities of source material. 40.22 Section 40.22 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.22 Small quantities of source material. (a) A general license is hereby issued authorizing commercial and industrial...

Monopoly Profits: The Market for Taxi Licenses.

ERIC Educational Resources Information Center

Keane, Michael

1981-01-01

Presents a case study dealing with open versus closed markets for use in college economics classes. Using the example of the taxi license monopoly in Dublin, Ireland, students examine how theories of supply and demand explain the characteristics of open and closed markets. (AM)

10 CFR 40.46 - Inalienability of licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Inalienability of licenses. 40.46 Section 40.46 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.46 Inalienability of... consent in writing. Transfer of Source Material ...

OpenDanubia - An integrated, modular simulation system to support regional water resource management

NASA Astrophysics Data System (ADS)

Muerth, M.; Waldmann, D.; Heinzeller, C.; Hennicker, R.; Mauser, W.

2012-04-01

The already completed, multi-disciplinary research project GLOWA-Danube has developed a regional scale, integrated modeling system, which was successfully applied on the 77,000 km2 Upper Danube basin to investigate the impact of Global Change on both the natural and anthropogenic water cycle. At the end of the last project phase, the integrated modeling system was transferred into the open source project OpenDanubia, which now provides both the core system as well as all major model components to the general public. First, this will enable decision makers from government, business and management to use OpenDanubia as a tool for proactive management of water resources in the context of global change. Secondly, the model framework to support integrated simulations and all simulation models developed for OpenDanubia in the scope of GLOWA-Danube are further available for future developments and research questions. OpenDanubia allows for the investigation of water-related scenarios considering different ecological and economic aspects to support both scientists and policy makers to design policies for sustainable environmental management. OpenDanubia is designed as a framework-based, distributed system. The model system couples spatially distributed physical and socio-economic process during run-time, taking into account their mutual influence. To simulate the potential future impacts of Global Change on agriculture, industrial production, water supply, households and tourism businesses, so-called deep actor models are implemented in OpenDanubia. All important water-related fluxes and storages in the natural environment are implemented in OpenDanubia as spatially explicit, process-based modules. This includes the land surface water and energy balance, dynamic plant water uptake, ground water recharge and flow as well as river routing and reservoirs. Although the complete system is relatively demanding on data requirements and hardware requirements, the modular structure and the generic core system (Core Framework, Actor Framework) allows the application in new regions and the selection of a reduced number of modules for simulation. As part of the Open Source Initiative in GLOWA-Danube (opendanubia.glowa-danube.de) a comprehensive documentation for the system installation was created and both the program code of the framework and of all major components is licensed under the GNU General Public License. In addition, some helpful programs and scripts necessary for the operation and processing of input and result data sets are provided.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

PubMed

Hart, Reece K; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A

2015-01-15

Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature

PubMed Central

Hart, Reece K.; Rico, Rudolph; Hare, Emily; Garcia, John; Westbrook, Jody; Fusaro, Vincent A.

2015-01-01

Summary: Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature guidelines endorsed by the Human Genome Variation Society (HGVS). Despite the widespread use of the standard, no freely available and comprehensive programming libraries are available. Here we report an open-source and easy-to-use Python library that facilitates the parsing, manipulation, formatting and validation of variants according to the HGVS specification. The current implementation focuses on the subset of the HGVS recommendations that precisely describe sequence-level variation relevant to the application of high-throughput sequencing to clinical diagnostics. Availability and implementation: The package is released under the Apache 2.0 open-source license. Source code, documentation and issue tracking are available at http://bitbucket.org/hgvs/hgvs/. Python packages are available at PyPI (https://pypi.python.org/pypi/hgvs). Contact: reecehart@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25273102

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

PubMed

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

2005-10-30

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

Continuous integration for concurrent MOOSE framework and application development on GitHub

DOE PAGES

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.; ...

2015-11-20

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Continuous integration for concurrent MOOSE framework and application development on GitHub

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

Slaughter, Andrew E.; Peterson, John W.; Gaston, Derek R.

For the past several years, Idaho National Laboratory’s MOOSE framework team has employed modern software engineering techniques (continuous integration, joint application/framework source code repos- itories, automated regression testing, etc.) in developing closed-source multiphysics simulation software (Gaston et al., Journal of Open Research Software vol. 2, article e10, 2014). In March 2014, the MOOSE framework was released under an open source license on GitHub, significantly expanding and diversifying the pool of current active and potential future contributors on the project. Despite this recent growth, the same philosophy of concurrent framework and application development continues to guide the project’s development roadmap. Severalmore » specific practices, including techniques for managing multiple repositories, conducting automated regression testing, and implementing a cascading build process are discussed in this short paper. Furthermore, special attention is given to describing the manner in which these practices naturally synergize with the GitHub API and GitHub-specific features such as issue tracking, Pull Requests, and project forks.« less

Nmrglue: an open source Python package for the analysis of multidimensional NMR data.

PubMed

Helmus, Jonathan J; Jaroniec, Christopher P

2013-04-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license.

Nmrglue: An Open Source Python Package for the Analysis of Multidimensional NMR Data

PubMed Central

Helmus, Jonathan J.; Jaroniec, Christopher P.

2013-01-01

Nmrglue, an open source Python package for working with multidimensional NMR data, is described. When used in combination with other Python scientific libraries, nmrglue provides a highly flexible and robust environment for spectral processing, analysis and visualization and includes a number of common utilities such as linear prediction, peak picking and lineshape fitting. The package also enables existing NMR software programs to be readily tied together, currently facilitating the reading, writing and conversion of data stored in Bruker, Agilent/Varian, NMRPipe, Sparky, SIMPSON, and Rowland NMR Toolkit file formats. In addition to standard applications, the versatility offered by nmrglue makes the package particularly suitable for tasks that include manipulating raw spectrometer data files, automated quantitative analysis of multidimensional NMR spectra with irregular lineshapes such as those frequently encountered in the context of biomacromolecular solid-state NMR, and rapid implementation and development of unconventional data processing methods such as covariance NMR and other non-Fourier approaches. Detailed documentation, install files and source code for nmrglue are freely available at http://nmrglue.com. The source code can be redistributed and modified under the New BSD license. PMID:23456039

An open source device for operant licking in rats.

PubMed

Longley, Matthew; Willis, Ethan L; Tay, Cindy X; Chen, Hao

2017-01-01

We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior.

An open source device for operant licking in rats

PubMed Central

Longley, Matthew; Willis, Ethan L.; Tay, Cindy X.

2017-01-01

We created an easy-to-use device for operant licking experiments and another device that records environmental variables. Both devices use the Raspberry Pi computer to obtain data from multiple input devices (e.g., radio frequency identification tag readers, touch and motion sensors, environmental sensors) and activate output devices (e.g., LED lights, syringe pumps) as needed. Data gathered from these devices are stored locally on the computer but can be automatically transferred to a remote server via a wireless network. We tested the operant device by training rats to obtain either sucrose or water under the control of a fixed ratio, a variable ratio, or a progressive ratio reinforcement schedule. The lick data demonstrated that the device has sufficient precision and time resolution to record the fast licking behavior of rats. Data from the environment monitoring device also showed reliable measurements. By providing the source code and 3D design under an open source license, we believe these examples will stimulate innovation in behavioral studies. The source code can be found at http://github.com/chen42/openbehavior. PMID:28229020

The LaueUtil toolkit for Laue photocrystallography. I. Rapid orientation matrix determination for intermediate-size-unit-cell Laue data

PubMed Central

Kalinowski, Jarosław A.; Makal, Anna; Coppens, Philip

2011-01-01

A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the experimental patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice with the corresponding pattern of a monochromatic data set on the same material. This technique is applied to the complete data set and thus eliminates problems often encountered when single frames with a limited number of peaks are to be used for orientation matrix determination. Application of the method to a series of Laue data sets on organometallic crystals is described. The corresponding program is available under a Mozilla Public License-like open-source license. PMID:22199400

Seismic Analysis Code (SAC): Development, porting, and maintenance within a legacy code base

NASA Astrophysics Data System (ADS)

Savage, B.; Snoke, J. A.

2017-12-01

The Seismic Analysis Code (SAC) is the result of toil of many developers over almost a 40-year history. Initially a Fortran-based code, it has undergone major transitions in underlying bit size from 16 to 32, in the 1980s, and 32 to 64 in 2009; as well as a change in language from Fortran to C in the late 1990s. Maintenance of SAC, the program and its associated libraries, have tracked changes in hardware and operating systems including the advent of Linux in the early 1990, the emergence and demise of Sun/Solaris, variants of OSX processors (PowerPC and x86), and Windows (Cygwin). Traces of these systems are still visible in source code and associated comments. A major concern while improving and maintaining a routinely used, legacy code is a fear of introducing bugs or inadvertently removing favorite features of long-time users. Prior to 2004, SAC was maintained and distributed by LLNL (Lawrence Livermore National Lab). In that year, the license was transferred from LLNL to IRIS (Incorporated Research Institutions for Seismology), but the license is not open source. However, there have been thousands of downloads a year of the package, either source code or binaries for specific system. Starting in 2004, the co-authors have maintained the SAC package for IRIS. In our updates, we fixed bugs, incorporated newly introduced seismic analysis procedures (such as EVALRESP), added new, accessible features (plotting and parsing), and improved the documentation (now in HTML and PDF formats). Moreover, we have added modern software engineering practices to the development of SAC including use of recent source control systems, high-level tests, and scripted, virtualized environments for rapid testing and building. Finally, a "sac-help" listserv (administered by IRIS) was setup for SAC-related issues and is the primary avenue for users seeking advice and reporting bugs. Attempts are always made to respond to issues and bugs in a timely fashion. For the past thirty-plus years, SAC files contained a fixed-length header. Time and distance-related values are stored in single precision, which has become a problem with the increase in desired precision for data compared to thirty years ago. A future goal is to address this precision problem, but in a backward compatible manner. We would also like to transition SAC to a more open source license.

Integrating Clinical Trial Imaging Data Resources Using Service-Oriented Architecture and Grid Computing

PubMed Central

Cladé, Thierry; Snyder, Joshua C.

2010-01-01

Clinical trials which use imaging typically require data management and workflow integration across several parties. We identify opportunities for all parties involved to realize benefits with a modular interoperability model based on service-oriented architecture and grid computing principles. We discuss middleware products for implementation of this model, and propose caGrid as an ideal candidate due to its healthcare focus; free, open source license; and mature developer tools and support. PMID:20449775

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination

PubMed Central

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-01-01

Abstract Motivation Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Implementation Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. General features Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Availability Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. PMID:29025122

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

PubMed

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

2014-10-01

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

Survey of Non-Rigid Registration Tools in Medicine.

PubMed

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

2017-02-01

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

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

PubMed

Duez, Marc; Giraud, Mathieu; Herbert, Ryan; Rocher, Tatiana; Salson, Mikaël; Thonier, Florian

2016-01-01

The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia. Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing

PubMed Central

Duez, Marc; Herbert, Ryan; Rocher, Tatiana; Salson, Mikaël; Thonier, Florian

2016-01-01

Background The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia. Methods and Results Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications. PMID:27835690

UManSysProp v1.0: an online and open-source facility for molecular property prediction and atmospheric aerosol calculations

NASA Astrophysics Data System (ADS)

Topping, David; Barley, Mark; Bane, Michael K.; Higham, Nicholas; Aumont, Bernard; Dingle, Nicholas; McFiggans, Gordon

2016-03-01

In this paper we describe the development and application of a new web-based facility, UManSysProp (http://umansysprop.seaes.manchester.ac.uk), for automating predictions of molecular and atmospheric aerosol properties. Current facilities include pure component vapour pressures, critical properties, and sub-cooled densities of organic molecules; activity coefficient predictions for mixed inorganic-organic liquid systems; hygroscopic growth factors and CCN (cloud condensation nuclei) activation potential of mixed inorganic-organic aerosol particles; and absorptive partitioning calculations with/without a treatment of non-ideality. The aim of this new facility is to provide a single point of reference for all properties relevant to atmospheric aerosol that have been checked for applicability to atmospheric compounds where possible. The group contribution approach allows users to upload molecular information in the form of SMILES (Simplified Molecular Input Line Entry System) strings and UManSysProp will automatically extract the relevant information for calculations. Built using open-source chemical informatics, and hosted at the University of Manchester, the facilities are provided via a browser and device-friendly web interface, or can be accessed using the user's own code via a JSON API (application program interface). We also provide the source code for all predictive techniques provided on the site, covered by the GNU GPL (General Public License) license to encourage development of a user community. We have released this via a Github repository (doi:10.5281/zenodo.45143). In this paper we demonstrate its use with specific examples that can be simulated using the web-browser interface.

Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses.

PubMed

Menegidio, Fabiano B; Jabes, Daniela L; Costa de Oliveira, Regina; Nunes, Luiz R

2018-02-01

This manuscript introduces and describes Dugong, a Docker image based on Ubuntu 16.04, which automates installation of more than 3500 bioinformatics tools (along with their respective libraries and dependencies), in alternative computational environments. The software operates through a user-friendly XFCE4 graphic interface that allows software management and installation by users not fully familiarized with the Linux command line and provides the Jupyter Notebook to assist in the delivery and exchange of consistent and reproducible protocols and results across laboratories, assisting in the development of open science projects. Source code and instructions for local installation are available at https://github.com/DugongBioinformatics, under the MIT open source license. Luiz.nunes@ufabc.edu.br. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments.

PubMed

Martin, Daniel B; Holzman, Ted; May, Damon; Peterson, Amelia; Eastham, Ashley; Eng, Jimmy; McIntosh, Martin

2008-11-01

Multiple reaction monitoring (MRM) mass spectrometry identifies and quantifies specific peptides in a complex mixture with very high sensitivity and speed and thus has promise for the high throughput screening of clinical samples for candidate biomarkers. We have developed an interactive software platform, called MRMer, for managing highly complex MRM-MS experiments, including quantitative analyses using heavy/light isotopic peptide pairs. MRMer parses and extracts information from MS files encoded in the platform-independent mzXML data format. It extracts and infers precursor-product ion transition pairings, computes integrated ion intensities, and permits rapid visual curation for analyses exceeding 1000 precursor-product pairs. Results can be easily output for quantitative comparison of consecutive runs. Additionally MRMer incorporates features that permit the quantitative analysis experiments including heavy and light isotopic peptide pairs. MRMer is open source and provided under the Apache 2.0 license.

CHRONOS architecture: Experiences with an open-source services-oriented architecture for geoinformatics

USGS Publications Warehouse

Fils, D.; Cervato, C.; Reed, J.; Diver, P.; Tang, X.; Bohling, G.; Greer, D.

2009-01-01

CHRONOS's purpose is to transform Earth history research by seamlessly integrating stratigraphic databases and tools into a virtual on-line stratigraphic record. In this paper, we describe the various components of CHRONOS's distributed data system, including the encoding of semantic and descriptive data into a service-based architecture. We give examples of how we have integrated well-tested resources available from the open-source and geoinformatic communities, like the GeoSciML schema and the simple knowledge organization system (SKOS), into the services-oriented architecture to encode timescale and phylogenetic synonymy data. We also describe on-going efforts to use geospatially enhanced data syndication and informally including semantic information by embedding it directly into the XHTML Document Object Model (DOM). XHTML DOM allows machine-discoverable descriptive data such as licensing and citation information to be incorporated directly into data sets retrieved by users. ?? 2008 Elsevier Ltd. All rights reserved.

An open-source platform to study uniaxial stress effects on nanoscale devices

NASA Astrophysics Data System (ADS)

Signorello, G.; Schraff, M.; Zellekens, P.; Drechsler, U.; Bürge, M.; Steinauer, H. R.; Heller, R.; Tschudy, M.; Riel, H.

2017-05-01

We present an automatic measurement platform that enables the characterization of nanodevices by electrical transport and optical spectroscopy as a function of the uniaxial stress. We provide insights into and detailed descriptions of the mechanical device, the substrate design and fabrication, and the instrument control software, which is provided under open-source license. The capability of the platform is demonstrated by characterizing the piezo-resistance of an InAs nanowire device using a combination of electrical transport and Raman spectroscopy. The advantages of this measurement platform are highlighted by comparison with state-of-the-art piezo-resistance measurements in InAs nanowires. We envision that the systematic application of this methodology will provide new insights into the physics of nanoscale devices and novel materials for electronics, and thus contribute to the assessment of the potential of strain as a technology booster for nanoscale electronics.

RINGMesh: A programming library for developing mesh-based geomodeling applications

NASA Astrophysics Data System (ADS)

Pellerin, Jeanne; Botella, Arnaud; Bonneau, François; Mazuyer, Antoine; Chauvin, Benjamin; Lévy, Bruno; Caumon, Guillaume

2017-07-01

RINGMesh is a C++ open-source programming library for manipulating discretized geological models. It is designed to ease the development of applications and workflows that use discretized 3D models. It is neither a geomodeler, nor a meshing software. RINGMesh implements functionalities to read discretized surface-based or volumetric structural models and to check their validity. The models can be then exported in various file formats. RINGMesh provides data structures to represent geological structural models, either defined by their discretized boundary surfaces, and/or by discretized volumes. A programming interface allows to develop of new geomodeling methods, and to plug in external software. The goal of RINGMesh is to help researchers to focus on the implementation of their specific method rather than on tedious tasks common to many applications. The documented code is open-source and distributed under the modified BSD license. It is available at https://www.ring-team.org/index.php/software/ringmesh.

Understanding the Role of Licenses and Evolution in Open Architecture Software Ecosystems

DTIC Science & Technology

2010-11-29

to a penalty for failing to comply with a collection of information if it does not display a currently valid OMB control number. 1. REPORT DATE 29...OA, since the (possibly empty) set of available license rights for an OA system depends on: (a) how and why OSS and open APIs are located within the...other compo- nents whose licenses may conflict with them or fail to match [2, 15]; the system integrator can decide to insert software shims using

10 CFR 40.3 - License requirements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false License requirements. 40.3 Section 40.3 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Provisions § 40.3 License requirements. A... material as defined in this part or any source material after removal from its place of deposit in nature...

77 FR 66647 - License Amendment Request to Byproduct Material License 06-31445-01 for Light Sources, Inc...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-06

... NUCLEAR REGULATORY COMMISSION [Docket No. 03038458; NRC-2012-0267] License Amendment Request to Byproduct Material License 06-31445- 01 for Light Sources, Inc., Orange, CT AGENCY: Nuclear Regulatory... Nuclear Materials Safety, Region I, 2100 Renaissance Blvd., King of Prussia, Pennsylvania 19406-2713...

Crawling The Web for Libre: Selecting, Integrating, Extending and Releasing Open Source Software

NASA Astrophysics Data System (ADS)

Truslove, I.; Duerr, R. E.; Wilcox, H.; Savoie, M.; Lopez, L.; Brandt, M.

2012-12-01

Libre is a project developed by the National Snow and Ice Data Center (NSIDC). Libre is devoted to liberating science data from its traditional constraints of publication, location, and findability. Libre embraces and builds on the notion of making knowledge freely available, and both Creative Commons licensed content and Open Source Software are crucial building blocks for, as well as required deliverable outcomes of the project. One important aspect of the Libre project is to discover cryospheric data published on the internet without prior knowledge of the location or even existence of that data. Inspired by well-known search engines and their underlying web crawling technologies, Libre has explored tools and technologies required to build a search engine tailored to allow users to easily discover geospatial data related to the polar regions. After careful consideration, the Libre team decided to base its web crawling work on the Apache Nutch project (http://nutch.apache.org). Nutch is "an open source web-search software project" written in Java, with good documentation, a significant user base, and an active development community. Nutch was installed and configured to search for the types of data of interest, and the team created plugins to customize the default Nutch behavior to better find and categorize these data feeds. This presentation recounts the Libre team's experiences selecting, using, and extending Nutch, and working with the Nutch user and developer community. We will outline the technical and organizational challenges faced in order to release the project's software as Open Source, and detail the steps actually taken. We distill these experiences into a set of heuristics and recommendations for using, contributing to, and releasing Open Source Software.

Getting Open Source Right for Big Data Analytics: Software Sharing, Governance, Collaboration and Most of All, Fun!

NASA Astrophysics Data System (ADS)

Mattmann, C. A.

2013-12-01

A wave of open source big data analytic infrastructure is currently shaping government, private sector, and academia. Projects are consuming, adapting, and contributing back to various ecosystems of software e.g., the Apache Hadoop project and its ecosystem of related efforts including Hive, HBase, Pig, Oozie, Ambari, Knox, Tez and Yarn, to name a few; the Berkeley AMPLab stack which includes Spark, Shark, Mesos, Tachyon, BlinkDB, MLBase, and other emerging efforts; MapR and its related stack of technologies, offerings from commercial companies building products around these tools e.g., Hortonworks Data Platform (HDP), Cloudera's CDH project, etc. Though the technologies all offer different capabilities including low latency support/in-memory, versus record oriented file I/O, high availability, support for the Map Reduce programming paradigm or other dataflow/workflow constructs, there is a common thread that binds these products - they are all released under an open source license e.g., Apache2, MIT, BSD, GPL/LGPL, etc.; all thrive in various ecosystems, such as Apache, or Berkeley AMPLab; all are developed collaboratively, and all technologies provide plug in architecture models and methodologies for allowing others to contribute, and participate via various community models. This talk will cover the open source aspects and governance aspects of the aforementioned Big Data ecosystems and point out the differences, subtleties, and implications of those differences. The discussion will be by example, using several national deployments and Big Data initiatives stemming from the Administration including DARPA's XDATA program; NASA's CMAC program; NSF's EarthCube and geosciences BigData projects. Lessons learned from these efforts in terms of the open source aspects of these technologies will help guide the AGU community in their use, deployment and understanding.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering.

PubMed

Nuñez, Isaac; Matute, Tamara; Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy; Federici, Fernán

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses.

Low cost and open source multi-fluorescence imaging system for teaching and research in biology and bioengineering

PubMed Central

Herrera, Roberto; Keymer, Juan; Marzullo, Timothy; Rudge, Timothy

2017-01-01

The advent of easy-to-use open source microcontrollers, off-the-shelf electronics and customizable manufacturing technologies has facilitated the development of inexpensive scientific devices and laboratory equipment. In this study, we describe an imaging system that integrates low-cost and open-source hardware, software and genetic resources. The multi-fluorescence imaging system consists of readily available 470 nm LEDs, a Raspberry Pi camera and a set of filters made with low cost acrylics. This device allows imaging in scales ranging from single colonies to entire plates. We developed a set of genetic components (e.g. promoters, coding sequences, terminators) and vectors following the standard framework of Golden Gate, which allowed the fabrication of genetic constructs in a combinatorial, low cost and robust manner. In order to provide simultaneous imaging of multiple wavelength signals, we screened a series of long stokes shift fluorescent proteins that could be combined with cyan/green fluorescent proteins. We found CyOFP1, mBeRFP and sfGFP to be the most compatible set for 3-channel fluorescent imaging. We developed open source Python code to operate the hardware to run time-lapse experiments with automated control of illumination and camera and a Python module to analyze data and extract meaningful biological information. To demonstrate the potential application of this integral system, we tested its performance on a diverse range of imaging assays often used in disciplines such as microbial ecology, microbiology and synthetic biology. We also assessed its potential use in a high school environment to teach biology, hardware design, optics, and programming. Together, these results demonstrate the successful integration of open source hardware, software, genetic resources and customizable manufacturing to obtain a powerful, low cost and robust system for education, scientific research and bioengineering. All the resources developed here are available under open source licenses. PMID:29140977

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

NASA Astrophysics Data System (ADS)

Thompson, C. K.; Plesea, L.; Hall, J. R.; Roberts, J. T.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; Huang, T.; McGann, J. M.; Chang, G.; Boller, R. A.; Ilavajhala, S.; Murphy, K. J.; Bingham, A. W.

2013-12-01

This presentation introduces OnEarth, a server side software package originally developed at the Jet Propulsion Laboratory (JPL), that facilitates network-based, minimum-latency geolocated image access independent of image size or spatial resolution. The key component in this package is the Meta Raster Format (MRF), a specialized raster file extension to the Geospatial Data Abstraction Library (GDAL) consisting of an internal indexed pyramid of image tiles. Imagery to be served is converted to the MRF format and made accessible online via an expandable set of server modules handling requests in several common protocols, including the Open Geospatial Consortium (OGC) compliant Web Map Tile Service (WMTS) as well as Tiled WMS and Keyhole Markup Language (KML). OnEarth has recently transitioned to open source status and is maintained and actively developed as part of GIBS (Global Imagery Browse Services), a collaborative project between JPL and Goddard Space Flight Center (GSFC). The primary function of GIBS is to enhance and streamline the data discovery process and to support near real-time (NRT) applications via the expeditious ingestion and serving of full-resolution imagery representing science products from across the NASA Earth Science spectrum. Open source software solutions are leveraged where possible in order to utilize existing available technologies, reduce development time, and enlist wider community participation. We will discuss some of the factors and decision points in transitioning OnEarth to a suitable open source paradigm, including repository and licensing agreement decision points, institutional hurdles, and perceived benefits. We will also provide examples illustrating how OnEarth is integrated within GIBS and other applications.

Open-Source Development of the Petascale Reactive Flow and Transport Code PFLOTRAN

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Andre, B.; Bisht, G.; Johnson, T.; Karra, S.; Lichtner, P. C.; Mills, R. T.

2013-12-01

Open-source software development has become increasingly popular in recent years. Open-source encourages collaborative and transparent software development and promotes unlimited free redistribution of source code to the public. Open-source development is good for science as it reveals implementation details that are critical to scientific reproducibility, but generally excluded from journal publications. In addition, research funds that would have been spent on licensing fees can be redirected to code development that benefits more scientists. In 2006, the developers of PFLOTRAN open-sourced their code under the U.S. Department of Energy SciDAC-II program. Since that time, the code has gained popularity among code developers and users from around the world seeking to employ PFLOTRAN to simulate thermal, hydraulic, mechanical and biogeochemical processes in the Earth's surface/subsurface environment. PFLOTRAN is a massively-parallel subsurface reactive multiphase flow and transport simulator designed from the ground up to run efficiently on computing platforms ranging from the laptop to leadership-class supercomputers, all from a single code base. The code employs domain decomposition for parallelism and is founded upon the well-established and open-source parallel PETSc and HDF5 frameworks. PFLOTRAN leverages modern Fortran (i.e. Fortran 2003-2008) in its extensible object-oriented design. The use of this progressive, yet domain-friendly programming language has greatly facilitated collaboration in the code's software development. Over the past year, PFLOTRAN's top-level data structures were refactored as Fortran classes (i.e. extendible derived types) to improve the flexibility of the code, ease the addition of new process models, and enable coupling to external simulators. For instance, PFLOTRAN has been coupled to the parallel electrical resistivity tomography code E4D to enable hydrogeophysical inversion while the same code base can be used as a third-party library to provide hydrologic flow, energy transport, and biogeochemical capability to the community land model, CLM, part of the open-source community earth system model (CESM) for climate. In this presentation, the advantages and disadvantages of open source software development in support of geoscience research at government laboratories, universities, and the private sector are discussed. Since the code is open-source (i.e. it's transparent and readily available to competitors), the PFLOTRAN team's development strategy within a competitive research environment is presented. Finally, the developers discuss their approach to object-oriented programming and the leveraging of modern Fortran in support of collaborative geoscience research as the Fortran standard evolves among compiler vendors.

10 CFR 40.41 - Terms and conditions of licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Terms and conditions of licenses. 40.41 Section 40.41 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.41 Terms and... the regulations in this part shall confine his possession and use of source or byproduct material to...

10 CFR 40.32 - General requirements for issuance of specific licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General requirements for issuance of specific licenses. 40.32 Section 40.32 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL License... applicant is qualified by reason of training and experience to use the source material for the purpose...

10 CFR 70.39 - Specific licenses for the manufacture or initial transfer of calibration or reference sources.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Specific licenses for the manufacture or initial transfer... manufacture or initial transfer of calibration or reference sources. (a) An application for a specific license to manufacture or initially transfer calibration or reference sources containing plutonium, for...

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

Not Available

Greenland's Mineral Resources Administration (MRA) plans a series of licensing rounds off western Greenland. Meanwhile, the MRA has declared the Jameson Land basin of east central Greenland as open acreage. Greenland Geological Survey (GGU), Copenhagen, has prepared a report on the geographical conditions, logistics, exploration history, and geological development of Jameson Land. The article emphasizes source and reservoir rocks, conceptual play types with six seismic examples, and thermal history with basin modeling. It also includes two interpreted regional seismic lines, a geological and an aeromagnetic map, depth structure, and isopach maps of selected formations.

Extensible Open-Source Zero-Footprint Web Viewer for Oncologic Imaging Research | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

The Tumor Imaging Metrics Core (TIMC), a CCSG Shared-Resource of the Dana-Farber/Harvard Cancer Center, has developed software for managing the workflow and image measurements for oncology clinical trials. This system currently is in use across the five Harvard hospitals to manage over 600 active clinical trials, with 800 users, and has been licensed and implemented at several other Cancer Centers, including Yale, Utah/Huntsman Cancer Institute, and UW/Seattle Cancer Care Alliance.

MYRaf: An Easy Aperture Photometry GUI for IRAF

NASA Astrophysics Data System (ADS)

Niaei, M. S.; KiliÇ, Y.; Özeren, F. F.

2015-07-01

We describe the design and development of MYRaf, a GUI (Graphical User Interface) that aims to be completely open-source under General Public License (GPL). MYRaf is an easy to use, reliable, and a fast IRAF aperture photometry GUI tool for those who are conversant with text-based software and command-line procedures in GNU/Linux OSs. MYRaf uses IRAF, PyRAF, matplotlib, ginga, alipy, and SExtractor with the general-purpose and high-level programming language Python, and uses the Qt framework.

Analogues as a check of predicted drift stability at Yucca Mountain, Nevada

USGS Publications Warehouse

Stuckless, J.S.

2006-01-01

Calculations made by the U.S. Department of Energy's Yucca Mountain Project as part of the licensing of a proposed geologic repository in southwestern Nevada for the disposal of high-level radioactive waste, predict that emplacement tunnels will remain open with little collapse long after ground support has disintegrated. This conclusion includes the effects of anticipated seismic events. Natural analogues cannot provide a quantitative test of this conclusion, but they can provide a reasonableness test by examining the naturally occuring and anthropogenic examples of stability of subterranean openings. Available data from a variety of sources, combined with limited observations by the author, show that natural underground openings tend to resist collapse for millions of years and that anthropogenic subterranean openings have remained open from before recorded history through today. This stability is true even in seismically active areas. In fact, the archaeological record is heavily skewed toward preservation of underground structures relative to those found at the surface.

A prospective international cooperative information technology platform built using open-source tools for improving the access to and safety of bone marrow transplantation in low- and middle-income countries.

PubMed

Agarwal, Rajat Kumar; Sedai, Amit; Dhimal, Sunil; Ankita, Kumari; Clemente, Luigi; Siddique, Sulman; Yaqub, Naila; Khalid, Sadaf; Itrat, Fatima; Khan, Anwar; Gilani, Sarah Khan; Marwah, Priya; Soni, Rajpreet; Missiry, Mohamed El; Hussain, Mohamed Hamed; Uderzo, Cornelio; Faulkner, Lawrence

2014-01-01

Jagriti Innovations developed a collaboration tool in partnership with the Cure2Children Foundation that has been used by health professionals in Italy, Pakistan, and India for the collaborative management of patients undergoing bone marrow transplantation (BMT) for thalassemia major since August 2008. This online open-access database covers data recording, analyzing, and reporting besides enabling knowledge exchange, telemedicine, capacity building, and quality assurance. As of February 2014, over 2400 patients have been registered and 112 BMTs have been performed with outcomes comparable to international standards, but at a fraction of the cost. This approach avoids medical emigration and contributes to local healthcare strengthening and competitiveness. This paper presents the experience and clinical outcomes associated with the use of this platform built using open-source tools and focusing on a locally pertinent tertiary care procedure-BMT. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Neptune: An astrophysical smooth particle hydrodynamics code for massively parallel computer architectures

NASA Astrophysics Data System (ADS)

Sandalski, Stou

Smooth particle hydrodynamics is an efficient method for modeling the dynamics of fluids. It is commonly used to simulate astrophysical processes such as binary mergers. We present a newly developed GPU accelerated smooth particle hydrodynamics code for astrophysical simulations. The code is named neptune after the Roman god of water. It is written in OpenMP parallelized C++ and OpenCL and includes octree based hydrodynamic and gravitational acceleration. The design relies on object-oriented methodologies in order to provide a flexible and modular framework that can be easily extended and modified by the user. Several pre-built scenarios for simulating collisions of polytropes and black-hole accretion are provided. The code is released under the MIT Open Source license and publicly available at http://code.google.com/p/neptune-sph/.

Undersea landslides: Extent and significance in the Pacific Ocean, an update

USGS Publications Warehouse

Lee, H.J.

2005-01-01

Submarine landslides are known to occur disproportionately in a limited number of environments including fjords, deltas, canyons, volcanic islands and the open continental slope. An evaluation of the progress that has been made in understanding Pacific Ocean submarine landslides over the last 15 years shows that mapping technologies have improved greatly, allowing a better interpretation of landslide features. Some features previously identified as landslides are being reinterpreted by some as sediment waves. Previously underappreciated environments for landslides such as deep-sea trenches are being recognized and lava deltas are being found to be landslide prone. Landslides are also being recognized much more commonly as a potential source of tsunamis. Landslides that have produced tsunamis in the past are being mapped and in some cases modeled. The flow characteristics of turbidity currents produced by landslides in canyon heads have recently been monitored and the source of these failures has been identified using repeated multibeam mapping. Finally, some landslide deposits are being dated as part of assessing risk to coastal cities from landslide-tsunamis. European Geosciences Union ?? 2005 Author(s). This work is licensed under a Creative Commons License.

Technology, conflict early warning systems, public health, and human rights.

PubMed

Pham, Phuong N; Vinck, Patrick

2012-12-15

Public health and conflict early warning are evolving rapidly in response to technology changes for the gathering, management, analysis and communication of data. It is expected that these changes will provide an unprecedented ability to monitor, detect, and respond to crises. One of the potentially most profound and lasting expected change affects the roles of the various actors in providing and sharing information and in responding to early warning. Communities and civil society actors have the opportunity to be empowered as a source of information, analysis, and response, while the role of traditional actors shifts toward supporting those communities and building resilience. However, by creating new roles, relationships, and responsibilities, technology changes raise major concerns and ethical challenges for practitioners, pressing the need for practical guidelines and actionable recommendations in line with existing ethical principles. Copyright © 2012 Pham and Vinck. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

A portable structural analysis library for reaction networks.

PubMed

Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri; Medley, Kyle; Sauro, Herbert M

2018-07-01

The topology of a reaction network can have a significant influence on the network's dynamical properties. Such influences can include constraints on network flows and concentration changes or more insidiously result in the emergence of feedback loops. These effects are due entirely to mass constraints imposed by the network configuration and are important considerations before any dynamical analysis is made. Most established simulation software tools usually carry out some kind of structural analysis of a network before any attempt is made at dynamic simulation. In this paper, we describe a portable software library, libStructural, that can carry out a variety of popular structural analyses that includes conservation analysis, flux dependency analysis and enumerating elementary modes. The library employs robust algorithms that allow it to be used on large networks with more than a two thousand nodes. The library accepts either a raw or fully labeled stoichiometry matrix or models written in SBML format. The software is written in standard C/C++ and comes with extensive on-line documentation and a test suite. The software is available for Windows, Mac OS X, and can be compiled easily on any Linux operating system. A language binding for Python is also available through the pip package manager making it simple to install on any standard Python distribution. The bulk of the source code is licensed under the open source BSD license with other parts using as either the MIT license or more simply public domain. All source is available on GitHub (https://github.com/sys-bio/Libstructural). Copyright © 2018 Elsevier B.V. All rights reserved.

NOAA's Data Catalog and the Federal Open Data Policy

NASA Astrophysics Data System (ADS)

Wengren, M. J.; de la Beaujardiere, J.

2014-12-01

The 2013 Open Data Policy Presidential Directive requires Federal agencies to create and maintain a 'public data listing' that includes all agency data that is currently or will be made publicly-available in the future. The directive requires the use of machine-readable and open formats that make use of 'common core' and extensible metadata formats according to the best practices published in an online repository called 'Project Open Data', to use open licenses where possible, and to adhere to existing metadata and other technology standards to promote interoperability. In order to meet the requirements of the Open Data Policy, the National Oceanic and Atmospheric Administration (NOAA) has implemented an online data catalog that combines metadata from all subsidiary NOAA metadata catalogs into a single master inventory. The NOAA Data Catalog is available to the public for search and discovery, providing access to the NOAA master data inventory through multiple means, including web-based text search, OGC CS-W endpoint, as well as a native Application Programming Interface (API) for programmatic query. It generates on a daily basis the Project Open Data JavaScript Object Notation (JSON) file required for compliance with the Presidential directive. The Data Catalog is based on the open source Comprehensive Knowledge Archive Network (CKAN) software and runs on the Amazon Federal GeoCloud. This presentation will cover topics including mappings of existing metadata in standard formats (FGDC-CSDGM and ISO 19115 XML ) to the Project Open Data JSON metadata schema, representation of metadata elements within the catalog, and compatible metadata sources used to feed the catalog to include Web Accessible Folder (WAF), Catalog Services for the Web (CS-W), and Esri ArcGIS.com. It will also discuss related open source technologies that can be used together to build a spatial data infrastructure compliant with the Open Data Policy.

Embracing Open Software Development in Solar Physics

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

Tracking Clouds with low cost GNSS chips aided by the Arduino platform

NASA Astrophysics Data System (ADS)

Hameed, Saji; Realini, Eugenio; Ishida, Shinya

2016-04-01

The Global Navigation Satellite System (GNSS) is a constellation of satellites that is used to provide geo-positioning services. Besides this application, the GNSS system is important for a wide range of scientific and civilian applications. For example, GNSS systems are routinely used in civilian applications such as surveying and scientific applications such as the study of crustal deformation. Another important scientific application of GNSS system is in meteorological research. Here it is mainly used to determine the total water vapour content of the troposphere, hereafter Precipitable Water Vapor (PWV). However, both GNSS receivers and software have prohibitively high price due to a variety of reasons. To overcome this somewhat artificial barrier we are exploring the use of low-cost GNSS receivers along with open source GNSS software for scientific research, in particular for GNSS meteorology research. To achieve this aim, we have developed a custom Arduino compatible data logging board that is able to operate together with a specific low-cost single frequency GNSS receiver chip from NVS Technologies AG. We have also developed an open-source software bundle that includes a new Arduino core for the Atmel324p chip, which is the main processor used in our custom logger. We have also developed software code that enables data collection, logging and parsing of the GNSS data stream. Additionally we have comprehensively evaluated the low power characteristics of the GNSS receiver and logger boards. Currently we are exploring the use of several openly source or free to use for research software to map GNSS delays to PWV. These include the open source goGPS (http://www.gogps-project.org/) and gLAB (http://gage.upc.edu/gLAB) and the openly available GAMIT software from Massachusetts Institute of Technology (MIT). We note that all the firmware and software developed as part of this project is available on an open source license.

OpenSQUID: A Flexible Open-Source Software Framework for the Control of SQUID Electronics

DOE PAGES

Jaeckel, Felix T.; Lafler, Randy J.; Boyd, S. T. P.

2013-02-06

We report commercially available computer-controlled SQUID electronics are usually delivered with software providing a basic user interface for adjustment of SQUID tuning parameters, such as bias current, flux offset, and feedback loop settings. However, in a research context it would often be useful to be able to modify this code and/or to have full control over all these parameters from researcher-written software. In the case of the STAR Cryoelectronics PCI/PFL family of SQUID control electronics, the supplied software contains modules for automatic tuning and noise characterization, but does not provide an interface for user code. On the other hand, themore » Magnicon SQUIDViewer software package includes a public application programming interface (API), but lacks auto-tuning and noise characterization features. To overcome these and other limitations, we are developing an "open-source" framework for controlling SQUID electronics which should provide maximal interoperability with user software, a unified user interface for electronics from different manufacturers, and a flexible platform for the rapid development of customized SQUID auto-tuning and other advanced features. Finally, we have completed a first implementation for the STAR Cryoelectronics hardware and have made the source code for this ongoing project available to the research community on SourceForge (http://opensquid.sourceforge.net) under the GNU public license.« less

Why open drug discovery needs four simple rules for licensing data and models.

PubMed

Williams, Antony J; Wilbanks, John; Ekins, Sean

2012-01-01

When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves.

RGG: A general GUI Framework for R scripts

PubMed Central

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

2009-01-01

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

A computational genomics pipeline for prokaryotic sequencing projects.

PubMed

Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

2010-08-01

New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

A New Architecture for Visualization: Open Mission Control Technologies

NASA Technical Reports Server (NTRS)

Trimble, Jay

2017-01-01

Open Mission Control Technologies (MCT) is a new architecture for visualisation of mission data. Driven by requirements for new mission capabilities, including distributed mission operations, access to data anywhere, customization by users, synthesis of multiple data sources, and flexibility for multi-mission adaptation, Open MCT provides users with an integrated customizable environment. Developed at NASAs Ames Research Center (ARC), in collaboration with NASAs Advanced Multimission Operations System (AMMOS) and NASAs Jet Propulsion Laboratory (JPL), Open MCT is getting its first mission use on the Jason 3 Mission, and is also available in the testbed for the Mars 2020 Rover and for development use for NASAs Resource Prospector Lunar Rover. The open source nature of the project provides for use outside of space missions, including open source contributions from a community of users. The defining features of Open MCT for mission users are data integration, end user composition and multiple views. Data integration provides access to mission data across domains in one place, making data such as activities, timelines, telemetry, imagery, event timers and procedures available in one place, without application switching. End user composition provides users with layouts, which act as a canvas to assemble visualisations. Multiple views provide the capability to view the same data in different ways, with live switching of data views in place. Open MCT is browser based, and works on the desktop as well as tablets and phones, providing access to data anywhere. An early use case for mobile data access took place on the Resource Prospector (RP) Mission Distributed Operations Test, in which rover engineers in the field were able to view telemetry on their phones. We envision this capability providing decision support to on console operators from off duty personnel. The plug-in architecture also allows for adaptation for different mission capabilities. Different data types and capabilities may be added or removed using plugins. An API provides a means to write new capabilities and to create data adaptors. Data plugins exist for mission data sources for NASA missions. Adaptors have been written by international and commercial users. Open MCT is open source. Open source enables collaborative development across organizations and also makes the product available outside of the space community, providing a potential source of usage and ideas to drive product design and development. The combination of open source with an Apache 2 license, and distribution on GitHub, has enabled an active community of users and contributors. The spectrum of users for Open MCT is, to our knowledge, unprecedented for mission software. In addition to our NASA users, we have, through open source, had users and inquires on projects ranging from Internet of Things, to radio hobbyists, to farming projects. We have an active community of contributors, enabling a flow of ideas inside and outside of the space community.

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.

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

Akyol, Bora A.; Allwardt, Craig H.; Beech, Zachary W.

VOLTTRON is a flexible, reliable, and scalable platform for distributed control and sensing. VOLTTRON serves in four primary roles: •A reference platform for researchers to quickly develop control applications for transactive energy. •A reference platform with flexible data store support for energy analytics applications either in academia or in commercial enterprise. •A platform from which commercial enterprise can develop products without license issues and easily integrate into their product line. •An accelerator to drive industry adoption of transactive energy and advanced building energy analytics. Pacific Northwest National Laboratory, with funding from the U.S. Department of Energy’s Building Technologies Office, developedmore » and maintains VOLTTRON as an open-source community project. VOLTTRON source code includes agent execution software; agents that perform critical services that enable and enhance VOLTTRON functionality; and numerous agents that utilize the platform to perform a specific function (fault detection, demand response, etc.). The platform supports energy, operational, and financial transactions between networked entities (equipment, organizations, buildings, grid, etc.) and enhance the control infrastructure of existing buildings through the use of open-source device communication, control protocols, and integrated analytics.« less

Software Application Profile: Opal and Mica: open-source software solutions for epidemiological data management, harmonization and dissemination.

PubMed

Doiron, Dany; Marcon, Yannick; Fortier, Isabel; Burton, Paul; Ferretti, Vincent

2017-10-01

Improving the dissemination of information on existing epidemiological studies and facilitating the interoperability of study databases are essential to maximizing the use of resources and accelerating improvements in health. To address this, Maelstrom Research proposes Opal and Mica, two inter-operable open-source software packages providing out-of-the-box solutions for epidemiological data management, harmonization and dissemination. Opal and Mica are two standalone but inter-operable web applications written in Java, JavaScript and PHP. They provide web services and modern user interfaces to access them. Opal allows users to import, manage, annotate and harmonize study data. Mica is used to build searchable web portals disseminating study and variable metadata. When used conjointly, Mica users can securely query and retrieve summary statistics on geographically dispersed Opal servers in real-time. Integration with the DataSHIELD approach allows conducting more complex federated analyses involving statistical models. Opal and Mica are open-source and freely available at [www.obiba.org] under a General Public License (GPL) version 3, and the metadata models and taxonomies that accompany them are available under a Creative Commons licence. © The Author 2017; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

NASA Technical Reports Server (NTRS)

Gilbertson, Christian; Welch, Bryan

2017-01-01

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

PubMed Central

Cock, Peter J. A.; Antao, Tiago; Chang, Jeffrey T.; Chapman, Brad A.; Cox, Cymon J.; Dalke, Andrew; Friedberg, Iddo; Hamelryck, Thomas; Kauff, Frank; Wilczynski, Bartek; de Hoon, Michiel J. L.

2009-01-01

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning. Availability: Biopython is freely available, with documentation and source code at www.biopython.org under the Biopython license. Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk. PMID:19304878

Smoke and mirrors: unanswered questions and misleading statements obscure the truth about organ sources in China.

PubMed

Rogers, Wendy A; Trey, Torsten; Fiatarone Singh, Maria; Bridgett, Madeleine; Bramstedt, Katrina A; Lavee, Jacob

2016-08-01

This response refutes the claim made in a recent article that organs for transplantation in China will no longer be sourced from executed prisoners. We identify ongoing ethical problems due to the lack of transparent data on current numbers of transplants in China; implausible and conflicting claims about voluntary donations; and obfuscation about who counts as a voluntary donor. The big unanswered question in Chinese transplant ethics is the source of organs, and until there is an open and independently audited system in China, legitimate concerns remain about organ harvesting from prisoners of conscience. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

PubMed

Mungall, Christopher J; Emmert, David B

2007-07-01

A few years ago, FlyBase undertook to design a new database schema to store Drosophila data. It would fully integrate genomic sequence and annotation data with bibliographic, genetic, phenotypic and molecular data from the literature representing a distillation of the first 100 years of research on this major animal model system. In developing this new integrated schema, FlyBase also made a commitment to ensure that its design was generic, extensible and available as open source, so that it could be employed as the core schema of any model organism data repository, thereby avoiding redundant software development and potentially increasing interoperability. Our question was whether we could create a relational database schema that would be successfully reused. Chado is a relational database schema now being used to manage biological knowledge for a wide variety of organisms, from human to pathogens, especially the classes of information that directly or indirectly can be associated with genome sequences or the primary RNA and protein products encoded by a genome. Biological databases that conform to this schema can interoperate with one another, and with application software from the Generic Model Organism Database (GMOD) toolkit. Chado is distinctive because its design is driven by ontologies. The use of ontologies (or controlled vocabularies) is ubiquitous across the schema, as they are used as a means of typing entities. The Chado schema is partitioned into integrated subschemas (modules), each encapsulating a different biological domain, and each described using representations in appropriate ontologies. To illustrate this methodology, we describe here the Chado modules used for describing genomic sequences. GMOD is a collaboration of several model organism database groups, including FlyBase, to develop a set of open-source software for managing model organism data. The Chado schema is freely distributed under the terms of the Artistic License (http://www.opensource.org/licenses/artistic-license.php) from GMOD (www.gmod.org).

An open ecosystem engagement strategy through the lens of global food safety

PubMed Central

Stacey, Paul; Fons, Garin; Bernardo, Theresa M

2015-01-01

The Global Food Safety Partnership (GFSP) is a public/private partnership established through the World Bank to improve food safety systems through a globally coordinated and locally-driven approach. This concept paper aims to establish a framework to help GFSP fully leverage the potential of open models. In preparing this paper the authors spoke to many different GFSP stakeholders who asked questions about open models such as: what is it?what’s in it for me?why use an open rather than a proprietary model?how will open models generate equivalent or greater sustainable revenue streams compared to the current “traditional” approaches?  This last question came up many times with assertions that traditional service providers need to see opportunity for equivalent or greater revenue dollars before they will buy-in. This paper identifies open value propositions for GFSP stakeholders and proposes a framework for creating and structuring that value. Open Educational Resources (OER) were the primary open practice GFSP partners spoke to us about, as they provide a logical entry point for collaboration. Going forward, funders should consider requiring that educational resources and concomitant data resulting from their sponsorship should be open, as a public good. There are, however, many other forms of open practice that bring value to the GFSP. Nine different open strategies and tactics (Appendix A) are described, including: open content (including OER and open courseware), open data, open access (research), open government, open source software, open standards, open policy, open licensing and open hardware. It is recommended that all stakeholders proactively pursue "openness" as an operating principle. This paper presents an overall GFSP Open Ecosystem Engagement Strategy within which specific local case examples can be situated. Two different case examples, China and Colombia, are presented to show both project-based and crowd-sourced, direct-to-public paths through this ecosystem. PMID:26213614

OpenStereo: Open Source, Cross-Platform Software for Structural Geology Analysis

NASA Astrophysics Data System (ADS)

Grohmann, C. H.; Campanha, G. A.

2010-12-01

Free and open source software (FOSS) are increasingly seen as synonyms of innovation and progress. Freedom to run, copy, distribute, study, change and improve the software (through access to the source code) assure a high level of positive feedback between users and developers, which results in stable, secure and constantly updated systems. Several software packages for structural geology analysis are available to the user, with commercial licenses or that can be downloaded at no cost from the Internet. Some provide basic tools of stereographic projections such as plotting poles, great circles, density contouring, eigenvector analysis, data rotation etc, while others perform more specific tasks, such as paleostress or geotechnical/rock stability analysis. This variety also means a wide range of data formating for input, Graphical User Interface (GUI) design and graphic export format. The majority of packages is built for MS-Windows and even though there are packages for the UNIX-based MacOS, there aren't native packages for *nix (UNIX, Linux, BSD etc) Operating Systems (OS), forcing the users to run these programs with emulators or virtual machines. Those limitations lead us to develop OpenStereo, an open source, cross-platform software for stereographic projections and structural geology. The software is written in Python, a high-level, cross-platform programming language and the GUI is designed with wxPython, which provide a consistent look regardless the OS. Numeric operations (like matrix and linear algebra) are performed with the Numpy module and all graphic capabilities are provided by the Matplolib library, including on-screen plotting and graphic exporting to common desktop formats (emf, eps, ps, pdf, png, svg). Data input is done with simple ASCII text files, with values of dip direction and dip/plunge separated by spaces, tabs or commas. The user can open multiple file at the same time (or the same file more than once), and overlay different elements of each dataset (poles, great circles etc). The GUI shows the opened files in a tree structure, similar to “layers” of many illustration software, where the vertical order of the files in the tree reflects the drawing order of the selected elements. At this stage, the software performs plotting operations of poles to planes, lineations, great circles, density contours and rose diagrams. A set of statistics is calculated for each file and its eigenvalues and eigenvectors are used to suggest if the data is clustered about a mean value or distributed along a girdle. Modified Flinn, Triangular and histograms plots are also available. Next step of development will focus on tools as merging and rotation of datasets, possibility to save 'projects' and paleostress analysis. In its current state, OpenStereo requires Python, wxPython, Numpy and Matplotlib installed in the system. We recommend installing PythonXY or the Enthought Python Distribution on MS-Windows and MacOS machines, since all dependencies are provided. Most Linux distributions provide an easy way to install all dependencies through software repositories. OpenStereo is released under the GNU General Public License. Programmers willing to contribute are encouraged to contact the authors directly. FAPESP Grant #09/17675-5

A Kernel for Open Source Drug Discovery in Tropical Diseases

PubMed Central

Ortí, Leticia; Carbajo, Rodrigo J.; Pieper, Ursula; Eswar, Narayanan; Maurer, Stephen M.; Rai, Arti K.; Taylor, Ginger; Todd, Matthew H.; Pineda-Lucena, Antonio; Sali, Andrej; Marti-Renom, Marc A.

2009-01-01

Background Conventional patent-based drug development incentives work badly for the developing world, where commercial markets are usually small to non-existent. For this reason, the past decade has seen extensive experimentation with alternative R&D institutions ranging from private–public partnerships to development prizes. Despite extensive discussion, however, one of the most promising avenues—open source drug discovery—has remained elusive. We argue that the stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. Historically, open source software collaborations have almost never succeeded without such “kernels”. Methodology/Principal Findings Here, we use a computational pipeline for: (i) comparative structure modeling of target proteins, (ii) predicting the localization of ligand binding sites on their surfaces, and (iii) assessing the similarity of the predicted ligands to known drugs. Our kernel currently contains 143 and 297 protein targets from ten pathogen genomes that are predicted to bind a known drug or a molecule similar to a known drug, respectively. The kernel provides a source of potential drug targets and drug candidates around which an online open source community can nucleate. Using NMR spectroscopy, we have experimentally tested our predictions for two of these targets, confirming one and invalidating the other. Conclusions/Significance The TDI kernel, which is being offered under the Creative Commons attribution share-alike license for free and unrestricted use, can be accessed on the World Wide Web at http://www.tropicaldisease.org. We hope that the kernel will facilitate collaborative efforts towards the discovery of new drugs against parasites that cause tropical diseases. PMID:19381286

Development of an IHE MRRT-compliant open-source web-based reporting platform.

PubMed

Pinto Dos Santos, Daniel; Klos, G; Kloeckner, R; Oberle, R; Dueber, C; Mildenberger, P

2017-01-01

To develop a platform that uses structured reporting templates according to the IHE Management of Radiology Report Templates (MRRT) profile, and to implement this platform into clinical routine. The reporting platform uses standard web technologies (HTML / JavaScript and PHP / MySQL) only. Several freely available external libraries were used to simplify the programming. The platform runs on a standard web server, connects with the radiology information system (RIS) and PACS, and is easily accessible via a standard web browser. A prototype platform that allows structured reporting to be easily incorporated into the clinical routine was developed and successfully tested. To date, 797 reports were generated using IHE MRRT-compliant templates (many of them downloaded from the RSNA's radreport.org website). Reports are stored in a MySQL database and are easily accessible for further analyses. Development of an IHE MRRT-compliant platform for structured reporting is feasible using only standard web technologies. All source code will be made available upon request under a free license, and the participation of other institutions in further development is welcome. • A platform for structured reporting using IHE MRRT-compliant templates is presented. • Incorporating structured reporting into clinical routine is feasible. • Full source code will be provided upon request under a free license.

Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors.

PubMed

Wilson, Mandy L; Okumoto, Sakiko; Adam, Laura; Peccoud, Jean

2014-01-15

Expression vectors used in different biotechnology applications are designed with domain-specific rules. For instance, promoters, origins of replication or homologous recombination sites are host-specific. Similarly, chromosomal integration or viral delivery of an expression cassette imposes specific structural constraints. As de novo gene synthesis and synthetic biology methods permeate many biotechnology specialties, the design of application-specific expression vectors becomes the new norm. In this context, it is desirable to formalize vector design strategies applicable in different domains. Using the design of constructs to express genes in the chloroplast of Chlamydomonas reinhardtii as an example, we show that a vector design strategy can be formalized as a domain-specific language. We have developed a graphical editor of context-free grammars usable by biologists without prior exposure to language theory. This environment makes it possible for biologists to iteratively improve their design strategies throughout the course of a project. It is also possible to ensure that vectors designed with early iterations of the language are consistent with the latest iteration of the language. The context-free grammar editor is part of the GenoCAD application. A public instance of GenoCAD is available at http://www.genocad.org. GenoCAD source code is available from SourceForge and licensed under the Apache v2.0 open source license.

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2011 CFR

2011-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... License Exception. (2) Access and release restrictions. (i)[Reserved] (ii) Technology and source code. Technology and source code eligible for License Exception APP may not be released to nationals of Cuba, Iran...

Open by default: a proposed copyright license and waiver agreement for open access research and data in peer-reviewed journals

PubMed Central

2012-01-01

Copyright and licensing of scientific data, internationally, are complex and present legal barriers to data sharing, integration and reuse, and therefore restrict the most efficient transfer and discovery of scientific knowledge. Much data are included within scientific journal articles, their published tables, additional files (supplementary material) and reference lists. However, these data are usually published under licenses which are not appropriate for data. Creative Commons CC0 is an appropriate and increasingly accepted method for dedicating data to the public domain, to enable data reuse with the minimum of restrictions. BioMed Central is committed to working towards implementation of open data-compliant licensing in its publications. Here we detail a protocol for implementing a combined Creative Commons Attribution license (for copyrightable material) and Creative Commons CC0 waiver (for data) agreement for content published in peer-reviewed open access journals. We explain the differences between legal requirements for attribution in copyright, and cultural requirements in scholarship for giving individuals credit for their work through citation. We argue that publishing data in scientific journals under CC0 will have numerous benefits for individuals and society, and yet will have minimal implications for authors and minimal impact on current publishing and research workflows. We provide practical examples and definitions of data types, such as XML and tabular data, and specific secondary use cases for published data, including text mining, reproducible research, and open bibliography. We believe this proposed change to the current copyright and licensing structure in science publishing will help clarify what users – people and machines – of the published literature can do, legally, with journal articles and make research using the published literature more efficient. We further believe this model could be adopted across multiple publishers, and invite comment on this article from all stakeholders in scientific research. PMID:22958225

[Acoustic conditions in open plan offices - Pilot test results].

PubMed

Mikulski, Witold

The main source of noise in open plan office are conversations. Office work standards in such premises are attained by applying specific acoustic adaptation. This article presents the results of pilot tests and acoustic evaluation of open space rooms. Acoustic properties of 6 open plan office rooms were the subject of the tests. Evaluation parameters, measurement methods and criterial values were adopted according to the following standards: PN-EN ISO 3382- 3:2012, PN-EN ISO 3382-2:2010, PN-B-02151-4:2015-06 and PN-B-02151-3:2015-10. The reverberation time was 0.33- 0.55 s (maximum permissible value in offices - 0.6 s; the criterion was met), sound absorption coefficient in relation to 1 m2 of the room's plan was 0.77-1.58 m2 (minimum permissible value - 1.1 m2; 2 out of 6 rooms met the criterion), distraction distance was 8.5-14 m (maximum permissible value - 5 m; none of the rooms met the criterion), A-weighted sound pressure level of speech at a distance of 4 m was 43.8-54.7 dB (maximum permissible value - 48 dB; 2 out of 6 rooms met the criterion), spatial decay rate of the speech was 1.8-6.3 dB (minimum permissible value - 7 dB; none of the rooms met the criterion). Standard acoustic treatment, containing sound absorbing suspended ceiling, sound absorbing materials on the walls, carpet flooring and sound absorbing workplace barriers, is not sufficient. These rooms require specific advanced acoustic solutions. Med Pr 2016;67(5):653-662. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

The Organizational Impact of Open Educational Resources

NASA Astrophysics Data System (ADS)

Sclater, Niall

The open educational resource (OER) movement has been growing rapidly since 2001, stimulated by funding from benefactors such as the Hewlett Foundation and UNESCO, and providing educational content freely to institutions and learners across the world. Individuals and organizations are motivated by a variety of drivers to produce OERs, both altruistic and self-interested. There are parallels with the open source movement, where authors and others combine their efforts to provide a product which they and others can use freely and adapt to their own purposes. There are many different ways in which OER initiatives are organized and an infinite range of possibilities for how the OERs themselves are constituted. If institutions are to develop sustainable OER initiatives, they need to build successful change management initiatives, developing models for the production and quality assurance of OERs, licensing them through appropriate mechanisms such as the Creative Commons, and considering how the resources will be discovered and used by learners.

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

PubMed Central

Fried, Jake Y.; Luna, Augustin

2013-01-01

Purpose: The PathVisio-Faceted Search plugin helps users explore and understand complex pathways by overlaying experimental data and data from webservices, such as Ensembl BioMart, onto diagrams drawn using formalized notations in PathVisio. The plugin then provides a filtering mechanism, known as a faceted search, to find and highlight diagram nodes (e.g. genes and proteins) of interest based on imported data. The tool additionally provides a flexible scripting mechanism to handle complex queries. Availability: The PathVisio-Faceted Search plugin is compatible with PathVisio 3.0 and above. PathVisio is compatible with Windows, Mac OS X and Linux. The plugin, documentation, example diagrams and Groovy scripts are available at http://PathVisio.org/wiki/PathVisioFacetedSearchHelp. The plugin is free, open-source and licensed by the Apache 2.0 License. Contact: augustin@mail.nih.gov or jakeyfried@gmail.com PMID:23547033

Why Open Drug Discovery Needs Four Simple Rules for Licensing Data and Models

PubMed Central

Williams, Antony J.; Wilbanks, John; Ekins, Sean

2012-01-01

When we look at the rapid growth of scientific databases on the Internet in the past decade, we tend to take the accessibility and provenance of the data for granted. As we see a future of increased database integration, the licensing of the data may be a hurdle that hampers progress and usability. We have formulated four rules for licensing data for open drug discovery, which we propose as a starting point for consideration by databases and for their ultimate adoption. This work could also be extended to the computational models derived from such data. We suggest that scientists in the future will need to consider data licensing before they embark upon re-using such content in databases they construct themselves. PMID:23028298

The Ultracool Typing Kit - An Open-Source, Qualitative Spectral Typing GUI for L Dwarfs

NASA Astrophysics Data System (ADS)

Schwab, Ellianna; Cruz, Kelle; Núñez, Alejandro; Burgasser, Adam J.; Rice, Emily; Reid, Neill; Faherty, Jacqueline K.; BDNYC

2018-01-01

The Ultracool Typing Kit (UTK) is an open-source graphical user interface for classifying the NIR spectral types of L dwarfs, including field and low-gravity dwarfs spanning L0-L9. The user is able to input an NIR spectrum and qualitatively compare the input spectrum to a full suite of spectral templates, including low-gravity beta and gamma templates. The user can choose to view the input spectrum as both a band-by-band comparison with the templates and a full bandwidth comparison with NIR spectral standards. Once an optimal qualitative comparison is selected, the user can save their spectral type selection both graphically and to a database. Using UTK to classify 78 previously typed L dwarfs, we show that a band-by-band classification method more accurately agrees with optical spectral typing systems than previous L dwarf NIR classification schemes. UTK is written in python, released on Zenodo with a BSD-3 clause license and publicly available on the BDNYC Github page.

CACTI: free, open-source software for the sequential coding of behavioral interactions.

PubMed

Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

CFS MATLAB toolbox: An experiment builder for continuous flash suppression (CFS) task.

PubMed

Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka

2017-09-15

CFS toolbox is an open-source collection of MATLAB functions that utilizes PsychToolbox-3 (PTB-3). It is designed to allow a researcher to create and run continuous flash suppression experiments using a variety of experimental parameters (i.e., stimulus types and locations, noise characteristics, and experiment window settings). In a CFS experiment, one of the eyes at a time is presented with a dynamically changing noise pattern, while the other eye is concurrently presented with a static target stimulus, such as a Gabor patch. Due to the strong interocular suppression created by the dominant noise pattern mask, the target stimulus is rendered invisible for an extended duration. Very little knowledge of MATLAB is required for using the toolbox; experiments are generated by modifying csv files with the required parameters, and result data are output to text files for further analysis. The open-source code is available on the project page under a Creative Commons License ( http://www.mikkonuutinen.arkku.net/CFS_toolbox/ and https://bitbucket.org/mikkonuutinen/cfs_toolbox ).

Low Cost, Scalable Proteomics Data Analysis Using Amazon's Cloud Computing Services and Open Source Search Algorithms

PubMed Central

Halligan, Brian D.; Geiger, Joey F.; Vallejos, Andrew K.; Greene, Andrew S.; Twigger, Simon N.

2009-01-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step by step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center website (http://proteomics.mcw.edu/vipdac). PMID:19358578

Apis - a Digital Inventory of Archaeological Heritage Based on Remote Sensing Data

NASA Astrophysics Data System (ADS)

Doneus, M.; Forwagner, U.; Liem, J.; Sevara, C.

2017-08-01

Heritage managers are in need of dynamic spatial inventories of archaeological and cultural heritage that provide them with multipurpose tools to interactively understand information about archaeological heritage within its landscape context. Specifically, linking site information with the respective non-invasive prospection data is of increasing importance as it allows for the assessment of inherent uncertainties related to the use and interpretation of remote sensing data by the educated and knowledgeable heritage manager. APIS, the archaeological prospection information system of the Aerial Archive of the University of Vienna, is specifically designed to meet these needs. It provides storage and easy access to all data concerning aerial photographs and archaeological sites through a single GIS-based application. Furthermore, APIS has been developed in an open source environment, which allows it to be freely distributed and modified. This combination in one single open source system facilitates an easy workflow for data management, interpretation, storage, and retrieval. APIS and a sample dataset will be released free of charge under creative commons license in near future.

TEA: A Code Calculating Thermochemical Equilibrium Abundances

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. We tested the code against the method of Burrows & Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows & Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but with higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.

ScreenMasker: An Open-source Gaze-contingent Screen Masking Environment.

PubMed

Orlov, Pavel A; Bednarik, Roman

2016-09-01

The moving-window paradigm, based on gazecontingent technic, traditionally used in a studies of the visual perceptual span. There is a strong demand for new environments that could be employed by non-technical researchers. We have developed an easy-to-use tool with a graphical user interface (GUI) allowing both execution and control of visual gaze-contingency studies. This work describes ScreenMasker, an environment that allows create gaze-contingent textured displays used together with stimuli presentation software. ScreenMasker has an architecture that meets the requirements of low-latency real-time eye-movement experiments. It also provides a variety of settings and functions. Effective rendering times and performance are ensured by means of GPU processing under CUDA technology. Performance tests show ScreenMasker's latency to be 67-74 ms on a typical office computer, and high-end 144-Hz screen latencies of about 25-28 ms. ScreenMasker is an open-source system distributed under the GNU Lesser General Public License and is available at https://github.com/PaulOrlov/ScreenMasker .

Exo-Transmit: An Open-Source Code for Calculating Transmission Spectra for Exoplanet Atmospheres of Varied Composition

NASA Astrophysics Data System (ADS)

Kempton, Eliza M.-R.; Lupu, Roxana; Owusu-Asare, Albert; Slough, Patrick; Cale, Bryson

2017-04-01

We present Exo-Transmit, a software package to calculate exoplanet transmission spectra for planets of varied composition. The code is designed to generate spectra of planets with a wide range of atmospheric composition, temperature, surface gravity, and size, and is therefore applicable to exoplanets ranging in mass and size from hot Jupiters down to rocky super-Earths. Spectra can be generated with or without clouds or hazes with options to (1) include an optically thick cloud deck at a user-specified atmospheric pressure or (2) to augment the nominal Rayleigh scattering by a user-specified factor. The Exo-Transmit code is written in C and is extremely easy to use. Typically the user will only need to edit parameters in a single user input file in order to run the code for a planet of their choosing. Exo-Transmit is available publicly on Github with open-source licensing at https://github.com/elizakempton/Exo_Transmit.

What makes computational open source software libraries successful?

NASA Astrophysics Data System (ADS)

Bangerth, Wolfgang; Heister, Timo

2013-01-01

Software is the backbone of scientific computing. Yet, while we regularly publish detailed accounts about the results of scientific software, and while there is a general sense of which numerical methods work well, our community is largely unaware of best practices in writing the large-scale, open source scientific software upon which our discipline rests. This is particularly apparent in the commonly held view that writing successful software packages is largely the result of simply ‘being a good programmer’ when in fact there are many other factors involved, for example the social skill of community building. In this paper, we consider what we have found to be the necessary ingredients for successful scientific software projects and, in particular, for software libraries upon which the vast majority of scientific codes are built today. In particular, we discuss the roles of code, documentation, communities, project management and licenses. We also briefly comment on the impact on academic careers of engaging in software projects.

Low cost, scalable proteomics data analysis using Amazon's cloud computing services and open source search algorithms.

PubMed

Halligan, Brian D; Geiger, Joey F; Vallejos, Andrew K; Greene, Andrew S; Twigger, Simon N

2009-06-01

One of the major difficulties for many laboratories setting up proteomics programs has been obtaining and maintaining the computational infrastructure required for the analysis of the large flow of proteomics data. We describe a system that combines distributed cloud computing and open source software to allow laboratories to set up scalable virtual proteomics analysis clusters without the investment in computational hardware or software licensing fees. Additionally, the pricing structure of distributed computing providers, such as Amazon Web Services, allows laboratories or even individuals to have large-scale computational resources at their disposal at a very low cost per run. We provide detailed step-by-step instructions on how to implement the virtual proteomics analysis clusters as well as a list of current available preconfigured Amazon machine images containing the OMSSA and X!Tandem search algorithms and sequence databases on the Medical College of Wisconsin Proteomics Center Web site ( http://proteomics.mcw.edu/vipdac ).

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

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

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver, E-mail: jasmina@physics.ucf.edu

2016-07-01

We present an open-source Thermochemical Equilibrium Abundances (TEA) code that calculates the abundances of gaseous molecular species. The code is based on the methodology of White et al. and Eriksson. It applies Gibbs free-energy minimization using an iterative, Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature–pressure pairs. We tested the code against the method of Burrows and Sharp, the free thermochemical equilibrium code Chemical Equilibrium with Applications (CEA), and the example given by Burrows and Sharp. Using their thermodynamic data, TEA reproduces their final abundances, but withmore » higher precision. We also applied the TEA abundance calculations to models of several hot-Jupiter exoplanets, producing expected results. TEA is written in Python in a modular format. There is a start guide, a user manual, and a code document in addition to this theory paper. TEA is available under a reproducible-research, open-source license via https://github.com/dzesmin/TEA.« less

Open Babel: An open chemical toolbox

PubMed Central

2011-01-01

Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

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/ .

KaBOB: ontology-based semantic integration of biomedical databases.

PubMed

Livingston, Kevin M; Bada, Michael; Baumgartner, William A; Hunter, Lawrence E

2015-04-23

The ability to query many independent biological databases using a common ontology-based semantic model would facilitate deeper integration and more effective utilization of these diverse and rapidly growing resources. Despite ongoing work moving toward shared data formats and linked identifiers, significant problems persist in semantic data integration in order to establish shared identity and shared meaning across heterogeneous biomedical data sources. We present five processes for semantic data integration that, when applied collectively, solve seven key problems. These processes include making explicit the differences between biomedical concepts and database records, aggregating sets of identifiers denoting the same biomedical concepts across data sources, and using declaratively represented forward-chaining rules to take information that is variably represented in source databases and integrating it into a consistent biomedical representation. We demonstrate these processes and solutions by presenting KaBOB (the Knowledge Base Of Biomedicine), a knowledge base of semantically integrated data from 18 prominent biomedical databases using common representations grounded in Open Biomedical Ontologies. An instance of KaBOB with data about humans and seven major model organisms can be built using on the order of 500 million RDF triples. All source code for building KaBOB is available under an open-source license. KaBOB is an integrated knowledge base of biomedical data representationally based in prominent, actively maintained Open Biomedical Ontologies, thus enabling queries of the underlying data in terms of biomedical concepts (e.g., genes and gene products, interactions and processes) rather than features of source-specific data schemas or file formats. KaBOB resolves many of the issues that routinely plague biomedical researchers intending to work with data from multiple data sources and provides a platform for ongoing data integration and development and for formal reasoning over a wealth of integrated biomedical data.

10 CFR 40.25 - General license for use of certain industrial products or devices.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license for use of certain industrial products or devices. 40.25 Section 40.25 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL... person receiving the source material pursuant to such transfer. (e) Any person receiving, acquiring...

CheapStat: an open-source, "do-it-yourself" potentiostat for analytical and educational applications.

PubMed

Rowe, Aaron A; Bonham, Andrew J; White, Ryan J; Zimmer, Michael P; Yadgar, Ramsin J; Hobza, Tony M; Honea, Jim W; Ben-Yaacov, Ilan; Plaxco, Kevin W

2011-01-01

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license.

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database.

PubMed

Zappia, Luke; Phipson, Belinda; Oshlack, Alicia

2018-06-25

As single-cell RNA-sequencing (scRNA-seq) datasets have become more widespread the number of tools designed to analyse these data has dramatically increased. Navigating the vast sea of tools now available is becoming increasingly challenging for researchers. In order to better facilitate selection of appropriate analysis tools we have created the scRNA-tools database (www.scRNA-tools.org) to catalogue and curate analysis tools as they become available. Our database collects a range of information on each scRNA-seq analysis tool and categorises them according to the analysis tasks they perform. Exploration of this database gives insights into the areas of rapid development of analysis methods for scRNA-seq data. We see that many tools perform tasks specific to scRNA-seq analysis, particularly clustering and ordering of cells. We also find that the scRNA-seq community embraces an open-source and open-science approach, with most tools available under open-source licenses and preprints being extensively used as a means to describe methods. The scRNA-tools database provides a valuable resource for researchers embarking on scRNA-seq analysis and records the growth of the field over time.

CheapStat: An Open-Source, “Do-It-Yourself” Potentiostat for Analytical and Educational Applications

PubMed Central

Rowe, Aaron A.; Bonham, Andrew J.; White, Ryan J.; Zimmer, Michael P.; Yadgar, Ramsin J.; Hobza, Tony M.; Honea, Jim W.; Ben-Yaacov, Ilan; Plaxco, Kevin W.

2011-01-01

Although potentiostats are the foundation of modern electrochemical research, they have seen relatively little application in resource poor settings, such as undergraduate laboratory courses and the developing world. One reason for the low penetration of potentiostats is their cost, as even the least expensive commercially available laboratory potentiostats sell for more than one thousand dollars. An inexpensive electrochemical workstation could thus prove useful in educational labs, and increase access to electrochemistry-based analytical techniques for food, drug and environmental monitoring. With these motivations in mind, we describe here the CheapStat, an inexpensive (<$80), open-source (software and hardware), hand-held potentiostat that can be constructed by anyone who is proficient at assembling circuits. This device supports a number of potential waveforms necessary to perform cyclic, square wave, linear sweep and anodic stripping voltammetry. As we demonstrate, it is suitable for a wide range of applications ranging from food- and drug-quality testing to environmental monitoring, rapid DNA detection, and educational exercises. The device's schematics, parts lists, circuit board layout files, sample experiments, and detailed assembly instructions are available in the supporting information and are released under an open hardware license. PMID:21931613

78 FR 33691 - Distribution of Source Material to Exempt Persons and to General Licensees and Revision of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-05

... Distribution of Source Material to Exempt Persons and to General Licensees and Revision of General License and..., Distribution of Source Material to Exempt Persons and to General Licensees and Revision of General License and Exemptions (Distribution of Source Material Rule). The Distribution of Source Material Rule amended the NRC's...

Pyteomics--a Python framework for exploratory data analysis and rapid software prototyping in proteomics.

PubMed

Goloborodko, Anton A; Levitsky, Lev I; Ivanov, Mark V; Gorshkov, Mikhail V

2013-02-01

Pyteomics is a cross-platform, open-source Python library providing a rich set of tools for MS-based proteomics. It provides modules for reading LC-MS/MS data, search engine output, protein sequence databases, theoretical prediction of retention times, electrochemical properties of polypeptides, mass and m/z calculations, and sequence parsing. Pyteomics is available under Apache license; release versions are available at the Python Package Index http://pypi.python.org/pyteomics, the source code repository at http://hg.theorchromo.ru/pyteomics, documentation at http://packages.python.org/pyteomics. Pyteomics.biolccc documentation is available at http://packages.python.org/pyteomics.biolccc/. Questions on installation and usage can be addressed to pyteomics mailing list: pyteomics@googlegroups.com.

SPV: a JavaScript Signaling Pathway Visualizer.

PubMed

Calderone, Alberto; Cesareni, Gianni

2018-03-24

The visualization of molecular interactions annotated in web resources is useful to offer to users such information in a clear intuitive layout. These interactions are frequently represented as binary interactions that are laid out in free space where, different entities, cellular compartments and interaction types are hardly distinguishable. SPV (Signaling Pathway Visualizer) is a free open source JavaScript library which offers a series of pre-defined elements, compartments and interaction types meant to facilitate the representation of signaling pathways consisting of causal interactions without neglecting simple protein-protein interaction networks. freely available under Apache version 2 license; Source code: https://github.com/Sinnefa/SPV_Signaling_Pathway_Visualizer_v1.0. Language: JavaScript; Web technology: Scalable Vector Graphics; Libraries: D3.js. sinnefa@gmail.com.

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.

ProtVista: visualization of protein sequence annotations.

PubMed

Watkins, Xavier; Garcia, Leyla J; Pundir, Sangya; Martin, Maria J

2017-07-01

ProtVista is a comprehensive visualization tool for the graphical representation of protein sequence features in the UniProt Knowledgebase, experimental proteomics and variation public datasets. The complexity and relationships in this wealth of data pose a challenge in interpretation. Integrative visualization approaches such as provided by ProtVista are thus essential for researchers to understand the data and, for instance, discover patterns affecting function and disease associations. ProtVista is a JavaScript component released as an open source project under the Apache 2 License. Documentation and source code are available at http://ebi-uniprot.github.io/ProtVista/ . martin@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. 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

SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.

PubMed

Curtis, Darren S; Phillips, Aaron R; Callister, Stephen J; Conlan, Sean; McCue, Lee Ann

2013-10-15

At the rate that prokaryotic genomes can now be generated, comparative genomics studies require a flexible method for quickly and accurately predicting orthologs among the rapidly changing set of genomes available. SPOCS implements a graph-based ortholog prediction method to generate a simple tab-delimited table of orthologs and in addition, html files that provide a visualization of the predicted ortholog/paralog relationships to which gene/protein expression metadata may be overlaid. A SPOCS web application is freely available at http://cbb.pnnl.gov/portal/tools/spocs.html. Source code for Linux systems is also freely available under an open source license at http://cbb.pnnl.gov/portal/software/spocs.html; the Boost C++ libraries and BLAST are required.

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

PubMed

Loening, Andreas Markus; Gambhir, Sanjiv Sam

2003-07-01

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

An automated workflow for parallel processing of large multiview SPIM recordings

PubMed Central

Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

2016-01-01

Summary: Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. Availability and implementation: The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT. The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows. Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction. Contact: schmied@mpi-cbg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26628585

An automated workflow for parallel processing of large multiview SPIM recordings.

PubMed

Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

2016-04-01

Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction : schmied@mpi-cbg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.

PubMed

Forth, Thomas; McConkey, Glenn A; Westhead, David R

2010-09-15

An application has been developed to help with the creation and editing of Systems Biology Markup Language (SBML) format metabolic networks up to the organism scale. Networks are defined as a collection of Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND reactions with an optional associated Enzyme Classification (EC) number for each reaction. Additional custom reactions can be defined by the user. Reactions within the network can be assigned flux constraints and compartmentalization is supported for each reaction in addition to the support for reactions that occur across compartment boundaries. Exported networks are fully SBML L2V4 compatible with an optional L2V1 export for compatibility with old versions of the COBRA toolbox. The software runs in the free Microsoft Access 2007 Runtime (Microsoft Inc.), which is included with the installer and works on Windows XP SP2 or better. Full source code is viewable in the full version of Access 2007 or 2010. Users must have a license to use the KEGG LIGAND database (free academic licensing is available). Please go to www.bioinformatics.leeds.ac.uk/~pytf/metnetmaker for software download, help and tutorials.

77 FR 73545 - Implementation of the Local Community Radio Act of 2010; Revision of Service and Eligibility...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-11

... our FM translator licensing procedures and modify licensing and service rules for the low power FM... clarifications the comprehensive plan for licensing FM translators and LPFM stations adopted in the Fourth Report...-delayed processing of over 6,000 FM translator applications and establish a timeline for the opening of an...

A computational genomics pipeline for prokaryotic sequencing projects

PubMed Central

Kislyuk, Andrey O.; Katz, Lee S.; Agrawal, Sonia; Hagen, Matthew S.; Conley, Andrew B.; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C.; Sammons, Scott A.; Govil, Dhwani; Mair, Raydel D.; Tatti, Kathleen M.; Tondella, Maria L.; Harcourt, Brian H.; Mayer, Leonard W.; Jordan, I. King

2010-01-01

Motivation: New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. Results: We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. Availability and implementation: The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems. Contact: king.jordan@biology.gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20519285

10 CFR 61.23 - Standards for issuance of a license.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE Licenses § 61.23 Standards for issuance of a license. A license for the receipt, possession, and disposal of waste containing or contaminated with source, special nuclear, or byproduct material will be...

10 CFR 61.23 - Standards for issuance of a license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE Licenses § 61.23 Standards for issuance of a license. A license for the receipt, possession, and disposal of waste containing or contaminated with source, special nuclear, or byproduct material will be...

10 CFR 61.23 - Standards for issuance of a license.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE Licenses § 61.23 Standards for issuance of a license. A license for the receipt, possession, and disposal of waste containing or contaminated with source, special nuclear, or byproduct material will be...

10 CFR 61.23 - Standards for issuance of a license.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE Licenses § 61.23 Standards for issuance of a license. A license for the receipt, possession, and disposal of waste containing or contaminated with source, special nuclear, or byproduct material will be...

10 CFR 61.23 - Standards for issuance of a license.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE Licenses § 61.23 Standards for issuance of a license. A license for the receipt, possession, and disposal of waste containing or contaminated with source, special nuclear, or byproduct material will be...

Spatial rainfall data in open source environment

NASA Astrophysics Data System (ADS)

Schuurmans, Hanneke; Maarten Verbree, Jan; Leijnse, Hidde; van Heeringen, Klaas-Jan; Uijlenhoet, Remko; Bierkens, Marc; van de Giesen, Nick; Gooijer, Jan; van den Houten, Gert

2013-04-01

Since January 2013 The Netherlands have access to innovative high-quality rainfall data that is used for watermanagers. This product is innovative because of the following reasons. (i) The product is developed in a 'golden triangle' construction - corporation between government, business and research. (ii) Second the rainfall products are developed according to the open-source GPL license. The initiative comes from a group of water boards in the Netherlands that joined their forces to fund the development of a new rainfall product. Not only data from Dutch radar stations (as is currently done by the Dutch meteorological organization KNMI) is used but also data from radars in Germany and Belgium. After a radarcomposite is made, it is adjusted according to data from raingauges (ground truth). This results in 9 different rainfall products that give for each moment the best rainfall data. Specific knowledge is necessary to develop these kind of data. Therefore a pool of experts (KNMI, Deltares and 3 universities) participated in the development. The philosophy of the developers (being corporations) is that products like this should be developed in open source. This way knowledge is shared and the whole community is able to make suggestions for improvement. In our opinion this is the only way to make real progress in product development. Furthermore the financial resources of government organizations are optimized. More info (in Dutch): www.nationaleregenradar.nl

Evaluation of DICOM viewer software for workflow integration in clinical trials

NASA Astrophysics Data System (ADS)

Haak, Daniel; Page, Charles E.; Kabino, Klaus; Deserno, Thomas M.

2015-03-01

The digital imaging and communications in medicine (DICOM) protocol is nowadays the leading standard for capture, exchange and storage of image data in medical applications. A broad range of commercial, free, and open source software tools supporting a variety of DICOM functionality exists. However, different from patient's care in hospital, DICOM has not yet arrived in electronic data capture systems (EDCS) for clinical trials. Due to missing integration, even just the visualization of patient's image data in electronic case report forms (eCRFs) is impossible. Four increasing levels for integration of DICOM components into EDCS are conceivable, raising functionality but also demands on interfaces with each level. Hence, in this paper, a comprehensive evaluation of 27 DICOM viewer software projects is performed, investigating viewing functionality as well as interfaces for integration. Concerning general, integration, and viewing requirements the survey involves the criteria (i) license, (ii) support, (iii) platform, (iv) interfaces, (v) two-dimensional (2D) and (vi) three-dimensional (3D) image viewing functionality. Optimal viewers are suggested for applications in clinical trials for 3D imaging, hospital communication, and workflow. Focusing on open source solutions, the viewers ImageJ and MicroView are superior for 3D visualization, whereas GingkoCADx is advantageous for hospital integration. Concerning workflow optimization in multi-centered clinical trials, we suggest the open source viewer Weasis. Covering most use cases, an EDCS and PACS interconnection with Weasis is suggested.

10 CFR 40.44 - Amendment of licenses at request of licensee.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Amendment of licenses at request of licensee. 40.44 Section 40.44 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.44 Amendment of licenses at request of licensee. Applications for amendment of a license shall be filed on NRC...

10 CFR 40.43 - Renewal of licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Renewal of licenses. 40.43 Section 40.43 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.43 Renewal of licenses. (a) Application for renewal of a specific license must be filed on NRC Form 313 and in accordance with § 40.31. (b...

Inexpensive Open-Source Data Logging in the Field

NASA Astrophysics Data System (ADS)

Wickert, A. D.

2013-12-01

I present a general-purpose open-source field-capable data logger, which provides a mechanism to develop dense networks of inexpensive environmental sensors. This data logger was developed as a low-power variant of the Arduino open-source development system, and is named the ALog ("Arduino Logger") BottleLogger (it is slim enough to fit inside a Nalgene water bottle) version 1.0. It features an integrated high-precision real-time clock, SD card slot for high-volume data storage, and integrated power switching. The ALog can interface with sensors via six analog/digital pins, two digital pins, and one digital interrupt pin that can read event-based inputs, such as those from a tipping-bucket rain gauge. We have successfully tested the ALog BottleLogger with ultrasonic rangefinders (for water stage and snow accumulation and melt), temperature sensors, tipping-bucket rain gauges, soil moisture and water potential sensors, resistance-based tools to measure frost heave, and cameras that it triggers based on events. The source code for the ALog, including functions to interface with a a range of commercially-available sensors, is provided as an Arduino C++ library with example implementations. All schematics, circuit board layouts, and source code files are open-source and freely available under GNU GPL v3.0 and Creative Commons Attribution-ShareAlike 3.0 Unported licenses. Through this work, we hope to foster a community-driven movement to collect field environmental data on a budget that permits citizen-scientists and researchers from low-income countries to collect the same high-quality data as researchers in wealthy countries. These data can provide information about global change to managers, governments, scientists, and interested citizens worldwide. Watertight box with ALog BottleLogger data logger on the left and battery pack with 3 D cells on the right. Data can be collected for 3-5 years on one set of batteries.

10 CFR 40.71 - Modification and revocation of licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Modification and revocation of licenses. 40.71 Section 40.71 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Modification and Revocation of Licenses § 40.71 Modification and revocation of licenses. (a) The terms and conditions of each...

10 CFR 60.41 - Standards for issuance of a license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REPOSITORIES Licenses License Issuance and Amendment § 60.41 Standards for issuance of a license. A license to receive and possess source, special nuclear, or byproduct material at a geologic repository operations area may be issued by the Commission upon finding that: (a) Construction of the geologic repository...

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

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

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

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

OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

An Open-source Community Web Site To Support Ground-Water Model Testing

NASA Astrophysics Data System (ADS)

Kraemer, S. R.; Bakker, M.; Craig, J. R.

2007-12-01

A community wiki wiki web site has been created as a resource to support ground-water model development and testing. The Groundwater Gourmet wiki is a repository for user supplied analytical and numerical recipes, howtos, and examples. Members are encouraged to submit analytical solutions, including source code and documentation. A diversity of code snippets are sought in a variety of languages, including Fortran, C, C++, Matlab, Python. In the spirit of a wiki, all contributions may be edited and altered by other users, and open source licensing is promoted. Community accepted contributions are graduated into the library of analytic solutions and organized into either a Strack (Groundwater Mechanics, 1989) or Bruggeman (Analytical Solutions of Geohydrological Problems, 1999) classification. The examples section of the wiki are meant to include laboratory experiments (e.g., Hele Shaw), classical benchmark problems (e.g., Henry Problem), and controlled field experiments (e.g., Borden landfill and Cape Cod tracer tests). Although this work was reviewed by EPA and approved for publication, it may not necessarily reflect official Agency policy. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

MultiElec: A MATLAB Based Application for MEA Data Analysis.

PubMed

Georgiadis, Vassilis; Stephanou, Anastasis; Townsend, Paul A; Jackson, Thomas R

2015-01-01

We present MultiElec, an open source MATLAB based application for data analysis of microelectrode array (MEA) recordings. MultiElec displays an extremely user-friendly graphic user interface (GUI) that allows the simultaneous display and analysis of voltage traces for 60 electrodes and includes functions for activation-time determination, the production of activation-time heat maps with activation time and isoline display. Furthermore, local conduction velocities are semi-automatically calculated along with their corresponding vector plots. MultiElec allows ad hoc signal suppression, enabling the user to easily and efficiently handle signal artefacts and for incomplete data sets to be analysed. Voltage traces and heat maps can be simply exported for figure production and presentation. In addition, our platform is able to produce 3D videos of signal progression over all 60 electrodes. Functions are controlled entirely by a single GUI with no need for command line input or any understanding of MATLAB code. MultiElec is open source under the terms of the GNU General Public License as published by the Free Software Foundation, version 3. Both the program and source code are available to download from http://www.cancer.manchester.ac.uk/MultiElec/.

10 CFR 35.11 - License required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... material or discrete sources of radium-226 for which a specific medical use license is required in... persons, who possess and use accelerator-produced radioactive material or discrete sources of radium-226...

dsmcFoam+: An OpenFOAM based direct simulation Monte Carlo solver

NASA Astrophysics Data System (ADS)

White, C.; Borg, M. K.; Scanlon, T. J.; Longshaw, S. M.; John, B.; Emerson, D. R.; Reese, J. M.

2018-03-01

dsmcFoam+ is a direct simulation Monte Carlo (DSMC) solver for rarefied gas dynamics, implemented within the OpenFOAM software framework, and parallelised with MPI. It is open-source and released under the GNU General Public License in a publicly available software repository that includes detailed documentation and tutorial DSMC gas flow cases. This release of the code includes many features not found in standard dsmcFoam, such as molecular vibrational and electronic energy modes, chemical reactions, and subsonic pressure boundary conditions. Since dsmcFoam+ is designed entirely within OpenFOAM's C++ object-oriented framework, it benefits from a number of key features: the code emphasises extensibility and flexibility so it is aimed first and foremost as a research tool for DSMC, allowing new models and test cases to be developed and tested rapidly. All DSMC cases are as straightforward as setting up any standard OpenFOAM case, as dsmcFoam+ relies upon the standard OpenFOAM dictionary based directory structure. This ensures that useful pre- and post-processing capabilities provided by OpenFOAM remain available even though the fully Lagrangian nature of a DSMC simulation is not typical of most OpenFOAM applications. We show that dsmcFoam+ compares well to other well-known DSMC codes and to analytical solutions in terms of benchmark results.

FRED (a Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations.

PubMed

Grefenstette, John J; Brown, Shawn T; Rosenfeld, Roni; DePasse, Jay; Stone, Nathan T B; Cooley, Phillip C; Wheaton, William D; Fyshe, Alona; Galloway, David D; Sriram, Anuroop; Guclu, Hasan; Abraham, Thomas; Burke, Donald S

2013-10-08

Mathematical and computational models provide valuable tools that help public health planners to evaluate competing health interventions, especially for novel circumstances that cannot be examined through observational or controlled studies, such as pandemic influenza. The spread of diseases like influenza depends on the mixing patterns within the population, and these mixing patterns depend in part on local factors including the spatial distribution and age structure of the population, the distribution of size and composition of households, employment status and commuting patterns of adults, and the size and age structure of schools. Finally, public health planners must take into account the health behavior patterns of the population, patterns that often vary according to socioeconomic factors such as race, household income, and education levels. FRED (a Framework for Reconstructing Epidemic Dynamics) is a freely available open-source agent-based modeling system based closely on models used in previously published studies of pandemic influenza. This version of FRED uses open-access census-based synthetic populations that capture the demographic and geographic heterogeneities of the population, including realistic household, school, and workplace social networks. FRED epidemic models are currently available for every state and county in the United States, and for selected international locations. State and county public health planners can use FRED to explore the effects of possible influenza epidemics in specific geographic regions of interest and to help evaluate the effect of interventions such as vaccination programs and school closure policies. FRED is available under a free open source license in order to contribute to the development of better modeling tools and to encourage open discussion of modeling tools being used to evaluate public health policies. We also welcome participation by other researchers in the further development of FRED.

77 FR 43866 - Notice of Intent To Grant a Partially Exclusive License

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

... No. 11/ 671,089 entitled ``Wireless Sensing System Using Open-Circuit, Electrically-Conductive Spiral..., Virginia. The license may be limited to one or more fields of use. The patent rights in these inventions...

The EnzymeTracker: an open-source laboratory information management system for sample tracking.

PubMed

Triplet, Thomas; Butler, Gregory

2012-01-26

In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license.

The EnzymeTracker: an open-source laboratory information management system for sample tracking

PubMed Central

2012-01-01

Background In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone, as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary systems have been developed, which laboratories need to pay expensive license fees for. Those costs are usually prohibitive for most laboratories and prevent scientists from benefiting from more sophisticated data management systems. Results In this paper, we propose the EnzymeTracker, a web-based laboratory information management system for sample tracking, as an open-source and flexible alternative that aims at facilitating entry, mining and sharing of experimental biological data. The EnzymeTracker features online spreadsheets and tools for monitoring numerous experiments conducted by several collaborators to identify and characterize samples. It also provides libraries of shared data such as protocols, and administration tools for data access control using OpenID and user/team management. Our system relies on a database management system for efficient data indexing and management and a user-friendly AJAX interface that can be accessed over the Internet. The EnzymeTracker facilitates data entry by dynamically suggesting entries and providing smart data-mining tools to effectively retrieve data. Our system features a number of tools to visualize and annotate experimental data, and export highly customizable reports. It also supports QR matrix barcoding to facilitate sample tracking. Conclusions The EnzymeTracker was designed to be easy to use and offers many benefits over spreadsheets, thus presenting the characteristics required to facilitate acceptance by the scientific community. It has been successfully used for 20 months on a daily basis by over 50 scientists. The EnzymeTracker is freely available online at http://cubique.fungalgenomics.ca/enzymedb/index.html under the GNU GPLv3 license. PMID:22280360

10 CFR 40.34 - Special requirements for issuance of specific licenses.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Special requirements for issuance of specific licenses. 40.34 Section 40.34 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL License Applications § 40.34 Special requirements for issuance of specific licenses. (a) An application for a specific...

10 CFR 40.33 - Issuance of a license for a uranium enrichment facility.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Issuance of a license for a uranium enrichment facility. 40.33 Section 40.33 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL License Applications § 40.33 Issuance of a license for a uranium enrichment facility. (a) The Commission...

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web.

PubMed

Taylor, Stephen; Noble, Roger

2014-09-15

Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. © The Author 2014. Published by Oxford University Press.

A-Track: A new approach for detection of moving objects in FITS images

NASA Astrophysics Data System (ADS)

Atay, T.; Kaplan, M.; Kilic, Y.; Karapinar, N.

2016-10-01

We have developed a fast, open-source, cross-platform pipeline, called A-Track, for detecting the moving objects (asteroids and comets) in sequential telescope images in FITS format. The pipeline is coded in Python 3. The moving objects are detected using a modified line detection algorithm, called MILD. We tested the pipeline on astronomical data acquired by an SI-1100 CCD with a 1-meter telescope. We found that A-Track performs very well in terms of detection efficiency, stability, and processing time. The code is hosted on GitHub under the GNU GPL v3 license.

MetExploreViz: web component for interactive metabolic network visualization.

PubMed

Chazalviel, Maxime; Frainay, Clément; Poupin, Nathalie; Vinson, Florence; Merlet, Benjamin; Gloaguen, Yoann; Cottret, Ludovic; Jourdan, Fabien

2017-09-15

MetExploreViz is an open source web component that can be easily embedded in any web site. It provides features dedicated to the visualization of metabolic networks and pathways and thus offers a flexible solution to analyze omics data in a biochemical context. Documentation and link to GIT code repository (GPL 3.0 license)are available at this URL: http://metexplore.toulouse.inra.fr/metexploreViz/doc /. Tutorial is available at this URL. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

SYNCSA--R tool for analysis of metacommunities based on functional traits and phylogeny of the community components.

PubMed

Debastiani, Vanderlei J; Pillar, Valério D

2012-08-01

SYNCSA is an R package for the analysis of metacommunities based on functional traits and phylogeny of the community components. It offers tools to calculate several matrix correlations that express trait-convergence assembly patterns, trait-divergence assembly patterns and phylogenetic signal in functional traits at the species pool level and at the metacommunity level. SYNCSA is a package for the R environment, under a GPL-2 open-source license and freely available on CRAN official web server for R (http://cran.r-project.org). vanderleidebastiani@yahoo.com.br.

pez: phylogenetics for the environmental sciences.

PubMed

Pearse, William D; Cadotte, Marc W; Cavender-Bares, Jeannine; Ives, Anthony R; Tucker, Caroline M; Walker, Steve C; Helmus, Matthew R

2015-09-01

pez is an R package that permits measurement, modelling and simulation of phylogenetic structure in ecological data. pez contains the first implementation of many methods in R, and aggregates existing data structures and methods into a single, coherent package. pez is released under the GPL v3 open-source license, available on the Internet from CRAN (http://cran.r-project.org). The package is under active development, and the authors welcome contributions (see http://github.com/willpearse/pez). will.pearse@gmail.com. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Picante: R tools for integrating phylogenies and ecology.

PubMed

Kembel, Steven W; Cowan, Peter D; Helmus, Matthew R; Cornwell, William K; Morlon, Helene; Ackerly, David D; Blomberg, Simon P; Webb, Campbell O

2010-06-01

Picante is a software package that provides a comprehensive set of tools for analyzing the phylogenetic and trait diversity of ecological communities. The package calculates phylogenetic diversity metrics, performs trait comparative analyses, manipulates phenotypic and phylogenetic data, and performs tests for phylogenetic signal in trait distributions, community structure and species interactions. Picante is a package for the R statistical language and environment written in R and C, released under a GPL v2 open-source license, and freely available on the web (http://picante.r-forge.r-project.org) and from CRAN (http://cran.r-project.org).

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

PubMed

Rosset, Antoine; Spadola, Luca; Ratib, Osman

2004-09-01

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

78 FR 4469 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses and Combined Licenses...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-22

... controverted. In addition, the requestor/petitioner shall provide a brief explanation of the bases for the... pressurizer PORV block valves provide isolation for a postulated stuck-open or leaking PORV. Isolation is...

10 CFR 40.35 - Conditions of specific licenses issued pursuant to § 40.34.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Conditions of specific licenses issued pursuant to § 40.34. 40.35 Section 40.35 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL... § 40.25 and a copy of Form NRC 244 to each person to whom he transfers source material in a product or...

Youpi: YOUr processing PIpeline

NASA Astrophysics Data System (ADS)

Monnerville, Mathias; Sémah, Gregory

2012-03-01

Youpi is a portable, easy to use web application providing high level functionalities to perform data reduction on scientific FITS images. Built on top of various open source reduction tools released to the community by TERAPIX (http://terapix.iap.fr), Youpi can help organize data, manage processing jobs on a computer cluster in real time (using Condor) and facilitate teamwork by allowing fine-grain sharing of results and data. Youpi is modular and comes with plugins which perform, from within a browser, various processing tasks such as evaluating the quality of incoming images (using the QualityFITS software package), computing astrometric and photometric solutions (using SCAMP), resampling and co-adding FITS images (using SWarp) and extracting sources and building source catalogues from astronomical images (using SExtractor). Youpi is useful for small to medium-sized data reduction projects; it is free and is published under the GNU General Public License.

Apollo: a community resource for genome annotation editing

PubMed Central

Ed, Lee; Nomi, Harris; Mark, Gibson; Raymond, Chetty; Suzanna, Lewis

2009-01-01

Summary: Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Availability: Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo. Contact: elee@berkeleybop.org PMID:19439563

Apollo: a community resource for genome annotation editing.

PubMed

Lee, Ed; Harris, Nomi; Gibson, Mark; Chetty, Raymond; Lewis, Suzanna

2009-07-15

Apollo is a genome annotation-editing tool with an easy to use graphical interface. It is a component of the GMOD project, with ongoing development driven by the community. Recent additions to the software include support for the generic feature format version 3 (GFF3), continuous transcriptome data, a full Chado database interface, integration with remote services for on-the-fly BLAST and Primer BLAST analyses, graphical interfaces for configuring user preferences and full undo of all edit operations. Apollo's user community continues to grow, including its use as an educational tool for college and high-school students. Apollo is a Java application distributed under a free and open source license. Installers for Windows, Linux, Unix, Solaris and Mac OS X are available at http://apollo.berkeleybop.org, and the source code is available from the SourceForge CVS repository at http://gmod.cvs.sourceforge.net/gmod/apollo.

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.

Technical Note: FreeCT_ICD: An Open Source Implementation of a Model-Based Iterative Reconstruction Method using Coordinate Descent Optimization for CT Imaging Investigations.

PubMed

Hoffman, John M; Noo, Frédéric; Young, Stefano; Hsieh, Scott S; McNitt-Gray, Michael

2018-06-01

To facilitate investigations into the impacts of acquisition and reconstruction parameters on quantitative imaging, radiomics and CAD using CT imaging, we previously released an open source implementation of a conventional weighted filtered backprojection reconstruction called FreeCT_wFBP. Our purpose was to extend that work by providing an open-source implementation of a model-based iterative reconstruction method using coordinate descent optimization, called FreeCT_ICD. Model-based iterative reconstruction offers the potential for substantial radiation dose reduction, but can impose substantial computational processing and storage requirements. FreeCT_ICD is an open source implementation of a model-based iterative reconstruction method that provides a reasonable tradeoff between these requirements. This was accomplished by adapting a previously proposed method that allows the system matrix to be stored with a reasonable memory requirement. The method amounts to describing the attenuation coefficient using rotating slices that follow the helical geometry. In the initially-proposed version, the rotating slices are themselves described using blobs. We have replaced this description by a unique model that relies on tri-linear interpolation together with the principles of Joseph's method. This model offers an improvement in memory requirement while still allowing highly accurate reconstruction for conventional CT geometries. The system matrix is stored column-wise and combined with an iterative coordinate descent (ICD) optimization. The result is FreeCT_ICD, which is a reconstruction program developed on the Linux platform using C++ libraries and the open source GNU GPL v2.0 license. The software is capable of reconstructing raw projection data of helical CT scans. In this work, the software has been described and evaluated by reconstructing datasets exported from a clinical scanner which consisted of an ACR accreditation phantom dataset and a clinical pediatric thoracic scan. For the ACR phantom, image quality was comparable to clinical reconstructions as well as reconstructions using open-source FreeCT_wFBP software. The pediatric thoracic scan also yielded acceptable results. In addition, we did not observe any deleterious impact in image quality associated with the utilization of rotating slices. These evaluations also demonstrated reasonable tradeoffs in storage requirements and computational demands. FreeCT_ICD is an open-source implementation of a model-based iterative reconstruction method that extends the capabilities of previously released open source reconstruction software and provides the ability to perform vendor-independent reconstructions of clinically acquired raw projection data. This implementation represents a reasonable tradeoff between storage and computational requirements and has demonstrated acceptable image quality in both simulated and clinical image datasets. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Open Data as Open Educational Resources: Towards Transversal Skills and Global Citizenship

ERIC Educational Resources Information Center

Atenas, Javiera; Havemann, Leo; Priego, Ernesto

2015-01-01

Open Data is the name given to datasets which have been generated by international organisations, governments, NGOs and academic researchers, and made freely available online and openly-licensed. These datasets can be used by educators as Open Educational Resources (OER) to support different teaching and learning activities, allowing students to…

10 CFR 40.42 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Expiration and termination of licenses and decommissioning of sites and separate buildings or outdoor areas. 40.42 Section 40.42 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.42 Expiration and termination of licenses and...

10 CFR 40.42 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Expiration and termination of licenses and decommissioning of sites and separate buildings or outdoor areas. 40.42 Section 40.42 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.42 Expiration and termination of licenses and...

10 CFR 40.42 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Expiration and termination of licenses and decommissioning of sites and separate buildings or outdoor areas. 40.42 Section 40.42 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.42 Expiration and termination of licenses and...

10 CFR 40.42 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Expiration and termination of licenses and decommissioning of sites and separate buildings or outdoor areas. 40.42 Section 40.42 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.42 Expiration and termination of licenses and...

10 CFR 40.42 - Expiration and termination of licenses and decommissioning of sites and separate buildings or...

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Expiration and termination of licenses and decommissioning of sites and separate buildings or outdoor areas. 40.42 Section 40.42 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Licenses § 40.42 Expiration and termination of licenses and...

BioBlend: automating pipeline analyses within Galaxy and CloudMan.

PubMed

Sloggett, Clare; Goonasekera, Nuwan; Afgan, Enis

2013-07-01

We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs. BioBlend makes it easy for bioinformaticians to automate end-to-end large data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provide the required infrastructure and automate complex analyses over large datasets within the familiar Galaxy environment. http://bioblend.readthedocs.org/. Automated installation of BioBlend is available via PyPI (e.g. pip install bioblend). Alternatively, the source code is available from the GitHub repository (https://github.com/afgane/bioblend) under the MIT open source license. The library has been tested and is working on Linux, Macintosh and Windows-based systems.

GenomeDiagram: a python package for the visualization of large-scale genomic data.

PubMed

Pritchard, Leighton; White, Jennifer A; Birch, Paul R J; Toth, Ian K

2006-03-01

We present GenomeDiagram, a flexible, open-source Python module for the visualization of large-scale genomic, comparative genomic and other data with reference to a single chromosome or other biological sequence. GenomeDiagram may be used to generate publication-quality vector graphics, rastered images and in-line streamed graphics for webpages. The package integrates with datatypes from the BioPython project, and is available for Windows, Linux and Mac OS X systems. GenomeDiagram is freely available as source code (under GNU Public License) at http://bioinf.scri.ac.uk/lp/programs.html, and requires Python 2.3 or higher, and recent versions of the ReportLab and BioPython packages. A user manual, example code and images are available at http://bioinf.scri.ac.uk/lp/programs.html.

The Open AUC Project.

PubMed

Cölfen, Helmut; Laue, Thomas M; Wohlleben, Wendel; Schilling, Kristian; Karabudak, Engin; Langhorst, Bradley W; Brookes, Emre; Dubbs, Bruce; Zollars, Dan; Rocco, Mattia; Demeler, Borries

2010-02-01

Progress in analytical ultracentrifugation (AUC) has been hindered by obstructions to hardware innovation and by software incompatibility. In this paper, we announce and outline the Open AUC Project. The goals of the Open AUC Project are to stimulate AUC innovation by improving instrumentation, detectors, acquisition and analysis software, and collaborative tools. These improvements are needed for the next generation of AUC-based research. The Open AUC Project combines on-going work from several different groups. A new base instrument is described, one that is designed from the ground up to be an analytical ultracentrifuge. This machine offers an open architecture, hardware standards, and application programming interfaces for detector developers. All software will use the GNU Public License to assure that intellectual property is available in open source format. The Open AUC strategy facilitates collaborations, encourages sharing, and eliminates the chronic impediments that have plagued AUC innovation for the last 20 years. This ultracentrifuge will be equipped with multiple and interchangeable optical tracks so that state-of-the-art electronics and improved detectors will be available for a variety of optical systems. The instrument will be complemented by a new rotor, enhanced data acquisition and analysis software, as well as collaboration software. Described here are the instrument, the modular software components, and a standardized database that will encourage and ease integration of data analysis and interpretation software.

10 CFR 32.74 - Manufacture and distribution of sources or devices containing byproduct material for medical use.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Manufacture and distribution of sources or devices... SPECIFIC DOMESTIC LICENSES TO MANUFACTURE OR TRANSFER CERTAIN ITEMS CONTAINING BYPRODUCT MATERIAL Generally Licensed Items § 32.74 Manufacture and distribution of sources or devices containing byproduct material for...

10 CFR 40.22 - Small quantities of source material.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Small quantities of source material. 40.22 Section 40.22 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.22 Small... (15.4 lb) of uranium, removed during the treatment of drinking water, at any one time. A person may...

PlasmaPy: initial development of a Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas; Leonard, Andrew J.; Stańczak, Dominik; Haggerty, Colby C.; Parashar, Tulasi N.; Huang, Yu-Min; PlasmaPy Community

2017-10-01

We report on initial development of PlasmaPy: an open source community-driven Python package for plasma physics. PlasmaPy seeks to provide core functionality that is needed for the formation of a fully open source Python ecosystem for plasma physics. PlasmaPy prioritizes code readability, consistency, and maintainability while using best practices for scientific computing such as version control, continuous integration testing, embedding documentation in code, and code review. We discuss our current and planned capabilities, including features presently under development. The development roadmap includes features such as fluid and particle simulation capabilities, a Grad-Shafranov solver, a dispersion relation solver, atomic data retrieval methods, and tools to analyze simulations and experiments. We describe several ways to contribute to PlasmaPy. PlasmaPy has a code of conduct and is being developed under a BSD license, with a version 0.1 release planned for 2018. The success of PlasmaPy depends on active community involvement, so anyone interested in contributing to this project should contact the authors. This work was partially supported by the U.S. Department of Energy.

Extending a CAD-Based Cartesian Mesh Generator for the Lattice Boltzmann Method

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

Cantrell, J Nathan; Inclan, Eric J; Joshi, Abhijit S

2012-01-01

This paper describes the development of a custom preprocessor for the PaRAllel Thermal Hydraulics simulations using Advanced Mesoscopic methods (PRATHAM) code based on an open-source mesh generator, CartGen [1]. PRATHAM is a three-dimensional (3D) lattice Boltzmann method (LBM) based parallel flow simulation software currently under development at the Oak Ridge National Laboratory. The LBM algorithm in PRATHAM requires a uniform, coordinate system-aligned, non-body-fitted structured mesh for its computational domain. CartGen [1], which is a GNU-licensed open source code, already comes with some of the above needed functionalities. However, it needs to be further extended to fully support the LBM specificmore » preprocessing requirements. Therefore, CartGen is being modified to (i) be compiler independent while converting a neutral-format STL (Stereolithography) CAD geometry to a uniform structured Cartesian mesh, (ii) provide a mechanism for PRATHAM to import the mesh and identify the fluid/solid domains, and (iii) provide a mechanism to visually identify and tag the domain boundaries on which to apply different boundary conditions.« less

CACTI: Free, Open-Source Software for the Sequential Coding of Behavioral Interactions

PubMed Central

Glynn, Lisa H.; Hallgren, Kevin A.; Houck, Jon M.; Moyers, Theresa B.

2012-01-01

The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery. PMID:22815713

Mitigating Evidentiary Bias in Planning and Policy-Making Comment on "Reflective Practice: How the World Bank Explored Its Own Biases?"

PubMed

Parkhurst, Justin

2016-07-20

The field of cognitive psychology has increasingly provided scientific insights to explore how humans are subject to unconscious sources of evidentiary bias, leading to errors that can affect judgement and decision-making. Increasingly these insights are being applied outside the realm of individual decision-making to the collective arena of policy-making as well. A recent editorial in this journal has particularly lauded the work of the World Bank for undertaking an open and critical reflection on sources of unconscious bias in its own expert staff that could undermine achievement of its key goals. The World Bank case indeed serves as a remarkable case of a global policy-making agency making its own critical reflections transparent for all to see. Yet the recognition that humans are prone to cognitive errors has been known for centuries, and the scientific exploration of such biases provided by cognitive psychology is now well-established. What still remains to be developed, however, is a widespread body of work that can inform efforts to institutionalise strategies to mitigate the multiple sources and forms of evidentiary bias arising within administrative and policy-making environments. Addressing this gap will require a programme of conceptual and empirical work that supports robust development and evaluation of institutional bias mitigation strategies. The cognitive sciences provides a scientific basis on which to proceed, but a critical priority will now be the application of that science to improve policy-making within those agencies taking responsibility for social welfare and development programmes. © 2017 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

ENKI - An Open Source environmental modelling platfom

NASA Astrophysics Data System (ADS)

Kolberg, S.; Bruland, O.

2012-04-01

The ENKI software framework for implementing spatio-temporal models is now released under the LGPL license. Originally developed for evaluation and comparison of distributed hydrological model compositions, ENKI can be used for simulating any time-evolving process over a spatial domain. The core approach is to connect a set of user specified subroutines into a complete simulation model, and provide all administrative services needed to calibrate and run that model. This includes functionality for geographical region setup, all file I/O, calibration and uncertainty estimation etc. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines and various model compositions in a fixed framework. The open-source license and modular design of ENKI will also facilitate rapid dissemination of new methods to institutions engaged in operational water resource management. ENKI uses a plug-in structure to invoke separately compiled subroutines, separately built as dynamic-link libraries (dlls). The source code of an ENKI routine is highly compact, with a narrow framework-routine interface allowing the main program to recognise the number, types, and names of the routine's variables. The framework then exposes these variables to the user within the proper context, ensuring that distributed maps coincide spatially, time series exist for input variables, states are initialised, GIS data sets exist for static map data, manually or automatically calibrated values for parameters etc. By using function calls and memory data structures to invoke routines and facilitate information flow, ENKI provides good performance. For a typical distributed hydrological model setup in a spatial domain of 25000 grid cells, 3-4 time steps simulated per second should be expected. Future adaptation to parallel processing may further increase this speed. New modifications to ENKI include a full separation of API and user interface, making it possible to run ENKI from GIS programs and other software environments. ENKI currently compiles under Windows and Visual Studio only, but ambitions exist to remove the platform and compiler dependencies.

PyPedia: using the wiki paradigm as crowd sourcing environment for bioinformatics protocols.

PubMed

Kanterakis, Alexandros; Kuiper, Joël; Potamias, George; Swertz, Morris A

2015-01-01

Today researchers can choose from many bioinformatics protocols for all types of life sciences research, computational environments and coding languages. Although the majority of these are open source, few of them possess all virtues to maximize reuse and promote reproducible science. Wikipedia has proven a great tool to disseminate information and enhance collaboration between users with varying expertise and background to author qualitative content via crowdsourcing. However, it remains an open question whether the wiki paradigm can be applied to bioinformatics protocols. We piloted PyPedia, a wiki where each article is both implementation and documentation of a bioinformatics computational protocol in the python language. Hyperlinks within the wiki can be used to compose complex workflows and induce reuse. A RESTful API enables code execution outside the wiki. Initial content of PyPedia contains articles for population statistics, bioinformatics format conversions and genotype imputation. Use of the easy to learn wiki syntax effectively lowers the barriers to bring expert programmers and less computer savvy researchers on the same page. PyPedia demonstrates how wiki can provide a collaborative development, sharing and even execution environment for biologists and bioinformaticians that complement existing resources, useful for local and multi-center research teams. PyPedia is available online at: http://www.pypedia.com. The source code and installation instructions are available at: https://github.com/kantale/PyPedia_server. The PyPedia python library is available at: https://github.com/kantale/pypedia. PyPedia is open-source, available under the BSD 2-Clause License.

Focusing on Prevention: The Social and Economic Rights of Children Vulnerable to Sex Trafficking.

PubMed

Duger, Angela

2015-06-11

The commercial sexual exploitation of children ("CSEC") is an egregious human rights and public health violation that occurs every day across the US. Although there has been positive change in the US to bring attention to CSEC and to reform laws and policies to assist CSEC victims, scant attention and resources have been dedicated to prevention efforts. This paper critiques current US strategies to address CSEC and highlights the limitations of an interventionist framework that narrows its focus to anti-trafficking efforts. As an alternative, the paper proposes a human rights-based approach focusing on the fulfillment of economic and social rights of children as a prevention strategy in the U.S. Copyright 2015 Duger. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

[Ultraviolet exposure from indoor tanning devices as a potential source of health risks: Basic knowledge of the proper use of these devices for practical users, physicians and solarium staff].

PubMed

Malinowska-Borowska, Jolanta; Janosik, Elżbieta

2017-07-26

Bearing in mind the adverse health effects of exposure to ultraviolet (UV) radiation in solarium, especially the risk of carcinogenesis, there is a need to adopt legal regulations by relevant Polish authorities. They should set out the principles for indoor tanning studios operation, supervision and service of the technical parameters of tanning devices and training programs to provide the staff with professional knowledge and other aspects of safety in these facilities. The mechanism of the harmful effects of ultraviolet radiation on the human body, scale of overexposure, resulting from excessive sunbathing are described. Methods for estimating UV exposure and possible actions aimed at reducing the overexposure and preventing from cancer development caused by UV are also presented in this paper. Med Pr 2017;68(5):653-665. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Human rights versus legal control over women's reproductive self-determination.

PubMed

Uberoi, Diya; de Bruyn, Maria

2013-06-14

States have a duty under international human rights law to protect people's health. Nonetheless, while some health-related policies and laws protect basic human rights, others violate fundamental rights when they criminalize, prohibit, and restrict access to necessary health services. For example, laws and regulations related to protection of life from conception, contraception, actions of pregnant women, and abortion can harm women and place women and health care providers in jeopardy of legal penalization. Given the adverse consequences of punitive and restrictive laws related to pregnancy, advocates, civil society groups, human rights groups, and government institutions must work together to promote, protect, and fulfill women's fundamental reproductive rights. Copyright © 2013 Uberoi and de Bruyn. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

[Health and quality of life vs. occupational activity].

PubMed

Kowalska, Małgorzata; Szemik, Szymon

The level of quality of life and health status of the population largely depends on the determinants related to occupational activity. The results of reviewed bibliography indicate a significant and growing importance of employment conditions on the quality of life and population health status in most countries of the world, especially in those with market economy. Of the evaluated determinants the following factors should be listed in particular: sources and the amount of income, stability of the income and employment, the nature of work and the degree of job satisfaction, as well as autonomy and career prospects. Moreover, they proved that the situation of persisting and long-term unemployment and precarious employment leads to a significant deterioration in the quality of life and health, especially among young people. In conclusion, the study of quality of life and population health status should take into consideration factors related to occupational activity. Med Pr 2016;67(5):663-671. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Estimate of radon exposure in geothermal spas in Poland.

PubMed

Walczak, Katarzyna; Olszewski, Jerzy; Zmyślony, Marek

2016-01-01

Geothermal waters may contain soluble, radioactive radon gas. Spa facilities that use geothermal water may be a source of an increased radiation dose to people who stay there. It has been necessary to assess the exposure to radon among people: workers and visitors of spa centers that use geothermal waters. In 2013, workers of the Nofer Institute of Occupational Medicine measured concentrations of radon over the geothermal water surfaces in 9 selected Polish spa centers which use geothermal water for recreational and medicinal purposes. The measurements were performed by active dosimetry using Lucas scintillation cells. According to our research, the doses received by the personnel in Polish geothermal spas are < 0.6 mSv/year. In 1 of the investigated spas, the estimated annual dose to the staff may exceed 3 mSv/year. In Polish geothermal spas, neither the workers nor the visitors are at risk of receiving doses that exceed the safe limits. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

Acquiring Data by Mining the Past: Pairing Communities with Environmental Monitoring Methods through Open Online Collaborative Replication

NASA Astrophysics Data System (ADS)

Lippincott, M.; Lewis, E. S.; Gehrke, G. E.; Wise, A.; Pyle, S.; Sinatra, V.; Bland, G.; Bydlowski, D.; Henry, A.; Gilberts, P. A.

2016-12-01

Community groups are interested in low-cost sensors to monitor their environment. However, many new commercial sensors are unknown devices without peer-reviewed evaluations of data quality or pathways to regulatory acceptance, and the time to achieve these outcomes may be beyond a community's patience and attention. Rather than developing a device from scratch or validating a new commercial product, a workflow is presented whereby existing technologies, especially those that are out of patent, are replicated through open online collaboration between communities affected by environmental pollution, volunteers, academic institutions, and existing open hardware and open source software projects. Technology case studies will be presented, focusing primarily on a passive PM monitor based on the UNC Passive Monitor. Stages of the project will be detailed moving from identifying community needs, reviewing existing technology, partnership development, technology replication, IP review and licensing, data quality assurance (in process), and field evaluation with community partners (in process), with special attention to partnership development and technology review. We have leveraged open hardware and open source software to lower the cost and access barriers of existing technologies for PM10-2.5 and other atmospheric measures that have already been validated through peer review. Existing validation of and regulatory familiarity with a technology enables a rapid pathway towards collecting data, shortening the time it takes for communities to leverage data in environmental management decisions. Online collaboration requires rigorous documentation that aids in spreading research methods and promoting deep engagement by interested community researchers outside academia. At the same time, careful choice of technology and the use of small-scale fabrication through laser cutting, 3D printing, and open, shared repositories of plans and software enables educational engagement that broadens a project's reach.

48 CFR 908.7101-7 - Government license tags.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Government license tags... ACQUISITION PLANNING REQUIRED SOURCES OF SUPPLIES AND SERVICES Acquisition of Special Items 908.7101-7 Government license tags. (a) Government license tags shall be procured and assignments recorded by DOE...

10 CFR 40.26 - General license for possession and storage of byproduct material as defined in this part.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license for possession and storage of byproduct material as defined in this part. 40.26 Section 40.26 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.26 General license for possession and storage of...

10 CFR 40.28 - General license for custody and long-term care of uranium or thorium byproduct materials disposal...

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license for custody and long-term care of uranium or thorium byproduct materials disposal sites. 40.28 Section 40.28 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.28 General license for custody and...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

10 CFR 34.1 - Purpose and scope.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATORY COMMISSION LICENSES FOR INDUSTRIAL RADIOGRAPHY AND RADIATION SAFETY REQUIREMENTS FOR INDUSTRIAL... issuance of licenses for the use of sealed sources containing byproduct material and radiation safety requirements for persons using these sealed sources in industrial radiography. The provisions and requirements...

WebProtégé: a collaborative Web-based platform for editing biomedical ontologies.

PubMed

Horridge, Matthew; Tudorache, Tania; Nuylas, Csongor; Vendetti, Jennifer; Noy, Natalya F; Musen, Mark A

2014-08-15

WebProtégé is an open-source Web application for editing OWL 2 ontologies. It contains several features to aid collaboration, including support for the discussion of issues, change notification and revision-based change tracking. WebProtégé also features a simple user interface, which is geared towards editing the kinds of class descriptions and annotations that are prevalent throughout biomedical ontologies. Moreover, it is possible to configure the user interface using views that are optimized for editing Open Biomedical Ontology (OBO) class descriptions and metadata. Some of these views are shown in the Supplementary Material and can be seen in WebProtégé itself by configuring the project as an OBO project. WebProtégé is freely available for use on the Web at http://webprotege.stanford.edu. It is implemented in Java and JavaScript using the OWL API and the Google Web Toolkit. All major browsers are supported. For users who do not wish to host their ontologies on the Stanford servers, WebProtégé is available as a Web app that can be run locally using a Servlet container such as Tomcat. Binaries, source code and documentation are available under an open-source license at http://protegewiki.stanford.edu/wiki/WebProtege. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

cPath: open source software for collecting, storing, and querying biological pathways.

PubMed

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-11-13

Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling.

A Review of the Impact of the Human Rights in Healthcare Programme in England and Wales.

PubMed

Dyer, Lindsey

2015-12-10

This article provides the background to an analysis of the Human Rights in Healthcare Programme in England and Wales. Using evidence from source materials, summary publications, and official reports, it charts a small but important change in the relationship between health and human rights and shows how a small number of National Health Service organizations used a human rights-based approach (HRBA) to develop resources aimed at improving the quality of health services and health outcomes. Through a case study of one participating organization, it examines the development of approaches to measuring the outcomes and impacts of HRBAs. The article argues that because of the way the Programme was set up, it is not likely to provide the level of evidence of impact required to bring about a profound change in the relationship between human rights and health care. There is a need for a different approach that considers the big human rights questions that need to be asked. Copyright © 2015 Dyer. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

An economic justification for open access to essential medicine patents in developing countries.

PubMed

Flynn, Sean; Hollis, Aidan; Palmedo, Mike

2009-01-01

This paper offers an economic rationale for compulsory licensing of needed medicines in developing countries. The patent system is based on a trade-off between the "deadweight losses" caused by market power and the incentive to innovate created by increased profits from monopoly pricing during the period of the patent. However, markets for essential medicines under patent in developing countries with high income inequality are characterized by highly convex demand curves, producing large deadweight losses relative to potential profits when monopoly firms exercise profit-maximizing pricing strategies. As a result, these markets are systematically ill-suited to exclusive marketing rights, a problem which can be corrected through compulsory licensing. Open licenses that permit any qualified firm to supply the market on the same terms, such as may be available under licenses of right or essential facility legal standards, can be used to mitigate the negative effects of government-granted patents, thereby increasing overall social welfare.

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

Klise, Katherine A.; Siirola, John Daniel; Hart, David

The Water Security Toolkit (WST) is a suite of open source software tools that can be used by water utilities to create response strategies to reduce the impact of contamination in a water distribution network . WST includes hydraulic and water quality modeling software , optimizati on methodologies , and visualization tools to identify: (1) sensor locations to detect contamination, (2) locations in the network in which the contamination was introduced, (3) hydrants to remove contaminated water from the distribution system, (4) locations in the network to inject decontamination agents to inactivate, remove, or destroy contaminants, (5) locations in themore » network to take grab sample s to help identify the source of contamination and (6) valves to close in order to isolate contaminate d areas of the network. This user manual describes the different components of WST , along w ith examples and case studies. License Notice The Water Security Toolkit (WST) v.1.2 Copyright c 2012 Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000, there is a non-exclusive license for use of this work by or on behalf of the U.S. government. This software is distributed under the Revised BSD License (see below). In addition, WST leverages a variety of third-party software packages, which have separate licensing policies: Acro Revised BSD License argparse Python Software Foundation License Boost Boost Software License Coopr Revised BSD License Coverage BSD License Distribute Python Software Foundation License / Zope Public License EPANET Public Domain EPANET-ERD Revised BSD License EPANET-MSX GNU Lesser General Public License (LGPL) v.3 gcovr Revised BSD License GRASP AT&T Commercial License for noncommercial use; includes randomsample and sideconstraints executable files LZMA SDK Public Domain nose GNU Lesser General Public License (LGPL) v.2.1 ordereddict MIT License pip MIT License PLY BSD License PyEPANET Revised BSD License Pyro MIT License PyUtilib Revised BSD License PyYAML MIT License runpy2 Python Software Foundation License setuptools Python Software Foundation License / Zope Public License six MIT License TinyXML zlib License unittest2 BSD License Utilib Revised BSD License virtualenv MIT License Vol Common Public License vpykit Revised BSD License Additionally, some precompiled WST binary distributions might bundle other third-party executables files: Coliny Revised BSD License (part of Acro project) Dakota GNU Lesser General Public License (LGPL) v.2.1 PICO Revised BSD License (part of Acro project) i Revised BSD License Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of Sandia National Laboratories nor Sandia Corporation nor the names of its con- tributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IM- PLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL SANDIA CORPORATION BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUD- ING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ii Acknowledgements This work was supported by the U.S. Environmental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The material in this document has been subject to technical and policy review by the U.S. EPA, and approved for publication. The views expressed by individual authors, however, are their own, and do not necessarily reflect those of the U.S. Environmental Protection Agency. Mention of trade names, products, or services does not convey official U.S. EPA approval, endorsement, or recommendation. The Water Security Toolkit is an extension of the Threat Ensemble Vulnerability Assessment-Sensor Place- ment Optimization Tool (TEVA-SPOT), which was also developed with funding from the U.S. Environ- mental Protection Agency through its Office of Research and Development (Interagency Agreement # DW8992192801). The authors acknowledge the following individuals for their contributions to the devel- opment of TEVA-SPOT: Jonathan Berry (Sandia National Laboratories), Erik Boman (Sandia National Laboratories), Lee Ann Riesen (Sandia National Laboratories), James Uber (University of Cincinnati), and Jean-Paul Watson (Sandia National Laboratories). iii Acronyms ATUS American Time-Use Survey BLAS Basic linear algebra sub-routines CFU Colony-forming unit CVAR Conditional value at risk CWS Contamination warning system EA Evolutionary algorithm EDS Event detection system EPA U.S. Environmental Protection Agency EC Extent of Contamination ERD EPANET results database file GLPK GNU Linear Programming Kit GRASP Greedy randomized adaptive sampling process HEX Hexadecimal HTML HyperText markup language INP EPANET input file LP Linear program MC Mass consumed MILP Mixed integer linear program MIP Mixed integer program MSX Multi-species extension for EPANET NFD Number of failed detections NS Number of sensors NZD Non-zero demand PD Population dosed PE Population exposed PK Population killed TAI Threat assessment input file TCE Tailed-conditioned expectation TD Time to detection TEC Timed extent of contamination TEVA Threat ensemble vulnerability assessment TSB Tryptic soy broth TSG Threat scenario generation file TSI Threat simulation input file VAR Value at risk VC Volume consumed WST Water Security Toolkit YML YAML configuration file format for WST iv Symbols Notation Definition Example { , } set brackets { 1,2,3 } means a set containing the values 1,2, and 3. [?] is an element of s [?] S means that s is an element of the set S . [?] for all s = 1 [?] s [?] S means that the statement s = 1 is true for all s in set S . P summation P n i =1 s i means s 1 + s 2 + * * * + s n . \\ set minus S \\ T means the set that contains all those elements of S that are not in set T . %7C given %7C is used to define conditional probability. P ( s %7C t ) means the prob- ability of s occurring given that t occurs. %7C ... %7C cardinality Cardinality of a set is the number of elements of the set. If set S = { 2,4,6 } , then %7C S %7C = 3. v« less

The State of Open Source Electronic Health Record Projects: A Software Anthropology Study

PubMed Central

2017-01-01

Background Electronic health records (EHR) are a key tool in managing and storing patients’ information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers’ motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. Objective This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. Methods This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were “certified” EHRs. Health care F/OSS developers were also surveyed using an online survey. Results At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45% (45/99) of developers do not work in the health care field. Conclusion The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States. PMID:28235750

10 CFR 40.23 - General license for carriers of transient shipments of natural uranium other than in the form of...

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false General license for carriers of transient shipments of natural uranium other than in the form of ore or ore residue. 40.23 Section 40.23 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Licenses § 40.23 General license for...

Gallbladder removal - open - discharge

MedlinePlus

... your eyes turns yellow. Your stools are a gray color. Alternative Names Cholelithiasis - open discharge; Biliary calculus - ... any medical emergency or for the diagnosis or treatment of any medical condition. A licensed physician should ...

GALARIO: a GPU accelerated library for analysing radio interferometer observations

NASA Astrophysics Data System (ADS)

Tazzari, Marco; Beaujean, Frederik; Testi, Leonardo

2018-06-01

We present GALARIO, a computational library that exploits the power of modern graphical processing units (GPUs) to accelerate the analysis of observations from radio interferometers like Atacama Large Millimeter and sub-millimeter Array or the Karl G. Jansky Very Large Array. GALARIO speeds up the computation of synthetic visibilities from a generic 2D model image or a radial brightness profile (for axisymmetric sources). On a GPU, GALARIO is 150 faster than standard PYTHON and 10 times faster than serial C++ code on a CPU. Highly modular, easy to use, and to adopt in existing code, GALARIO comes as two compiled libraries, one for Nvidia GPUs and one for multicore CPUs, where both have the same functions with identical interfaces. GALARIO comes with PYTHON bindings but can also be directly used in C or C++. The versatility and the speed of GALARIO open new analysis pathways that otherwise would be prohibitively time consuming, e.g. fitting high-resolution observations of large number of objects, or entire spectral cubes of molecular gas emission. It is a general tool that can be applied to any field that uses radio interferometer observations. The source code is available online at http://github.com/mtazzari/galario under the open source GNU Lesser General Public License v3.

Enabling systematic, harmonised and large-scale biofilms data computation: the Biofilms Experiment Workbench.

PubMed

Pérez-Rodríguez, Gael; Glez-Peña, Daniel; Azevedo, Nuno F; Pereira, Maria Olívia; Fdez-Riverola, Florentino; Lourenço, Anália

2015-03-01

Biofilms are receiving increasing attention from the biomedical community. Biofilm-like growth within human body is considered one of the key microbial strategies to augment resistance and persistence during infectious processes. The Biofilms Experiment Workbench is a novel software workbench for the operation and analysis of biofilms experimental data. The goal is to promote the interchange and comparison of data among laboratories, providing systematic, harmonised and large-scale data computation. The workbench was developed with AIBench, an open-source Java desktop application framework for scientific software development in the domain of translational biomedicine. Implementation favours free and open-source third-parties, such as the R statistical package, and reaches for the Web services of the BiofOmics database to enable public experiment deposition. First, we summarise the novel, free, open, XML-based interchange format for encoding biofilms experimental data. Then, we describe the execution of common scenarios of operation with the new workbench, such as the creation of new experiments, the importation of data from Excel spreadsheets, the computation of analytical results, the on-demand and highly customised construction of Web publishable reports, and the comparison of results between laboratories. A considerable and varied amount of biofilms data is being generated, and there is a critical need to develop bioinformatics tools that expedite the interchange and comparison of microbiological and clinical results among laboratories. We propose a simple, open-source software infrastructure which is effective, extensible and easy to understand. The workbench is freely available for non-commercial use at http://sing.ei.uvigo.es/bew under LGPL license. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

10 CFR 40.5 - Communications.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Communications. 40.5 Section 40.5 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL General Provisions § 40.5 Communications. (a... Administrators. (ii) Health and safety design review of sealed sources and devices and approval, for licensing...

15 CFR 740.7 - Computers (APP).

Code of Federal Regulations, 2010 CFR

2010-01-01

... 4A003. (2) Technology and software. License Exception APP authorizes exports of technology and software... programmability. (ii) Technology and source code. Technology and source code eligible for License Exception APP..., reexports and transfers (in-country) for nuclear, chemical, biological, or missile end-users and end-uses...

76 FR 31507 - Domestic Licensing of Source Material-Amendments/Integrated Safety Analysis

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-01

... Licensing of Source Material--Amendments/Integrated Safety Analysis AGENCY: Nuclear Regulatory Commission... rule announced the availability of a draft regulatory analysis for public comment. This document... in Section XI, ``Regulatory Analysis.'' The correct ADAMS accession number is ML102380243. DATES: The...

10 CFR 30.3 - Activities requiring license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... that possesses and uses accelerator-produced radioactive material or discrete sources of radium-226 for...-produced radioactive material or discrete sources of radium-226 for which a specific license is required in... section, all other licensees, who possess and use accelerator-produced radioactive material or discrete...

10 CFR 32.201 - Serialization of nationally tracked sources.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Serialization of nationally tracked sources. 32.201 Section 32.201 Energy NUCLEAR REGULATORY COMMISSION SPECIFIC DOMESTIC LICENSES TO MANUFACTURE OR TRANSFER CERTAIN ITEMS CONTAINING BYPRODUCT MATERIAL Specifically Licensed Items § 32.201 Serialization of...

10 CFR 32.201 - Serialization of nationally tracked sources.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Serialization of nationally tracked sources. 32.201 Section 32.201 Energy NUCLEAR REGULATORY COMMISSION SPECIFIC DOMESTIC LICENSES TO MANUFACTURE OR TRANSFER CERTAIN ITEMS CONTAINING BYPRODUCT MATERIAL Specifically Licensed Items § 32.201 Serialization of...

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.

PubMed

Brynildsrud, Ola; Bohlin, Jon; Scheffer, Lonneke; Eldholm, Vegard

2016-11-25

Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary .

ConKit: a python interface to contact predictions.

PubMed

Simkovic, Felix; Thomas, Jens M H; Rigden, Daniel J

2017-07-15

Recent advances in protein residue contact prediction algorithms have led to the emergence of many new methods and a variety of file formats. We present ConKit , an open source, modular and extensible Python interface which allows facile conversion between formats and provides an interface to analyses of sequence alignments and sets of contact predictions. ConKit is available via the Python Package Index. The documentation can be found at http://www.conkit.org . ConKit is licensed under the BSD 3-Clause. hlfsimko@liverpool.ac.uk or drigden@liverpool.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Livermore Big Artificial Neural Network Toolkit

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

Essen, Brian Van; Jacobs, Sam; Kim, Hyojin

2016-07-01

LBANN is a toolkit that is designed to train artificial neural networks efficiently on high performance computing architectures. It is optimized to take advantages of key High Performance Computing features to accelerate neural network training. Specifically it is optimized for low-latency, high bandwidth interconnects, node-local NVRAM, node-local GPU accelerators, and high bandwidth parallel file systems. It is built on top of the open source Elemental distributed-memory dense and spars-direct linear algebra and optimization library that is released under the BSD license. The algorithms contained within LBANN are drawn from the academic literature and implemented to work within a distributed-memory framework.

Evol and ProDy for bridging protein sequence evolution and structural dynamics

PubMed Central

Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet

2014-01-01

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

Tracking PACS usage with open source tools.

PubMed

French, Todd L; Langer, Steve G

2011-08-01

A typical choice faced by Picture Archiving and Communication System (PACS) administrators is deciding how many PACS workstations are needed and where they should be sited. Oftentimes, the social consequences of having too few are severe enough to encourage oversupply and underutilization. This is costly, at best in terms of hardware and electricity, and at worst (depending on the PACS licensing and support model) in capital costs and maintenance fees. The PACS administrator needs tools to asses accurately the use to which her fleet is being subjected, and thus make informed choices before buying more workstations. Lacking a vended solution for this challenge, we developed our own.

Validation of thermal effects of LED package by using Elmer finite element simulation method

NASA Astrophysics Data System (ADS)

Leng, Lai Siang; Retnasamy, Vithyacharan; Mohamad Shahimin, Mukhzeer; Sauli, Zaliman; Taniselass, Steven; Bin Ab Aziz, Muhamad Hafiz; Vairavan, Rajendaran; Kirtsaeng, Supap

2017-02-01

The overall performance of the Light-emitting diode, LED package is critically affected by the heat attribution. In this study, open source software - Elmer FEM has been utilized to study the thermal analysis of the LED package. In order to perform a complete simulation study, both Salome software and ParaView software were introduced as Pre and Postprocessor. The thermal effect of the LED package was evaluated by this software. The result has been validated with commercially licensed software based on previous work. The percentage difference from both simulation results is less than 5% which is tolerable and comparable.

76 FR 78173 - Options for Developing the Regulatory Basis for Streamlining Non-Power Reactor License Renewal...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-16

... Emergency Preparedness AGENCY: Nuclear Regulatory Commission. ACTION: Notice of public meeting. SUMMARY: The... non-power reactor license renewal and non-power reactor emergency preparedness. This meeting is a... potential enhancements to emergency preparedness requirements. This meeting is open to the public. DATES...

78 FR 75386 - Entergy Operations, Inc.; Combined License Application for River Bend Station Unit 3, Exemption...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-11

... Combined License Application To Comply With Enhancements to Emergency Preparedness Rule AGENCY: Nuclear... an exemption from addressing enhancements to the Emergency Preparedness (EP) rules in their Combined... to Emergency Preparedness Regulations. EOI's requested exemption is seen as an open-ended, one-time...

Identifying Tensions in the Use of Open Licenses in OER Repositories

ERIC Educational Resources Information Center

Amiel, Tel; Soares, Tiago Chagas

2016-01-01

We present an analysis of 50 repositories for educational content conducted through an "audit system" that helped us classify these repositories, their software systems, promoters, and how they communicated their licensing practices. We randomly accessed five resources from each repository to investigate the alignment of licensing…

31 CFR 561.504 - Transactions related to closing a correspondent account or payable-through account.

Code of Federal Regulations, 2011 CFR

2011-07-01

... accounts or payable-through accounts for the foreign financial institution are authorized to: (1) Process... TREASURY IRANIAN FINANCIAL SANCTIONS REGULATIONS Licenses, Authorizations, and Statements of Licensing... opening or maintaining of a correspondent account or a payable-through account for a foreign financial...

77 FR 71404 - Notice of Intent to License Government-Owned Inventions; Intent to License on a Partially...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-30

... DEPARTMENT OF DEFENSE Department of the Army Notice of Intent to License Government-Owned Inventions; Intent to License on a Partially-Exclusive Basis AGENCY: Department of the Army, DoD. ACTION..., issued 07/ 28/2009 and entitled ``Radiation source with self-aligning optics,'' U.S. Patent 7,852,469...

The Role of Open Access and Open Educational Resources: A Distance Learning Perspective

ERIC Educational Resources Information Center

Hatzipanagos, Stylianos; Gregson, Jon

2015-01-01

The paper explores the role of Open Access (in licensing, publishing and sharing research data) and Open Educational Resources within Distance Education, with a focus on the context of the University of London International Programmes. We report on a case study where data were gathered from librarians and programme directors relating to existing…

Open Access

ERIC Educational Resources Information Center

Suber, Peter

2012-01-01

The Internet lets us share perfect copies of our work with a worldwide audience at virtually no cost. We take advantage of this revolutionary opportunity when we make our work "open access": digital, online, free of charge, and free of most copyright and licensing restrictions. Open access is made possible by the Internet and copyright-holder…

10 CFR 40.38 - Ineligibility of certain applicants.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Ineligibility of certain applicants. 40.38 Section 40.38 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL License Applications § 40.38... security of the United States; or (2) The maintenance of a reliable and economical domestic source of...

10 CFR 40.61 - Records.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Records. 40.61 Section 40.61 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL Records, Reports, and Inspections § 40.61 Records. (a) Each person who receives source or byproduct material pursuant to a license issued pursuant to the regulations...

10 CFR 40.36 - Financial assurance and recordkeeping for decommissioning.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Financial assurance and recordkeeping for decommissioning. 40.36 Section 40.36 Energy NUCLEAR REGULATORY COMMISSION DOMESTIC LICENSING OF SOURCE MATERIAL... licenses authorizing the receipt, possession, and use of source material for uranium or thorium milling, or...

10 CFR 70.19 - General license for calibration or reference sources.

Code of Federal Regulations, 2010 CFR

2010-01-01

... State who holds a specific license issued by the Commission or the Atomic Energy Commission which... the Commission or the Atomic Energy Commission which authorizes him to receive, possess, use and... effect on January 1, 1975. The receipt, possession, use and transfer of this source, Model ___, Serial No...

76 FR 44865 - Domestic Licensing of Source Material-Amendments/Integrated Safety Analysis

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-27

... NUCLEAR REGULATORY COMMISSION 10 CFR Part 40 RIN 3150-AI50 [NRC-2009-0079 and NRC-2011-0080] Domestic Licensing of Source Material--Amendments/Integrated Safety Analysis AGENCY: Nuclear Regulatory Commission. ACTION: Extension of public comment period and public meeting. SUMMARY: The U.S. Nuclear...

CMOST: an open-source framework for the microsimulation of colorectal cancer screening strategies.

PubMed

Prakash, Meher K; Lang, Brian; Heinrich, Henriette; Valli, Piero V; Bauerfeind, Peter; Sonnenberg, Amnon; Beerenwinkel, Niko; Misselwitz, Benjamin

2017-06-05

Colorectal cancer (CRC) is a leading cause of cancer-related mortality. CRC incidence and mortality can be reduced by several screening strategies, including colonoscopy, but randomized CRC prevention trials face significant obstacles such as the need for large study populations with long follow-up. Therefore, CRC screening strategies will likely be designed and optimized based on computer simulations. Several computational microsimulation tools have been reported for estimating efficiency and cost-effectiveness of CRC prevention. However, none of these tools is publicly available. There is a need for an open source framework to answer practical questions including testing of new screening interventions and adapting findings to local conditions. We developed and implemented a new microsimulation model, Colon Modeling Open Source Tool (CMOST), for modeling the natural history of CRC, simulating the effects of CRC screening interventions, and calculating the resulting costs. CMOST facilitates automated parameter calibration against epidemiological adenoma prevalence and CRC incidence data. Predictions of CMOST were highly similar compared to a large endoscopic CRC prevention study as well as predictions of existing microsimulation models. We applied CMOST to calculate the optimal timing of a screening colonoscopy. CRC incidence and mortality are reduced most efficiently by a colonoscopy between the ages of 56 and 59; while discounted life years gained (LYG) is maximal at 49-50 years. With a dwell time of 13 years, the most cost-effective screening is at 59 years, at $17,211 discounted USD per LYG. While cost-efficiency varied according to dwell time it did not influence the optimal time point of screening interventions within the tested range. Predictions of CMOST are highly similar compared to a randomized CRC prevention trial as well as those of other microsimulation tools. This open source tool will enable health-economics analyses in for various countries, health-care scenarios and CRC prevention strategies. CMOST is freely available under the GNU General Public License at https://gitlab.com/misselwb/CMOST.

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

10 CFR 51.54 - Environmental report-manufacturing license.

Code of Federal Regulations, 2012 CFR

2012-01-01

... evaluation of alternative energy sources. (b) Each applicant for an amendment to a manufacturing license... 10 Energy 2 2012-01-01 2012-01-01 false Environmental report-manufacturing license. 51.54 Section 51.54 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR...

10 CFR 51.54 - Environmental report-manufacturing license.

Code of Federal Regulations, 2011 CFR

2011-01-01

... evaluation of alternative energy sources. (b) Each applicant for an amendment to a manufacturing license... 10 Energy 2 2011-01-01 2011-01-01 false Environmental report-manufacturing license. 51.54 Section 51.54 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR...

10 CFR 51.54 - Environmental report-manufacturing license.

Code of Federal Regulations, 2014 CFR

2014-01-01

... evaluation of alternative energy sources. (b) Each applicant for an amendment to a manufacturing license... 10 Energy 2 2014-01-01 2014-01-01 false Environmental report-manufacturing license. 51.54 Section 51.54 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR...

10 CFR 51.54 - Environmental report-manufacturing license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... evaluation of alternative energy sources. (b) Each applicant for an amendment to a manufacturing license... 10 Energy 2 2010-01-01 2010-01-01 false Environmental report-manufacturing license. 51.54 Section 51.54 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR...

10 CFR 51.54 - Environmental report-manufacturing license.

Code of Federal Regulations, 2013 CFR

2013-01-01

... evaluation of alternative energy sources. (b) Each applicant for an amendment to a manufacturing license... 10 Energy 2 2013-01-01 2013-01-01 false Environmental report-manufacturing license. 51.54 Section 51.54 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) ENVIRONMENTAL PROTECTION REGULATIONS FOR...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2011 CFR

2011-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2010 CFR

2010-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2012 CFR

2012-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2013 CFR

2013-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

10 CFR 61.3 - License required.

Code of Federal Regulations, 2014 CFR

2014-01-01

... REGULATORY COMMISSION (CONTINUED) LICENSING REQUIREMENTS FOR LAND DISPOSAL OF RADIOACTIVE WASTE General Provisions § 61.3 License required. (a) No person may receive, possess, and dispose of radioactive waste containing source, special nuclear, or byproduct material at a land disposal facility unless authorized by a...

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

PubMed

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-05

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments

PubMed Central

Ingargiola, Antonino; Laurence, Ted; Boutelle, Robert; Weiss, Shimon; Michalet, Xavier

2016-01-01

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license. PMID:26745406

Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors

DOE PAGES

Ingargiola, A.; Laurence, T. A.; Boutelle, R.; ...

2015-12-23

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

78 FR 24404 - Auction of Lower and Upper Paging Band Licenses Scheduled for July 16, 2013; Notice of Filing...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-25

...This document announces the procedures and minimum opening bids for the upcoming auction of licenses in the lower and upper paging bands (Auction 95). This document is intended to familiarize prospective applicants with the procedures and other requirements for participation in the auction.

Investigating the Perceptions, Use, and Impact of Open Textbooks: A Survey of Post-Secondary Students in British Columbia

ERIC Educational Resources Information Center

Jhangiani, Rajiv; Jhangiani, Surita

2017-01-01

Unrelenting increases in the price of college textbooks have prompted the development and adoption of open textbooks, educational resources that are openly licensed and available to students free of cost. Although several studies have investigated U.S. students' perceptions and use of open textbooks, there are no published studies of this kind in…

The State of Open Source Electronic Health Record Projects: A Software Anthropology Study.

PubMed

Alsaffar, Mona; Yellowlees, Peter; Odor, Alberto; Hogarth, Michael

2017-02-24

Electronic health records (EHR) are a key tool in managing and storing patients' information. Currently, there are over 50 open source EHR systems available. Functionality and usability are important factors for determining the success of any system. These factors are often a direct reflection of the domain knowledge and developers' motivations. However, few published studies have focused on the characteristics of free and open source software (F/OSS) EHR systems and none to date have discussed the motivation, knowledge background, and demographic characteristics of the developers involved in open source EHR projects. This study analyzed the characteristics of prevailing F/OSS EHR systems and aimed to provide an understanding of the motivation, knowledge background, and characteristics of the developers. This study identified F/OSS EHR projects on SourceForge and other websites from May to July 2014. Projects were classified and characterized by license type, downloads, programming languages, spoken languages, project age, development status, supporting materials, top downloads by country, and whether they were "certified" EHRs. Health care F/OSS developers were also surveyed using an online survey. At the time of the assessment, we uncovered 54 open source EHR projects, but only four of them had been successfully certified under the Office of the National Coordinator for Health Information Technology (ONC Health IT) Certification Program. In the majority of cases, the open source EHR software was downloaded by users in the United States (64.07%, 148,666/232,034), underscoring that there is a significant interest in EHR open source applications in the United States. A survey of EHR open source developers was conducted and a total of 103 developers responded to the online questionnaire. The majority of EHR F/OSS developers (65.3%, 66/101) are participating in F/OSS projects as part of a paid activity and only 25.7% (26/101) of EHR F/OSS developers are, or have been, health care providers in their careers. In addition, 45% (45/99) of developers do not work in the health care field. The research presented in this study highlights some challenges that may be hindering the future of health care F/OSS. A minority of developers have been health care professionals, and only 55% (54/99) work in the health care field. This undoubtedly limits the ability of functional design of F/OSS EHR systems from being a competitive advantage over prevailing commercial EHR systems. Open source software seems to be a significant interest to many; however, given that only four F/OSS EHR systems are ONC-certified, this interest is unlikely to yield significant adoption of these systems in the United States. Although the Health Information Technology for Economic and Clinical Health (HITECH) act was responsible for a substantial infusion of capital into the EHR marketplace, the lack of a corporate entity in most F/OSS EHR projects translates to a marginal capacity to market the respective F/OSS system and to navigate certification. This likely has further disadvantaged F/OSS EHR adoption in the United States. ©Mona Alsaffar, Peter Yellowlees, Alberto Odor, Michael Hogarth. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 24.02.2017.

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

Ingargiola, A.; Laurence, T. A.; Boutelle, R.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode (SPAD), photomultiplier tube (PMT) or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. Themore » format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. As a result, to encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.« less

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

PubMed

Stoet, Gijsbert

2010-11-01

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

A collection of open source applications for mass spectrometry data mining.

PubMed

Gallardo, Óscar; Ovelleiro, David; Gay, Marina; Carrascal, Montserrat; Abian, Joaquin

2014-10-01

We present several bioinformatics applications for the identification and quantification of phosphoproteome components by MS. These applications include a front-end graphical user interface that combines several Thermo RAW formats to MASCOT™ Generic Format extractors (EasierMgf), two graphical user interfaces for search engines OMSSA and SEQUEST (OmssaGui and SequestGui), and three applications, one for the management of databases in FASTA format (FastaTools), another for the integration of search results from up to three search engines (Integrator), and another one for the visualization of mass spectra and their corresponding database search results (JsonVisor). These applications were developed to solve some of the common problems found in proteomic and phosphoproteomic data analysis and were integrated in the workflow for data processing and feeding on our LymPHOS database. Applications were designed modularly and can be used standalone. These tools are written in Perl and Python programming languages and are supported on Windows platforms. They are all released under an Open Source Software license and can be freely downloaded from our software repository hosted at GoogleCode. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

IPeak: An open source tool to combine results from multiple MS/MS search engines.

PubMed

Wen, Bo; Du, Chaoqin; Li, Guilin; Ghali, Fawaz; Jones, Andrew R; Käll, Lukas; Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Feng, Qiang; Xu, Xun; Wang, Jun

2015-09-01

Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present an open source software tool, termed IPeak, a peptide identification pipeline that is designed to combine the Percolator post-processing algorithm and multi-search strategy to enhance the sensitivity of peptide identifications without compromising accuracy. IPeak provides a graphical user interface (GUI) as well as a command-line interface, which is implemented in JAVA and can work on all three major operating system platforms: Windows, Linux/Unix and OS X. IPeak has been designed to work with the mzIdentML standard from the Proteomics Standards Initiative (PSI) as an input and output, and also been fully integrated into the associated mzidLibrary project, providing access to the overall pipeline, as well as modules for calling Percolator on individual search engine result files. The integration thus enables IPeak (and Percolator) to be used in conjunction with any software packages implementing the mzIdentML data standard. IPeak is freely available and can be downloaded under an Apache 2.0 license at https://code.google.com/p/mzidentml-lib/. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A high-throughput system for high-quality tomographic reconstruction of large datasets at Diamond Light Source

PubMed Central

Atwood, Robert C.; Bodey, Andrew J.; Price, Stephen W. T.; Basham, Mark; Drakopoulos, Michael

2015-01-01

Tomographic datasets collected at synchrotrons are becoming very large and complex, and, therefore, need to be managed efficiently. Raw images may have high pixel counts, and each pixel can be multidimensional and associated with additional data such as those derived from spectroscopy. In time-resolved studies, hundreds of tomographic datasets can be collected in sequence, yielding terabytes of data. Users of tomographic beamlines are drawn from various scientific disciplines, and many are keen to use tomographic reconstruction software that does not require a deep understanding of reconstruction principles. We have developed Savu, a reconstruction pipeline that enables users to rapidly reconstruct data to consistently create high-quality results. Savu is designed to work in an ‘orthogonal’ fashion, meaning that data can be converted between projection and sinogram space throughout the processing workflow as required. The Savu pipeline is modular and allows processing strategies to be optimized for users' purposes. In addition to the reconstruction algorithms themselves, it can include modules for identification of experimental problems, artefact correction, general image processing and data quality assessment. Savu is open source, open licensed and ‘facility-independent’: it can run on standard cluster infrastructure at any institution. PMID:25939626

RandSpg: An open-source program for generating atomistic crystal structures with specific spacegroups

NASA Astrophysics Data System (ADS)

Avery, Patrick; Zurek, Eva

2017-04-01

A new algorithm, RANDSPG, that can be used to generate trial crystal structures with specific space groups and compositions is described. The program has been designed for systems where the atoms are independent of one another, and it is therefore primarily suited towards inorganic systems. The structures that are generated adhere to user-defined constraints such as: the lattice shape and size, stoichiometry, set of space groups to be generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally specify if the most general Wyckoff position is to be occupied or constrain select atoms to specific Wyckoff positions. Extensive testing indicates that the algorithm is efficient and reliable. The library is lightweight, portable, dependency-free and is published under a license recognized by the Open Source Initiative. A web interface for the algorithm is publicly accessible at http://xtalopt.openmolecules.net/randSpg/randSpg.html. RANDSPG has also been interfaced with the XTALOPT evolutionary algorithm for crystal structure prediction, and it is illustrated that the use of symmetric lattices in the first generation of randomly created individuals decreases the number of structures that need to be optimized to find the global energy minimum.

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.

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

NASA Technical Reports Server (NTRS)

Samareh, Jamshid A.

2011-01-01

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

Open-Source Software for Modeling of Nanoelectronic Devices

NASA Technical Reports Server (NTRS)

Oyafuso, Fabiano; Hua, Hook; Tisdale, Edwin; Hart, Don

2004-01-01

The Nanoelectronic Modeling 3-D (NEMO 3-D) computer program has been upgraded to open-source status through elimination of license-restricted components. The present version functions equivalently to the version reported in "Software for Numerical Modeling of Nanoelectronic Devices" (NPO-30520), NASA Tech Briefs, Vol. 27, No. 11 (November 2003), page 37. To recapitulate: NEMO 3-D performs numerical modeling of the electronic transport and structural properties of a semiconductor device that has overall dimensions of the order of tens of nanometers. The underlying mathematical model represents the quantum-mechanical behavior of the device resolved to the atomistic level of granularity. NEMO 3-D solves the applicable quantum matrix equation on a Beowulf-class cluster computer by use of a parallel-processing matrix vector multiplication algorithm coupled to a Lanczos and/or Rayleigh-Ritz algorithm that solves for eigenvalues. A prior upgrade of NEMO 3-D incorporated a capability for a strain treatment, parameterized for bulk material properties of GaAs and InAs, for two tight-binding submodels. NEMO 3-D has been demonstrated in atomistic analyses of effects of disorder in alloys and, in particular, in bulk In(x)Ga(1-x)As and in In(0.6)Ga(0.4)As quantum dots.

The world’s user-generated road map is more than 80% complete

PubMed Central

2017-01-01

OpenStreetMap, a crowdsourced geographic database, provides the only global-level, openly licensed source of geospatial road data, and the only national-level source in many countries. However, researchers, policy makers, and citizens who want to make use of OpenStreetMap (OSM) have little information about whether it can be relied upon in a particular geographic setting. In this paper, we use two complementary, independent methods to assess the completeness of OSM road data in each country in the world. First, we undertake a visual assessment of OSM data against satellite imagery, which provides the input for estimates based on a multilevel regression and poststratification model. Second, we fit sigmoid curves to the cumulative length of contributions, and use them to estimate the saturation level for each country. Both techniques may have more general use for assessing the development and saturation of crowd-sourced data. Our results show that in many places, researchers and policymakers can rely on the completeness of OSM, or will soon be able to do so. We find (i) that globally, OSM is ∼83% complete, and more than 40% of countries—including several in the developing world—have a fully mapped street network; (ii) that well-governed countries with good Internet access tend to be more complete, and that completeness has a U-shaped relationship with population density—both sparsely populated areas and dense cities are the best mapped; and (iii) that existing global datasets used by the World Bank undercount roads by more than 30%. PMID:28797037

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events

PubMed Central

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-01-01

Background Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. Objective To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. Software architecture DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Results Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. Discussion This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. Conclusion The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License. PMID:17472749

Duke Surgery Patient Safety: an open-source application for anonymous reporting of adverse and near-miss surgical events.

PubMed

Pietrobon, Ricardo; Lima, Raquel; Shah, Anand; Jacobs, Danny O; Harker, Matthew; McCready, Mariana; Martins, Henrique; Richardson, William

2007-05-01

Studies have shown that 4% of hospitalized patients suffer from an adverse event caused by the medical treatment administered. Some institutions have created systems to encourage medical workers to report these adverse events. However, these systems often prove to be inadequate and/or ineffective for reviewing the data collected and improving the outcomes in patient safety. To describe the Web-application Duke Surgery Patient Safety, designed for the anonymous reporting of adverse and near-miss events as well as scheduled reporting to surgeons and hospital administration. SOFTWARE ARCHITECTURE: DSPS was developed primarily using Java language running on a Tomcat server and with MySQL database as its backend. Formal and field usability tests were used to aid in development of DSPS. Extensive experience with DSPS at our institution indicate that DSPS is easy to learn and use, has good speed, provides needed functionality, and is well received by both adverse-event reporters and administrators. This is the first description of an open-source application for reporting patient safety, which allows the distribution of the application to other institutions in addition for its ability to adapt to the needs of different departments. DSPS provides a mechanism for anonymous reporting of adverse events and helps to administer Patient Safety initiatives. The modifiable framework of DSPS allows adherence to evolving national data standards. The open-source design of DSPS permits surgical departments with existing reporting mechanisms to integrate them with DSPS. The DSPS application is distributed under the GNU General Public License.

cPath: open source software for collecting, storing, and querying biological pathways

PubMed Central

Cerami, Ethan G; Bader, Gary D; Gross, Benjamin E; Sander, Chris

2006-01-01

Background Biological pathways, including metabolic pathways, protein interaction networks, signal transduction pathways, and gene regulatory networks, are currently represented in over 220 diverse databases. These data are crucial for the study of specific biological processes, including human diseases. Standard exchange formats for pathway information, such as BioPAX, CellML, SBML and PSI-MI, enable convenient collection of this data for biological research, but mechanisms for common storage and communication are required. Results We have developed cPath, an open source database and web application for collecting, storing, and querying biological pathway data. cPath makes it easy to aggregate custom pathway data sets available in standard exchange formats from multiple databases, present pathway data to biologists via a customizable web interface, and export pathway data via a web service to third-party software, such as Cytoscape, for visualization and analysis. cPath is software only, and does not include new pathway information. Key features include: a built-in identifier mapping service for linking identical interactors and linking to external resources; built-in support for PSI-MI and BioPAX standard pathway exchange formats; a web service interface for searching and retrieving pathway data sets; and thorough documentation. The cPath software is freely available under the LGPL open source license for academic and commercial use. Conclusion cPath is a robust, scalable, modular, professional-grade software platform for collecting, storing, and querying biological pathways. It can serve as the core data handling component in information systems for pathway visualization, analysis and modeling. PMID:17101041

The Future of ECHO: Evaluating Open Source Possibilities

NASA Astrophysics Data System (ADS)

Pilone, D.; Gilman, J.; Baynes, K.; Mitchell, A. E.

2012-12-01

NASA's Earth Observing System ClearingHOuse (ECHO) is a format agnostic metadata repository supporting over 3000 collections and 100M science granules. ECHO exposes FTP and RESTful Data Ingest APIs in addition to both SOAP and RESTful search and order capabilities. Built on top of ECHO is a human facing search and order web application named Reverb. ECHO processes hundreds of orders, tens of thousands of searches, and 1-2M ingest actions each week. As ECHO's holdings, metadata format support, and visibility have increased, the ECHO team has received requests by non-NASA entities for copies of ECHO that can be run locally against their data holdings. ESDIS and the ECHO Team have begun investigations into various deployment and Open Sourcing models that can balance the real constraints faced by the ECHO project with the benefits of providing ECHO capabilities to a broader set of users and providers. This talk will discuss several release and Open Source models being investigated by the ECHO team along with the impacts those models are expected to have on the project. We discuss: - Addressing complex deployment or setup issues for potential users - Models of vetting code contributions - Balancing external (public) user requests versus our primary partners - Preparing project code for public release, including navigating licensing issues related to leveraged libraries - Dealing with non-free project dependencies such as commercial databases - Dealing with sensitive aspects of project code such as database passwords, authentication approaches, security through obscurity, etc. - Ongoing support for the released code including increased testing demands, bug fixes, security fixes, and new features.

78 FR 51753 - AUC, LLC Reno Creek, In Situ Project, New Source Material License Application

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-21

... NUCLEAR REGULATORY COMMISSION [Docket No. 040-09092; [NRC-2013-0164] AUC, LLC Reno Creek, In Situ Project, New Source Material License Application AGENCY: Nuclear Regulatory Commission. ACTION: Notice of..., AUC, LLC (AUC) submitted to the U.S. Nuclear Regulatory Commission (NRC) an application for a new...

10 CFR 171.16 - Annual fees: Materials licensees, holders of certificates of compliance, holders of sealed source...

Code of Federal Regulations, 2010 CFR

2010-01-01

... contained in devices used in industrial measuring systems, including x-ray fluorescence analyzers [Program... ores containing source material for extraction of metals other than uranium or thorium, including.... 4 Another license includes licenses for extraction of metals, heavy metals, and rare earths. 5 There...

10 CFR 60.3 - License required.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

10 CFR 60.3 - License required.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

10 CFR 60.3 - License required.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false License required. 60.3 Section 60.3 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) DISPOSAL OF HIGH-LEVEL RADIOACTIVE WASTES IN GEOLOGIC REPOSITORIES General Provisions § 60.3 License required. (a) DOE shall not receive or possess source, special nuclear, or...

10 CFR 60.22 - Filing and distribution of application.

Code of Federal Regulations, 2010 CFR

2010-01-01

... GEOLOGIC REPOSITORIES Licenses License Applications § 60.22 Filing and distribution of application. (a) An application for a construction authorization for a high-level radioactive waste repository at a geologic repository operations area, and an application for a license to receive and possess source, special nuclear...

Structuring the Multimedia Deal: Legal Issues--Part 1: Licensing in the Multimedia Arena.

ERIC Educational Resources Information Center

Gersh, David L.; Jeffrey, Sheri

1993-01-01

Provides an overview of legal issues related to licensing entertainment rights for multimedia source materials, including the grant of rights clause, copyright ownership, territory and languages, term provision, specifications, approvals/controls, royalties, guilds, bankruptcies, termination of the license, and confidentiality. Common mistakes…

Open Textbooks and Increased Student Access and Outcomes

ERIC Educational Resources Information Center

Feldstein, Andrew; Martin, Mirta; Hudson, Amy; Warren, Kiara; Hilton, John, III; Wiley, David

2012-01-01

This study reports findings from a year-long pilot study during which 991 students in 9 core courses in the Virginia State University School of Business replaced traditional textbooks with openly licensed books and other digital content. The university made a deliberate decision to use open textbooks that were copyrighted under the Creative…

Evaluating Human Rights Advocacy on Criminal Justice and Sex Work.

PubMed

Amon, Joseph; Wurth, Margaret; McLemore, Megan

2015-06-11

Between October 2011 and September 2013, we conducted research on the use, by police and/or prosecutors, of condom possession as evidence of intent to engage in prostitution-related offenses. We studied the practice in five large, geographically diverse cities in the U.S. To facilitate our advocacy on this issue, conducted concurrent to and following our research, we developed an advocacy framework consisting of six dimensions: (1) raising awareness, (2) building and engaging coalitions, (3) framing debate, (4) securing rhetorical commitments, (5) reforming law and policy, and (6) changing practice. Using a case study approach, we describe how this framework also provided a basis for the evaluation of our work, and discuss additional considerations and values related to the measurement and evaluation of human rights advocacy. Copyright 2015 Amon, Wurth, and McLemore. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

How Bioethics is Complementing Human Rights in Realizing Health Access for Clinical Trial Participants: The Case of Formative PrEP Access in South Africa.

PubMed

Singh, Jerome

2015-06-11

Following the demise of apartheid, human rights in South Africa are now constitutionally enshrined.The right to health in South Africa's Constitution has been credited with transforming the lives of millions of people by triggering programmatic reforms in HIV treatment and the prevention of mother to child transmission (MTCT) of HIV.However, a constitutionally enshrined right to health offers no guarantee that clinical trial participants will enjoy post-trial access to beneficial interventions. Using access to HIV pre-exposure prophylaxis (PrEP) in South Africa as an example, this paper argues that adherence to bioethics norms could realize the right to health for trial participants following the end of a clinical trial. Copyright 2015 Singh. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Correlates of violence in Guinea's Maison Centrale Prison: a statistical approach to documenting human rights abuses.

PubMed

Osborn, Ronald E

2010-12-15

Les Mêmes Droits Pour Tous (MDT) is a human rights NGO in Guinea, West Africa that focuses on the rights of prisoners in Maison Centrale, the country's largest prison located in the capital city of Conakry. In 2007, MDT completed a survey of the prison population to assess basic legal and human rights conditions. This article uses statistical tools to explore MDT's survey results in greater depth, shedding light on human rights violations in Guinea. It contributes to human rights literature that argues for greater use of econometric tools in rights reporting, and demonstrates how human rights practitioners and academics can work together to construct an etiology of violence and torture by state actors, as physical violence is perhaps the most extreme violation of the individual's right to health. Copyright © 2010 Osborn. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Four strategic pathways for the realization of the right to health through civil society actions: challenges and practical lessons learned in the Egyptian context.

PubMed

Sabae, Ayman

2014-12-11

This article examines four distinctly different, yet fully complementary, strategic pathways adopted by the Egyptian Initiative for Personal Rights (EIPR), an Egyptian independent human rights organization, in its practical efforts to protect and guarantee the realization of the right to health to all Egyptians. It reflects upon practical experiences, covering strategic options that include proposing new legislation to policy makers, participatory formulation of new laws from the ground up, public advocacy, coalition building, and litigation. It also examines several factors that affect the decision on which strategic pathway to follow. It reflects on the politico-economic settings, the presence of political will, the scope and extent of impacted stakeholders and the degree of complexity of the cause in question. Copyright © 2014 Sabae. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

iBiology: communicating the process of science.

PubMed

Goodwin, Sarah S

2014-08-01

The Internet hosts an abundance of science video resources aimed at communicating scientific knowledge, including webinars, massive open online courses, and TED talks. Although these videos are efficient at disseminating information for diverse types of users, they often do not demonstrate the process of doing science, the excitement of scientific discovery, or how new scientific knowledge is developed. iBiology (www.ibiology.org), a project that creates open-access science videos about biology research and science-related topics, seeks to fill this need by producing videos by science leaders that make their ideas, stories, and experiences available to anyone with an Internet connection. © 2014 Goodwin. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Computer-assisted learning in human and dental medicine.

PubMed

Höhne, S; Schumann, R R

2004-04-01

This article describes the development and application of new didactic methods for use in computer-assisted teaching and learning systems for training doctors and dentists. Taking the Meducase project as an example, didactic models and their technological implementation are explained, together with the limitations of imparting knowledge with the "new media". In addition, legal concepts for a progressive, pragmatic, and innovative distribution of knowledge to undergraduate students are presented. In conclusion, potential and visions for the wide use of electronic learning in the German and European universities in the future are discussed. Self-directed learning (SDL) is a key component in both undergraduate education and lifelong learning for medical practitioners. E-learning can already be used to promote SDL at undergraduate level. The Meducase project uses self-directed, constructive, case- and problem-oriented learning within a learning platform for medical and dental students. In the long run, e-learning programs can only be successful in education if there is consistent analysis and implementation of value-added factors and the development and use of media-didactic concepts matched to electronic learning. The use of innovative forms of licensing - open source licenses for software and similar licenses for content - facilitates continuous, free access to these programs for all students and teachers. These legal concepts offer the possibility of innovative knowledge distribution, quality assurance and standardization across specializations, university departments, and possibly even national borders.

DataPflex: a MATLAB-based tool for the manipulation and visualization of multidimensional datasets.

PubMed

Hendriks, Bart S; Espelin, Christopher W

2010-02-01

DataPflex is a MATLAB-based application that facilitates the manipulation and visualization of multidimensional datasets. The strength of DataPflex lies in the intuitive graphical user interface for the efficient incorporation, manipulation and visualization of high-dimensional data that can be generated by multiplexed protein measurement platforms including, but not limited to Luminex or Meso-Scale Discovery. Such data can generally be represented in the form of multidimensional datasets [for example (time x stimulation x inhibitor x inhibitor concentration x cell type x measurement)]. For cases where measurements are made in a combinational fashion across multiple dimensions, there is a need for a tool to efficiently manipulate and reorganize such data for visualization. DataPflex accepts data consisting of up to five arbitrary dimensions in addition to a measurement dimension. Data are imported from a simple .xls format and can be exported to MATLAB or .xls. Data dimensions can be reordered, subdivided, merged, normalized and visualized in the form of collections of line graphs, bar graphs, surface plots, heatmaps, IC50's and other custom plots. Open source implementation in MATLAB enables easy extension for custom plotting routines and integration with more sophisticated analysis tools. DataPflex is distributed under the GPL license (http://www.gnu.org/licenses/) together with documentation, source code and sample data files at: http://code.google.com/p/datapflex. Supplementary data available at Bioinformatics online.

Regulatory Technology Development Plan - Sodium Fast Reactor. Mechanistic Source Term - Trial Calculation. Work Plan

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

Grabaskas, David; Bucknor, Matthew; Jerden, James

2016-02-01

The overall objective of the SFR Regulatory Technology Development Plan (RTDP) effort is to identify and address potential impediments to the SFR regulatory licensing process. In FY14, an analysis by Argonne identified the development of an SFR-specific MST methodology as an existing licensing gap with high regulatory importance and a potentially long lead-time to closure. This work was followed by an initial examination of the current state-of-knowledge regarding SFR source term development (ANLART-3), which reported several potential gaps. Among these were the potential inadequacies of current computational tools to properly model and assess the transport and retention of radionuclides duringmore » a metal fuel pool-type SFR core damage incident. The objective of the current work is to determine the adequacy of existing computational tools, and the associated knowledge database, for the calculation of an SFR MST. To accomplish this task, a trial MST calculation will be performed using available computational tools to establish their limitations with regard to relevant radionuclide release/retention/transport phenomena. The application of existing modeling tools will provide a definitive test to assess their suitability for an SFR MST calculation, while also identifying potential gaps in the current knowledge base and providing insight into open issues regarding regulatory criteria/requirements. The findings of this analysis will assist in determining future research and development needs.« less

An open-source library for the numerical modeling of mass-transfer in solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Novaresio, Valerio; García-Camprubí, María; Izquierdo, Salvador; Asinari, Pietro; Fueyo, Norberto

2012-01-01

The generation of direct current electricity using solid oxide fuel cells (SOFCs) involves several interplaying transport phenomena. Their simulation is crucial for the design and optimization of reliable and competitive equipment, and for the eventual market deployment of this technology. An open-source library for the computational modeling of mass-transport phenomena in SOFCs is presented in this article. It includes several multicomponent mass-transport models ( i.e. Fickian, Stefan-Maxwell and Dusty Gas Model), which can be applied both within porous media and in porosity-free domains, and several diffusivity models for gases. The library has been developed for its use with OpenFOAM ®, a widespread open-source code for fluid and continuum mechanics. The library can be used to model any fluid flow configuration involving multicomponent transport phenomena and it is validated in this paper against the analytical solution of one-dimensional test cases. In addition, it is applied for the simulation of a real SOFC and further validated using experimental data. Program summaryProgram title: multiSpeciesTransportModels Catalogue identifier: AEKB_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKB_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License No. of lines in distributed program, including test data, etc.: 18 140 No. of bytes in distributed program, including test data, etc.: 64 285 Distribution format: tar.gz Programming language:: C++ Computer: Any x86 (the instructions reported in the paper consider only the 64 bit case for the sake of simplicity) Operating system: Generic Linux (the instructions reported in the paper consider only the open-source Ubuntu distribution for the sake of simplicity) Classification: 12 External routines: OpenFOAM® (version 1.6-ext) ( http://www.extend-project.de) Nature of problem: This software provides a library of models for the simulation of the steady state mass and momentum transport in a multi-species gas mixture, possibly in a porous medium. The software is particularly designed to be used as the mass-transport library for the modeling of solid oxide fuel cells (SOFC). When supplemented with other sub-models, such as thermal and charge-transport ones, it allows the prediction of the cell polarization curve and hence the cell performance. Solution method: Standard finite volume method (FVM) is used for solving all the conservation equations. The pressure-velocity coupling is solved using the SIMPLE algorithm (possibly adding a porous drag term if required). The mass transport can be calculated using different alternative models, namely Fick, Maxwell-Stefan or dusty gas model. The code adopts a segregated method to solve the resulting linear system of equations. The different regions of the SOFC, namely gas channels, electrodes and electrolyte, are solved independently, and coupled through boundary conditions. Restrictions: When extremely large species fluxes are considered, current implementation of the Neumann and Robin boundary conditions do not avoid negative values of molar and/or mass fractions, which finally end up with numerical instability. However this never happened in the documented runs. Eventually these boundary conditions could be reformulated to become more robust. Running time: From seconds to hours depending on the mesh size and number of species. For example, on a 64 bit machine with Intel Core Duo T8300 and 3 GBytes of RAM, the provided test run requires less than 1 second.

Galaxy Portal: interacting with the galaxy platform through mobile devices.

PubMed

Børnich, Claus; Grytten, Ivar; Hovig, Eivind; Paulsen, Jonas; Čech, Martin; Sandve, Geir Kjetil

2016-06-01

: We present Galaxy Portal app, an open source interface to the Galaxy system through smart phones and tablets. The Galaxy Portal provides convenient and efficient monitoring of job completion, as well as opportunities for inspection of results and execution history. In addition to being useful to the Galaxy community, we believe that the app also exemplifies a useful way of exploiting mobile interfaces for research/high-performance computing resources in general. The source is freely available under a GPL license on GitHub, along with user documentation and pre-compiled binaries and instructions for several platforms: https://github.com/Tarostar/QMLGalaxyPortal It is available for iOS version 7 (and newer) through the Apple App Store, and for Android through Google Play for version 4.1 (API 16) or newer. geirksa@ifi.uio.no. © The Author 2016. Published by Oxford University Press.

ImgLib2--generic image processing in Java.

PubMed

Pietzsch, Tobias; Preibisch, Stephan; Tomancák, Pavel; Saalfeld, Stephan

2012-11-15

ImgLib2 is an open-source Java library for n-dimensional data representation and manipulation with focus on image processing. It aims at minimizing code duplication by cleanly separating pixel-algebra, data access and data representation in memory. Algorithms can be implemented for classes of pixel types and generic access patterns by which they become independent of the specific dimensionality, pixel type and data representation. ImgLib2 illustrates that an elegant high-level programming interface can be achieved without sacrificing performance. It provides efficient implementations of common data types, storage layouts and algorithms. It is the data model underlying ImageJ2, the KNIME Image Processing toolbox and an increasing number of Fiji-Plugins. ImgLib2 is licensed under BSD. Documentation and source code are available at http://imglib2.net and in a public repository at https://github.com/imagej/imglib. Supplementary data are available at Bioinformatics Online. saalfeld@mpi-cbg.de

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

PubMed

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

13Check_RNA: A tool to evaluate 13C chemical shifts assignments of RNA.

PubMed

Icazatti, A A; Martin, O A; Villegas, M; Szleifer, I; Vila, J A

2018-06-19

Chemical shifts (CS) are an important source of structural information of macromolecules such as RNA. In addition to the scarce availability of CS for RNA, the observed values are prone to errors due to a wrong re-calibration or miss assignments. Different groups have dedicated their efforts to correct CS systematic errors on RNA. Despite this, there are not automated and freely available algorithms for correct assignments of RNA 13C CS before their deposition to the BMRB or re-reference already deposited CS with systematic errors. Based on an existent method we have implemented an open source python module to correct 13C CS (from here on 13Cexp) systematic errors of RNAs and then return the results in 3 formats including the nmrstar one. This software is available on GitHub at https://github.com/BIOS-IMASL/13Check_RNA under a MIT license. Supplementary data are available at Bioinformatics online.

esATAC: An Easy-to-use Systematic pipeline for ATAC-seq data analysis.

PubMed

Wei, Zheng; Zhang, Wei; Fang, Huan; Li, Yanda; Wang, Xiaowo

2018-03-07

ATAC-seq is rapidly emerging as one of the major experimental approaches to probe chromatin accessibility genome-wide. Here, we present "esATAC", a highly integrated easy-to-use R/Bioconductor package, for systematic ATAC-seq data analysis. It covers essential steps for full analyzing procedure, including raw data processing, quality control and downstream statistical analysis such as peak calling, enrichment analysis and transcription factor footprinting. esATAC supports one command line execution for preset pipelines, and provides flexible interfaces for building customized pipelines. esATAC package is open source under the GPL-3.0 license. It is implemented in R and C ++. Source code and binaries for Linux, MAC OS X and Windows are available through Bioconductor https://www.bioconductor.org/packages/release/bioc/html/esATAC.html). xwwang@tsinghua.edu.cn. Supplementary data are available at Bioinformatics online.

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

PubMed Central

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

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

PubMed

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

2012-08-01

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

The Victor C++ library for protein representation and advanced manipulation.

PubMed

Hirsh, Layla; Piovesan, Damiano; Giollo, Manuel; Ferrari, Carlo; Tosatto, Silvio C E

2015-04-01

Protein sequence and structure representation and manipulation require dedicated software libraries to support methods of increasing complexity. Here, we describe the VIrtual Constrution TOol for pRoteins (Victor) C++ library, an open source platform dedicated to enabling inexperienced users to develop advanced tools and gathering contributions from the community. The provided application examples cover statistical energy potentials, profile-profile sequence alignments and ab initio loop modeling. Victor was used over the last 15 years in several publications and optimized for efficiency. It is provided as a GitHub repository with source files and unit tests, plus extensive online documentation, including a Wiki with help files and tutorials, examples and Doxygen documentation. The C++ library and online documentation, distributed under a GPL license are available from URL: http://protein.bio.unipd.it/victor/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

BioRuby: bioinformatics software for the Ruby programming language.

PubMed

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

2010-10-15

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

SED-ED, a workflow editor for computational biology experiments written in SED-ML.

PubMed

Adams, Richard R

2012-04-15

The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.

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

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.

HTML5 PivotViewer: high-throughput visualization and querying of image data on the web

PubMed Central

Taylor, Stephen; Noble, Roger

2014-01-01

Motivation: Visualization and analysis of large numbers of biological images has generated a bottle neck in research. We present HTML5 PivotViewer, a novel, open source, platform-independent viewer making use of the latest web technologies that allows seamless access to images and associated metadata for each image. This provides a powerful method to allow end users to mine their data. Availability and implementation: Documentation, examples and links to the software are available from http://www.cbrg.ox.ac.uk/data/pivotviewer/. The software is licensed under GPLv2. Contact:  stephen.taylor@imm.ox.ac.uk and roger@coritsu.com PMID:24849578

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

PubMed Central

2015-01-01

Summary: dendextend is an R package for creating and comparing visually appealing tree diagrams. dendextend provides utility functions for manipulating dendrogram objects (their color, shape and content) as well as several advanced methods for comparing trees to one another (both statistically and visually). As such, dendextend offers a flexible framework for enhancing R's rich ecosystem of packages for performing hierarchical clustering of items. Availability and implementation: The dendextend R package (including detailed introductory vignettes) is available under the GPL-2 Open Source license and is freely available to download from CRAN at: (http://cran.r-project.org/package=dendextend) Contact: Tal.Galili@math.tau.ac.il PMID:26209431

76 FR 30404 - Advisory Committee On Reactor Safeguards; Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-25

... Room T2-B1, 11545 Rockville Pike, Rockville, Maryland 8:30 a.m.-8:35 a.m.: Opening Remarks by the ACRS... Alloy Cladding.'' 10:45 a.m.-11:45 a.m.: Revised Safety Evaluation Report Associated with the License... to the safety evaluation report associated with the license renewal application for the Hope Creek...

Natural analog studies: Licensing perspective

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

Bradbury, J.W.

1995-09-01

This report describes the licensing perspective of the term {open_quotes}natural analog studies{close_quotes} as used in CFR Part 60. It describes the misunderstandings related to its definition which has become evident during discussions at the U.S Nuclear Regulatory Commission meetings and tries to clarify the appropriate applications of natural analog studies to aspects of repository site characterization.

78 FR 47785 - Biweekly Notice; Applications and Amendments to Facility Operating Licenses and Combined Licenses...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-06

... correlation for the General Electric Nuclear Energy advanced fuel designs (i.e., GE14 and GNF2 fuels) used at... Electric Nuclear Energy in its report, ``10 CFR 21 Reportable Condition Notification: Potential to Exceed... failure-maximum demand open (PRFO) transient as reported by General Electric Nuclear Energy in its Part 21...

10 CFR 35.49 - Suppliers for sealed sources or devices for medical use.

Code of Federal Regulations, 2014 CFR

2014-01-01

... accordance with a license issued under 10 CFR part 30 and 10 CFR 32.74 of this chapter or equivalent requirements of an Agreement State; (b) Sealed sources or devices non-commercially transferred from a Part 35... in accordance with a license issued under 10 CFR part 30 or the equivalent requirements of an...

10 CFR 35.49 - Suppliers for sealed sources or devices for medical use.

Code of Federal Regulations, 2011 CFR

2011-01-01

... accordance with a license issued under 10 CFR Part 30 and 10 CFR 32.74 of this chapter or equivalent requirements of an Agreement State; (b) Sealed sources or devices non-commercially transferred from a Part 35... in accordance with a license issued under 10 CFR Part 30 or the equivalent requirements of an...

10 CFR 35.49 - Suppliers for sealed sources or devices for medical use.

Code of Federal Regulations, 2010 CFR

2010-01-01

... accordance with a license issued under 10 CFR Part 30 and 10 CFR 32.74 of this chapter or equivalent requirements of an Agreement State; (b) Sealed sources or devices non-commercially transferred from a Part 35... in accordance with a license issued under 10 CFR Part 30 or the equivalent requirements of an...

10 CFR 35.49 - Suppliers for sealed sources or devices for medical use.

Code of Federal Regulations, 2012 CFR

2012-01-01

... accordance with a license issued under 10 CFR Part 30 and 10 CFR 32.74 of this chapter or equivalent requirements of an Agreement State; (b) Sealed sources or devices non-commercially transferred from a Part 35... in accordance with a license issued under 10 CFR Part 30 or the equivalent requirements of an...

10 CFR 35.49 - Suppliers for sealed sources or devices for medical use.

Code of Federal Regulations, 2013 CFR

2013-01-01

... accordance with a license issued under 10 CFR Part 30 and 10 CFR 32.74 of this chapter or equivalent requirements of an Agreement State; (b) Sealed sources or devices non-commercially transferred from a Part 35... in accordance with a license issued under 10 CFR Part 30 or the equivalent requirements of an...

Questions of Quality in Repositories of Open Educational Resources: A Literature Review

ERIC Educational Resources Information Center

Atenas, Javiera; Havemann, Leo

2014-01-01

Open educational resources (OER) are teaching and learning materials which are freely available and openly licensed. Repositories of OER (ROER) are platforms that host and facilitate access to these resources. ROER should not just be designed to store this content--in keeping with the aims of the OER movement, they should support educators in…

Needs for and Utilization of OER in Distance Education: A Chinese Survey

ERIC Educational Resources Information Center

Chen, Qing; Panda, Santosh

2013-01-01

The recent developments within open educational resources (OERs) and open licensing have generated considerable interest among distance educators since open and distance learning is supposed to be the largest consumer/user of and contributor to OER. In China, given the policy of development and use of elaborate courses, conversion of radio and…

Hydropower resources at risk: The status of hydropower regulation and development - 1997

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

Hunt, R.T.; Hunt, J.A.

This report documents today`s hydropower licensing and development status based on published data as follows: (a) Federal Energy Regulatory Commission (FERC) databases, maintained by FERC`s Office of Hydropower Licensing, of: (1) operating FERC-regulated projects, federal projects, and known unlicensed projects; (2) surrendered licenses; and, (3) recent licensing and relicensing actions; (b) Energy Information Administration (EIA) data on installed capacity and generation from 1949 through 1995 for the various resources used to produce electricity in the U.S.; and, (c) FERC licensing orders, and environmental assessments or environmental impact statements for each individual project relicensed since 1980. The analysis conducted to preparemore » this paper includes the effects of all FERC hydropower licensing actions since 1980, and applies those findings to estimate the costs of hydropower licensing and development activity for the next 15 years. It also quantifies the national cost of hydropower regulation. The future estimates are quite conservative. The are presented in 1996 dollars without speculating on the effects of future inflation, license surrenders, conditions imposed through open-ended license articles, license terms greater than 30 years, or low water years. Instead, they show the most directly predictable influences on licensing outcomes using actual experiences since ECPA (after 1986).« less

10 CFR 39.1 - Purpose and scope.

Code of Federal Regulations, 2012 CFR

2012-01-01

... of licensed materials including sealed sources, radioactive tracers, radioactive markers, and uranium... authorizing the use of licensed material in tracer studies involving multiple wells, such as field flooding...

10 CFR 39.1 - Purpose and scope.

Code of Federal Regulations, 2011 CFR

2011-01-01

... of licensed materials including sealed sources, radioactive tracers, radioactive markers, and uranium... authorizing the use of licensed material in tracer studies involving multiple wells, such as field flooding...

10 CFR 39.1 - Purpose and scope.

Code of Federal Regulations, 2014 CFR

2014-01-01

... of licensed materials including sealed sources, radioactive tracers, radioactive markers, and uranium... authorizing the use of licensed material in tracer studies involving multiple wells, such as field flooding...

10 CFR 39.1 - Purpose and scope.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of licensed materials including sealed sources, radioactive tracers, radioactive markers, and uranium... authorizing the use of licensed material in tracer studies involving multiple wells, such as field flooding...

10 CFR 39.1 - Purpose and scope.

Code of Federal Regulations, 2013 CFR

2013-01-01

... of licensed materials including sealed sources, radioactive tracers, radioactive markers, and uranium... authorizing the use of licensed material in tracer studies involving multiple wells, such as field flooding...

XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

NASA Astrophysics Data System (ADS)

Lonie, David C.; Zurek, Eva

2011-02-01

The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely available to the scientific community for use and collaboration under the GNU Public License. Running time: User dependent. The program runs until stopped by the user.

Potential predatory and legitimate biomedical journals: can you tell the difference? A cross-sectional comparison.

PubMed

Shamseer, Larissa; Moher, David; Maduekwe, Onyi; Turner, Lucy; Barbour, Virginia; Burch, Rebecca; Clark, Jocalyn; Galipeau, James; Roberts, Jason; Shea, Beverley J

2017-03-16

The Internet has transformed scholarly publishing, most notably, by the introduction of open access publishing. Recently, there has been a rise of online journals characterized as 'predatory', which actively solicit manuscripts and charge publications fees without providing robust peer review and editorial services. We carried out a cross-sectional comparison of characteristics of potential predatory, legitimate open access, and legitimate subscription-based biomedical journals. On July 10, 2014, scholarly journals from each of the following groups were identified - potential predatory journals (source: Beall's List), presumed legitimate, fully open access journals (source: PubMed Central), and presumed legitimate subscription-based (including hybrid) journals (source: Abridged Index Medicus). MEDLINE journal inclusion criteria were used to screen and identify biomedical journals from within the potential predatory journals group. One hundred journals from each group were randomly selected. Journal characteristics (e.g., website integrity, look and feel, editors and staff, editorial/peer review process, instructions to authors, publication model, copyright and licensing, journal location, and contact) were collected by one assessor and verified by a second. Summary statistics were calculated. Ninety-three predatory journals, 99 open access, and 100 subscription-based journals were analyzed; exclusions were due to website unavailability. Many more predatory journals' homepages contained spelling errors (61/93, 66%) and distorted or potentially unauthorized images (59/93, 63%) compared to open access journals (6/99, 6% and 5/99, 5%, respectively) and subscription-based journals (3/100, 3% and 1/100, 1%, respectively). Thirty-one (33%) predatory journals promoted a bogus impact metric - the Index Copernicus Value - versus three (3%) open access journals and no subscription-based journals. Nearly three quarters (n = 66, 73%) of predatory journals had editors or editorial board members whose affiliation with the journal was unverified versus two (2%) open access journals and one (1%) subscription-based journal in which this was the case. Predatory journals charge a considerably smaller publication fee (median $100 USD, IQR $63-$150) than open access journals ($1865 USD, IQR $800-$2205) and subscription-based hybrid journals ($3000 USD, IQR $2500-$3000). We identified 13 evidence-based characteristics by which predatory journals may potentially be distinguished from presumed legitimate journals. These may be useful for authors who are assessing journals for possible submission or for others, such as universities evaluating candidates' publications as part of the hiring process.

Instructor and Student Experiences with Open Textbooks, from the California Open Online Library for Education (Cool4Ed)

ERIC Educational Resources Information Center

Ozdemir, Ozgur; Hendricks, Christina

2017-01-01

Open textbooks are similar to traditional textbooks except that they are free of cost and licensed to allow revision and reuse. Adopting open textbooks for higher education courses is a way to address the growing costs of traditional textbooks that lead some students to be unable to access them, and to allow instructors to tailor the books to…

Improving Software Sustainability: Lessons Learned from Profiles in Science.

PubMed

Gallagher, Marie E

2013-01-01

The Profiles in Science® digital library features digitized surrogates of historical items selected from the archival collections of the U.S. National Library of Medicine as well as collaborating institutions. In addition, it contains a database of descriptive, technical and administrative metadata. It also contains various software components that allow creation of the metadata, management of the digital items, and access to the items and metadata through the Profiles in Science Web site [1]. The choices made building the digital library were designed to maximize the sustainability and long-term survival of all of the components of the digital library [2]. For example, selecting standard and open digital file formats rather than proprietary formats increases the sustainability of the digital files [3]. Correspondingly, using non-proprietary software may improve the sustainability of the software--either through in-house expertise or through the open source community. Limiting our digital library software exclusively to open source software or to software developed in-house has not been feasible. For example, we have used proprietary operating systems, scanning software, a search engine, and office productivity software. We did this when either lack of essential capabilities or the cost-benefit trade-off favored using proprietary software. We also did so knowing that in the future we would need to replace or upgrade some of our proprietary software, analogous to migrating from an obsolete digital file format to a new format as the technological landscape changes. Since our digital library's start in 1998, all of its software has been upgraded or replaced, but the digitized items have not yet required migration to other formats. Technological changes that compelled us to replace proprietary software included the cost of product licensing, product support, incompatibility with other software, prohibited use due to evolving security policies, and product abandonment. Sometimes these changes happen on short notice, so we continually monitor our library's software for signs of endangerment. We have attempted to replace proprietary software with suitable in-house or open source software. When the replacement involves a standalone piece of software with a nearly equivalent version, such as replacing a commercial HTTP server with an open source HTTP server, the replacement is straightforward. Recently we replaced software that functioned not only as our search engine but also as the backbone of the architecture of our Web site. In this paper, we describe the lessons learned and the pros and cons of replacing this software with open source software.

Maximizing profits in international technology transfer

NASA Technical Reports Server (NTRS)

Straube, W.

1974-01-01

Maximum profit can be introduced into international technology transfer by observing the following: (1) ethical and open dealing between the parties; (2) maximum knowledge of all facts concerning the technology, the use of the technology, the market, competition, prices, and alternatives; (3) ability to coordinate exports, service, support activities, licensing and cross licensing; and (4) knowledgeable people which put these factors together.

78 FR 65982 - Auction of H Block Licenses in the 1915-1920 MHz and 1995-2000 MHz Bands Rescheduled for January...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-04

...This document announces the procedures, reserve price, and minimum opening bids for the upcoming auction of H Block licenses (Auction 96) and provides the revised schedule for Auction 96. This document is intended to familiarize prospective applicants with the procedures and other requirements for participation in the auction.

A GIS-based tool for an integrated assessment of spatial planning trade-offs with aquaculture.

PubMed

Gimpel, Antje; Stelzenmüller, Vanessa; Töpsch, Sandra; Galparsoro, Ibon; Gubbins, Matthew; Miller, David; Murillas, Arantza; Murray, Alexander G; Pınarbaşı, Kemal; Roca, Guillem; Watret, Robert

2018-06-15

The increasing demand for protein from aquaculture will trigger a global expansion of the sector in coastal and offshore waters. While contributing to food security, potential conflicts with other traditional activities such as fisheries or tourism are inevitable, thus calling for decision-support tools to assess aquaculture planning scenarios in a multi-use context. Here we introduce the AquaSpace tool, one of the first Geographic Information System (GIS)-based planning tools empowering an integrated assessment and mapping of 30 indicators reflecting economic, environmental, inter-sectorial and socio-cultural risks and opportunities for proposed aquaculture systems in a marine environment. A bottom-up process consulting more than 350 stakeholders from 10 countries across southern and northern Europe enabled the direct consideration of stakeholder needs when developing the GIS AddIn. The AquaSpace tool is an open source product and builds in the prospective use of open source datasets at a European scale, hence aiming to improve reproducibility and collaboration in aquaculture science and research. Tool outputs comprise detailed reports and graphics allowing key stakeholders such as planners or licensing authorities to evaluate and communicate alternative planning scenarios and to take more informed decisions. With the help of the German North Sea case study we demonstrate here the tool application at multiple spatial scales with different aquaculture systems and under a range of space-related development constraints. The computation of these aquaculture planning scenarios and the assessment of their trade-offs showed that it is entirely possible to identify aquaculture sites, that correspondent to multifarious potential challenges, for instance by a low conflict potential, a low risk of disease spread, a comparable high economic profit and a low impact on touristic attractions. We believe that a transparent visualisation of risks and opportunities of aquaculture planning scenarios helps an effective Marine Spatial Planning (MSP) process, supports the licensing process and simplifies investments. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Overview of the gaps in the health care legislation in Georgia: short-, medium-, and long-term priorities.

PubMed

Kiknadze, Nino; Beletsky, Leo

2013-12-12

After gaining independence following the dissolution of the Soviet Union, Georgia has aspired to become the region's leader in progressive legal reform. Particularly in the realm of health care regulation, Georgia has proceeded with extensive legislative reforms intended to modernize its health care system, and bring it in line with international standards. As part of a larger project to improve human rights in patient care, we conducted a study designed to identify gaps in the current Georgian health care legislation. Using a cross-site research framework based on the European Charter of Patients’ Rights, an interdisciplinary working group oversaw a comprehensive review of human rights legislation pertinent to health care settings using various sources, such as black letter law, expert opinions, court cases, research papers, reports, and complaints. The study identified a number of serious inconsistencies, gaps, and conflicts in the definition and coverage of terms used in the national legislative canon pertinent to human rights in patient care. These include inconsistent definitions of key terms "informed consent" and "medical malpractice" across the legislative landscape. Imprecise and overly broad drafting of legislation has left concepts like patient confidentiality and implied consent wide open to abuse. The field of health care provider rights was entirely missing from existing Georgian legislation. To our knowledge, this is the first study of its kind in Georgia. Gaps and inconsistencies uncovered were categorized based on a short-, medium-, and long-term action framework. Results were presented to key decision makers in Georgian ministerial and legislative institutions. Several of the major recommendations are currently being considered for inclusion into future legal reform. Copyright © 2013 Kiknadze and Beletsky. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Addressing the Local in Localization: A Case Study of Open Textbook Adoption by Three South African Teachers

ERIC Educational Resources Information Center

Jimes, Cynthia; Weiss, Shenandoah; Keep, Renae

2013-01-01

This article presents a case study of the adoption and use of open textbooks by three high school teachers in the KwaZulu-Natal province of South Africa. The textbooks, collaboratively authored and distributed through the South African initiative, Siyavula, are available online and are openly licensed, allowing teachers to freely use, modify,…

Portability and Usability of Open Educational Resources on Mobile Devices: A Study in the Context of Brazilian Educational Portals and Android-Based Devices

ERIC Educational Resources Information Center

da Silva, André Constantino; Freire, Fernanda Maria Pereira; Mourão, Vitor Hugo Miranda; da Cruz, Márcio Diógenes de Oliveira; da Rocha, Heloísa Vieira

2014-01-01

Open Educational Resources (OER) are freely accessible, openly licensed hypertext, audio, video, simulations, games and animations that are useful for teaching and learning purposes. In order to facilitate the location of such resources, educational content portals are being created, crowding contents that were produced by different teams with…

Emerging Issues: Open Educational Resources--How Science Teachers Can Use Open Educational Resources to Revitalize Lessons

ERIC Educational Resources Information Center

Charles, Karen; Rice, Olivia

2012-01-01

The term "open educational resources" (OERs) was first coined by UNESCO in 2005 and refers to "teaching, learning or research materials that are in the public domain or released with an intellectual property license that allows for free use, adaptation, and/or distribution." OERs offer educators what might be termed "value neutral" online…

Efficient visualization of high-throughput targeted proteomics experiments: TAPIR.

PubMed

Röst, Hannes L; Rosenberger, George; Aebersold, Ruedi; Malmström, Lars

2015-07-15

Targeted mass spectrometry comprises a set of powerful methods to obtain accurate and consistent protein quantification in complex samples. To fully exploit these techniques, a cross-platform and open-source software stack based on standardized data exchange formats is required. We present TAPIR, a fast and efficient Python visualization software for chromatograms and peaks identified in targeted proteomics experiments. The input formats are open, community-driven standardized data formats (mzML for raw data storage and TraML encoding the hierarchical relationships between transitions, peptides and proteins). TAPIR is scalable to proteome-wide targeted proteomics studies (as enabled by SWATH-MS), allowing researchers to visualize high-throughput datasets. The framework integrates well with existing automated analysis pipelines and can be extended beyond targeted proteomics to other types of analyses. TAPIR is available for all computing platforms under the 3-clause BSD license at https://github.com/msproteomicstools/msproteomicstools. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

NASA Astrophysics Data System (ADS)

Moore, Josh; Linkert, Melissa; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Li, Simon; Lindner, Dominik; Moore, William J.; Patterson, Andrew J.; Pindelski, Blazej; Ramalingam, Balaji; Rozbicki, Emil; Tarkowska, Aleksandra; Walczysko, Petr; Allan, Chris; Burel, Jean-Marie; Swedlow, Jason

2015-03-01

The Open Microscopy Environment (OME) has built and released Bio-Formats, a Java-based proprietary file format conversion tool and OMERO, an enterprise data management platform under open source licenses. In this report, we describe new versions of Bio-Formats and OMERO that are specifically designed to support large, multi-gigabyte or terabyte scale datasets that are routinely collected across most domains of biological and biomedical research. Bio- Formats reads image data directly from native proprietary formats, bypassing the need for conversion into a standard format. It implements the concept of a file set, a container that defines the contents of multi-dimensional data comprised of many files. OMERO uses Bio-Formats to read files natively, and provides a flexible access mechanism that supports several different storage and access strategies. These new capabilities of OMERO and Bio-Formats make them especially useful for use in imaging applications like digital pathology, high content screening and light sheet microscopy that create routinely large datasets that must be managed and analyzed.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations

NASA Astrophysics Data System (ADS)

Valiev, M.; Bylaska, E. J.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Van Dam, H. J. J.; Wang, D.; Nieplocha, J.; Apra, E.; Windus, T. L.; de Jong, W. A.

2010-09-01

The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and biological systems. Utilizing a common computational framework, diverse theoretical descriptions can be used to provide the best solution for a given scientific problem. Scalable parallel implementations and modular software design enable efficient utilization of current computational architectures. This paper provides an overview of NWChem focusing primarily on the core theoretical modules provided by the code and their parallel performance. Program summaryProgram title: NWChem Catalogue identifier: AEGI_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGI_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Open Source Educational Community License No. of lines in distributed program, including test data, etc.: 11 709 543 No. of bytes in distributed program, including test data, etc.: 680 696 106 Distribution format: tar.gz Programming language: Fortran 77, C Computer: all Linux based workstations and parallel supercomputers, Windows and Apple machines Operating system: Linux, OS X, Windows Has the code been vectorised or parallelized?: Code is parallelized Classification: 2.1, 2.2, 3, 7.3, 7.7, 16.1, 16.2, 16.3, 16.10, 16.13 Nature of problem: Large-scale atomistic simulations of chemical and biological systems require efficient and reliable methods for ground and excited solutions of many-electron Hamiltonian, analysis of the potential energy surface, and dynamics. Solution method: Ground and excited solutions of many-electron Hamiltonian are obtained utilizing density-functional theory, many-body perturbation approach, and coupled cluster expansion. These solutions or a combination thereof with classical descriptions are then used to analyze potential energy surface and perform dynamical simulations. Additional comments: Full documentation is provided in the distribution file. This includes an INSTALL file giving details of how to build the package. A set of test runs is provided in the examples directory. The distribution file for this program is over 90 Mbytes and therefore is not delivered directly when download or Email is requested. Instead a html file giving details of how the program can be obtained is sent. Running time: Running time depends on the size of the chemical system, complexity of the method, number of cpu's and the computational task. It ranges from several seconds for serial DFT energy calculations on a few atoms to several hours for parallel coupled cluster energy calculations on tens of atoms or ab-initio molecular dynamics simulation on hundreds of atoms.

76 FR 41308 - Strata Energy, Inc., Ross In Situ Recovery Uranium Project, Crook County, WY; Notice of Materials...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-13

..., Inc., Ross In Situ Recovery Uranium Project, Crook County, WY; Notice of Materials License Application...-4737, or by e-mail to [email protected] . The Ross In Situ Recovery Uranium Project License... source and byproduct materials license at its Ross In Situ Recovery Uranium Project site located in Crook...

Land use mapping from CBERS-2 images with open source tools by applying different classification algorithms

NASA Astrophysics Data System (ADS)

Sanhouse-García, Antonio J.; Rangel-Peraza, Jesús Gabriel; Bustos-Terrones, Yaneth; García-Ferrer, Alfonso; Mesas-Carrascosa, Francisco J.

2016-02-01

Land cover classification is often based on different characteristics between their classes, but with great homogeneity within each one of them. This cover is obtained through field work or by mean of processing satellite images. Field work involves high costs; therefore, digital image processing techniques have become an important alternative to perform this task. However, in some developing countries and particularly in Casacoima municipality in Venezuela, there is a lack of geographic information systems due to the lack of updated information and high costs in software license acquisition. This research proposes a low cost methodology to develop thematic mapping of local land use and types of coverage in areas with scarce resources. Thematic mapping was developed from CBERS-2 images and spatial information available on the network using open source tools. The supervised classification method per pixel and per region was applied using different classification algorithms and comparing them among themselves. Classification method per pixel was based on Maxver algorithms (maximum likelihood) and Euclidean distance (minimum distance), while per region classification was based on the Bhattacharya algorithm. Satisfactory results were obtained from per region classification, where overall reliability of 83.93% and kappa index of 0.81% were observed. Maxver algorithm showed a reliability value of 73.36% and kappa index 0.69%, while Euclidean distance obtained values of 67.17% and 0.61% for reliability and kappa index, respectively. It was demonstrated that the proposed methodology was very useful in cartographic processing and updating, which in turn serve as a support to develop management plans and land management. Hence, open source tools showed to be an economically viable alternative not only for forestry organizations, but for the general public, allowing them to develop projects in economically depressed and/or environmentally threatened areas.

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

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.

The Open Spectral Database: an open platform for sharing and searching spectral data.

PubMed

Chalk, Stuart J

2016-01-01

A number of websites make available spectral data for download (typically as JCAMP-DX text files) and one (ChemSpider) that also allows users to contribute spectral files. As a result, searching and retrieving such spectral data can be time consuming, and difficult to reuse if the data is compressed in the JCAMP-DX file. What is needed is a single resource that allows submission of JCAMP-DX files, export of the raw data in multiple formats, searching based on multiple chemical identifiers, and is open in terms of license and access. To address these issues a new online resource called the Open Spectral Database (OSDB) http://osdb.info/ has been developed and is now available. Built using open source tools, using open code (hosted on GitHub), providing open data, and open to community input about design and functionality, the OSDB is available for anyone to submit spectral data, making it searchable and available to the scientific community. This paper details the concept and coding, internal architecture, export formats, Representational State Transfer (REST) Application Programming Interface and options for submission of data. The OSDB website went live in November 2015. Concurrently, the GitHub repository was made available at https://github.com/stuchalk/OSDB/, and is open for collaborators to join the project, submit issues, and contribute code. The combination of a scripting environment (PHPStorm), a PHP Framework (CakePHP), a relational database (MySQL) and a code repository (GitHub) provides all the capabilities to easily develop REST based websites for ingestion, curation and exposure of open chemical data to the community at all levels. It is hoped this software stack (or equivalent ones in other scripting languages) will be leveraged to make more chemical data available for both humans and computers.

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

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

2008-01-01

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

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

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

2008-01-01

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

A resource management tool for public health continuity of operations during disasters.

PubMed

Turner, Anne M; Reeder, Blaine; Wallace, James C

2013-04-01

We developed and validated a user-centered information system to support the local planning of public health continuity of operations for the Community Health Services Division, Public Health - Seattle & King County, Washington. The Continuity of Operations Data Analysis (CODA) system was designed as a prototype developed using requirements identified through participatory design. CODA uses open-source software that links personnel contact and licensing information with needed skills and clinic locations for 821 employees at 14 public health clinics in Seattle and King County. Using a web-based interface, CODA can visualize locations of personnel in relationship to clinics to assist clinic managers in allocating public health personnel and resources under dynamic conditions. Based on user input, the CODA prototype was designed as a low-cost, user-friendly system to inventory and manage public health resources. In emergency conditions, the system can run on a stand-alone battery-powered laptop computer. A formative evaluation by managers of multiple public health centers confirmed the prototype design's usefulness. Emergency management administrators also provided positive feedback about the system during a separate demonstration. Validation of the CODA information design prototype by public health managers and emergency management administrators demonstrates the potential usefulness of building a resource management system using open-source technologies and participatory design principles.

The Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT): An Open-source Tool for Efficient Fitting of Astrometric and Radial Velocity Data

NASA Astrophysics Data System (ADS)

Mede, Kyle; Brandt, Timothy D.

2017-03-01

We present the Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT), a new, open-source suite to fit the orbital elements of planetary or stellar-mass companions to any combination of radial velocity and astrometric data. To explore the parameter space of Keplerian models, ExoSOFT may be operated with its own multistage sampling approach or interfaced with third-party tools such as emcee. In addition, ExoSOFT is packaged with a collection of post-processing tools to analyze and summarize the results. Although only a few systems have been observed with both radial velocity and direct imaging techniques, this number will increase, thanks to upcoming spacecraft and ground-based surveys. Providing both forms of data enables simultaneous fitting that can help break degeneracies in the orbital elements that arise when only one data type is available. The dynamical mass estimates this approach can produce are important when investigating the formation mechanisms and subsequent evolution of substellar companions. ExoSOFT was verified through fitting to artificial data and was implemented using the Python and Cython programming languages; it is available for public download at https://github.com/kylemede/ExoSOFT under GNU General Public License v3.

LakeMetabolizer: An R package for estimating lake metabolism from free-water oxygen using diverse statistical models

USGS Publications Warehouse

Winslow, Luke; Zwart, Jacob A.; Batt, Ryan D.; Dugan, Hilary; Woolway, R. Iestyn; Corman, Jessica; Hanson, Paul C.; Read, Jordan S.

2016-01-01

Metabolism is a fundamental process in ecosystems that crosses multiple scales of organization from individual organisms to whole ecosystems. To improve sharing and reuse of published metabolism models, we developed LakeMetabolizer, an R package for estimating lake metabolism from in situ time series of dissolved oxygen, water temperature, and, optionally, additional environmental variables. LakeMetabolizer implements 5 different metabolism models with diverse statistical underpinnings: bookkeeping, ordinary least squares, maximum likelihood, Kalman filter, and Bayesian. Each of these 5 metabolism models can be combined with 1 of 7 models for computing the coefficient of gas exchange across the air–water interface (k). LakeMetabolizer also features a variety of supporting functions that compute conversions and implement calculations commonly applied to raw data prior to estimating metabolism (e.g., oxygen saturation and optical conversion models). These tools have been organized into an R package that contains example data, example use-cases, and function documentation. The release package version is available on the Comprehensive R Archive Network (CRAN), and the full open-source GPL-licensed code is freely available for examination and extension online. With this unified, open-source, and freely available package, we hope to improve access and facilitate the application of metabolism in studies and management of lentic ecosystems.

A Resource Management Tool for Public Health Continuity of Operations During Disasters

PubMed Central

Turner, Anne M.; Reeder, Blaine; Wallace, James C.

2014-01-01

Objective We developed and validated a user-centered information system to support the local planning of public health continuity of operations for the Community Health Services Division, Public Health - Seattle & King County, Washington. Methods The Continuity of Operations Data Analysis (CODA) system was designed as a prototype developed using requirements identified through participatory design. CODA uses open-source software that links personnel contact and licensing information with needed skills and clinic locations for 821 employees at 14 public health clinics in Seattle and King County. Using a web-based interface, CODA can visualize locations of personnel in relationship to clinics to assist clinic managers in allocating public health personnel and resources under dynamic conditions. Results Based on user input, the CODA prototype was designed as a low-cost, user-friendly system to inventory and manage public health resources. In emergency conditions, the system can run on a stand-alone battery-powered laptop computer. A formative evaluation by managers of multiple public health centers confirmed the prototype design’s usefulness. Emergency management administrators also provided positive feedback about the system during a separate demonstration. Conclusions Validation of the CODA information design prototype by public health managers and emergency management administrators demonstrates the potential usefulness of building a resource management system using open-source technologies and participatory design principles. PMID:24618165

An open source framework for tracking and state estimation ('Stone Soup')

NASA Astrophysics Data System (ADS)

Thomas, Paul A.; Barr, Jordi; Balaji, Bhashyam; White, Kruger

2017-05-01

The ability to detect and unambiguously follow all moving entities in a state-space is important in multiple domains both in defence (e.g. air surveillance, maritime situational awareness, ground moving target indication) and the civil sphere (e.g. astronomy, biology, epidemiology, dispersion modelling). However, tracking and state estimation researchers and practitioners have difficulties recreating state-of-the-art algorithms in order to benchmark their own work. Furthermore, system developers need to assess which algorithms meet operational requirements objectively and exhaustively rather than intuitively or driven by personal favourites. We have therefore commenced the development of a collaborative initiative to create an open source framework for production, demonstration and evaluation of Tracking and State Estimation algorithms. The initiative will develop a (MIT-licensed) software platform for researchers and practitioners to test, verify and benchmark a variety of multi-sensor and multi-object state estimation algorithms. The initiative is supported by four defence laboratories, who will contribute to the development effort for the framework. The tracking and state estimation community will derive significant benefits from this work, including: access to repositories of verified and validated tracking and state estimation algorithms, a framework for the evaluation of multiple algorithms, standardisation of interfaces and access to challenging data sets. Keywords: Tracking,

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

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

2008-11-01

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

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

PubMed

Ceschin, Rafael; Panigrahy, Ashok; Gopalakrishnan, Vanathi

2015-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-09-01

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

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.

Distributed visualization of gridded geophysical data: the Carbon Data Explorer, version 0.2.3

NASA Astrophysics Data System (ADS)

Endsley, K. A.; Billmire, M. G.

2016-01-01

Due to the proliferation of geophysical models, particularly climate models, the increasing resolution of their spatiotemporal estimates of Earth system processes, and the desire to easily share results with collaborators, there is a genuine need for tools to manage, aggregate, visualize, and share data sets. We present a new, web-based software tool - the Carbon Data Explorer - that provides these capabilities for gridded geophysical data sets. While originally developed for visualizing carbon flux, this tool can accommodate any time-varying, spatially explicit scientific data set, particularly NASA Earth system science level III products. In addition, the tool's open-source licensing and web presence facilitate distributed scientific visualization, comparison with other data sets and uncertainty estimates, and data publishing and distribution.

Barista: A Framework for Concurrent Speech Processing by USC-SAIL

PubMed Central

Can, Doğan; Gibson, James; Vaz, Colin; Georgiou, Panayiotis G.; Narayanan, Shrikanth S.

2016-01-01

We present Barista, an open-source framework for concurrent speech processing based on the Kaldi speech recognition toolkit and the libcppa actor library. With Barista, we aim to provide an easy-to-use, extensible framework for constructing highly customizable concurrent (and/or distributed) networks for a variety of speech processing tasks. Each Barista network specifies a flow of data between simple actors, concurrent entities communicating by message passing, modeled after Kaldi tools. Leveraging the fast and reliable concurrency and distribution mechanisms provided by libcppa, Barista lets demanding speech processing tasks, such as real-time speech recognizers and complex training workflows, to be scheduled and executed on parallel (and/or distributed) hardware. Barista is released under the Apache License v2.0. PMID:27610047

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/

SAIL--a software system for sample and phenotype availability across biobanks and cohorts.

PubMed

Gostev, Mikhail; Fernandez-Banet, Julio; Rung, Johan; Dietrich, Joern; Prokopenko, Inga; Ripatti, Samuli; McCarthy, Mark I; Brazma, Alvis; Krestyaninova, Maria

2011-02-15

The Sample avAILability system-SAIL-is a web based application for searching, browsing and annotating biological sample collections or biobank entries. By providing individual-level information on the availability of specific data types (phenotypes, genetic or genomic data) and samples within a collection, rather than the actual measurement data, resource integration can be facilitated. A flexible data structure enables the collection owners to provide descriptive information on their samples using existing or custom vocabularies. Users can query for the available samples by various parameters combining them via logical expressions. The system can be scaled to hold data from millions of samples with thousands of variables. SAIL is available under Aferro-GPL open source license: https://github.com/sail.

BioSmalltalk: a pure object system and library for bioinformatics.

PubMed

Morales, Hernán F; Giovambattista, Guillermo

2013-09-15

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

The Bio-Community Perl toolkit for microbial ecology.

PubMed

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

2014-07-01

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

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption.

PubMed

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T

2018-03-23

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public).

Evol and ProDy for bridging protein sequence evolution and structural dynamics.

PubMed

Bakan, Ahmet; Dutta, Anindita; Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R; Bahar, Ivet

2014-09-15

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

InDEx: Open Source iOS and Android Software for Self-Reporting and Monitoring of Alcohol Consumption

PubMed Central

Leightley, Daniel; Puddephatt, Jo-Anne; Goodwin, Laura; Rona, Roberto; Fear, Nicola T.

2018-01-01

InDEx is a software package for reporting and monitoring alcohol consumption via a smartphone application. Consumption of alcohol is self-reported by the user, and the app provides a visual representation of drinking behaviour and offers feedback on consumption levels compared to the general population. InDEx is intended as an exemplar app, operating as a standalone smartphone application and is highly customisable for a variety of research domains. InDEx is written in JavaScript, using IONIC framework which is cross-platform and is available under the liberal GNU General Public License (v3). The software is available from GitHub (https://github.com/DrDanL/index-app-public). PMID:29795769

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

Barista: A Framework for Concurrent Speech Processing by USC-SAIL.

PubMed

Can, Doğan; Gibson, James; Vaz, Colin; Georgiou, Panayiotis G; Narayanan, Shrikanth S

2014-05-01

We present Barista, an open-source framework for concurrent speech processing based on the Kaldi speech recognition toolkit and the libcppa actor library. With Barista, we aim to provide an easy-to-use, extensible framework for constructing highly customizable concurrent (and/or distributed) networks for a variety of speech processing tasks. Each Barista network specifies a flow of data between simple actors, concurrent entities communicating by message passing, modeled after Kaldi tools. Leveraging the fast and reliable concurrency and distribution mechanisms provided by libcppa, Barista lets demanding speech processing tasks, such as real-time speech recognizers and complex training workflows, to be scheduled and executed on parallel (and/or distributed) hardware. Barista is released under the Apache License v2.0.

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

PubMed

Xirasagar, Sandhya; Gustafson, Scott F; Huang, Cheng-Cheng; Pan, Qinyan; Fostel, Jennifer; Boyer, Paul; Merrick, B Alex; Tomer, Kenneth B; Chan, Denny D; Yost, Kenneth J; Choi, Danielle; Xiao, Nianqing; Stasiewicz, Stanley; Bushel, Pierre; Waters, Michael D

2006-04-01

The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner. An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (http://www.cdisc.org/models/send/v2/index.html) which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (http://www.cdisc.org/models/sdtm/index.html) that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here. A universal modeling language (UML) depiction of the entire SysTox-OM is available at http://cebs.niehs.nih.gov and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov xirasagars@saic.com Supplementary data are available at Bioinformatics online.

Imfit: A Fast, Flexible Program for Astronomical Image Fitting

NASA Astrophysics Data System (ADS)

Erwin, Peter

2014-08-01

Imift is an open-source astronomical image-fitting program specialized for galaxies but potentially useful for other sources, which is fast, flexible, and highly extensible. Its object-oriented design allows new types of image components (2D surface-brightness functions) to be easily written and added to the program. Image functions provided with Imfit include Sersic, exponential, and Gaussian galaxy decompositions along with Core-Sersic and broken-exponential profiles, elliptical rings, and three components that perform line-of-sight integration through 3D luminosity-density models of disks and rings seen at arbitrary inclinations. Available minimization algorithms include Levenberg-Marquardt, Nelder-Mead simplex, and Differential Evolution, allowing trade-offs between speed and decreased sensitivity to local minima in the fit landscape. Minimization can be done using the standard chi^2 statistic (using either data or model values to estimate per-pixel Gaussian errors, or else user-supplied error images) or the Cash statistic; the latter is particularly appropriate for cases of Poisson data in the low-count regime. The C++ source code for Imfit is available under the GNU Public License.

Public Access and Open Access: Is There a Difference? | Poster

Cancer.gov

By Robin Meckley, Contributing Writer, and Tracie Frederick, Guest Writer Open access and public access—are they different concepts or are they the same? What do they mean for the researchers at NCI at Frederick? “Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions. What makes it possible is the Internet and the

The right to water in rural Punjab: assessing equitable access to water in the context of the ongoing Punjab Rural Water Supply Proejct.

PubMed

Samra, Shamsher; Crowley, Julia; Smith Fawzi, Mary C

2011-12-15

Although India is poised to meet its Millennium Development Goal for providing access to safe drinking water, there remains a worrying discrepancy in access between urban and rural areas. In 2006, 96% of the urban population versus 86% of the rural population obtained their drinking water from an improved water source. To increase access to potable water in rural areas, the World Bank and the state of Punjab have implemented the Punjab Rural Water Supply and Sanitation Project (PRWSS) to improve or construct water supply systems in 3,000 villages deemed to have inadequate access to clean drinking water. This study aimed to examine whether the right to water was fulfilled in six towns in rural Punjab during implementation of the PRWSS. The normative content of the right to water requires that water be of adequate quantity, safety, accessibility, affordability, and acceptability in terms of quality. While our findings suggest that the PRWSS improved water quality, they also indicate that access to water was limited due to affordability and the low socioeconomic status of some people living in the target communities. Copyright © 2011 Samra, Crowley, and Smith Fawzi. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

GobyWeb: Simplified Management and Analysis of Gene Expression and DNA Methylation Sequencing Data

PubMed Central

Dorff, Kevin C.; Chambwe, Nyasha; Zeno, Zachary; Simi, Manuele; Shaknovich, Rita; Campagne, Fabien

2013-01-01

We present GobyWeb, a web-based system that facilitates the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension mechanism. Analyses currently supported include quantification of gene expression for messenger and small RNA sequencing, estimation of DNA methylation (i.e., reduced bisulfite sequencing and whole genome methyl-seq), or the detection of pathogens in sequenced data. In contrast to previous analysis pipelines developed for analysis of HTS data, GobyWeb requires significantly less storage space, runs analyses efficiently on a parallel grid, scales gracefully to process tens or hundreds of multi-gigabyte samples, yet can be used effectively by researchers who are comfortable using a web browser. We conducted performance evaluations of the software and found it to either outperform or have similar performance to analysis programs developed for specialized analyses of HTS data. We found that most biologists who took a one-hour GobyWeb training session were readily able to analyze RNA-Seq data with state of the art analysis tools. GobyWeb can be obtained at http://gobyweb.campagnelab.org and is freely available for non-commercial use. GobyWeb plugins are distributed in source code and licensed under the open source LGPL3 license to facilitate code inspection, reuse and independent extensions http://github.com/CampagneLaboratory/gobyweb2-plugins. PMID:23936070

[Chemical analysis of wastewater as a new way of monitoring drugs and medicines consumption at workplace].

PubMed

Wiergowski, Marek; Sołtyszewski, Ireneusz; Sein Anand, Jacek

2015-01-01

The available information on the quality and frequency of illegal psychoactive substances used or medicines misused by workers, are often out of date at the time of its publication. This is due to the dynamic introduction of new synthetic drugs on the black market, changes in trends in the recreational use of medicines and the lack of readily available and reliable tests for fast identification. Strategy for detection of narcotic and non-medical psychoactive drugs use at workplace should embrace all possible sources of information. Classical sources of information on the use of psychoactive substances at the workplace include: statistical data (general information on trends and magnitude of drug and medicine addiction collected by the Polish National Police, the National Bureau for Drug Prevention and emergency medical services), surveys, psychomotor tests and qualitative and quantitative analyses of biological material. Of the new and promising methods, used throughout the world in recent years, chemical-toxicological analysis of surface water and wastewater deserve special mention. An increasing interest in the study of urban waste water can significantly complement the source of knowledge about drug and medicine addiction using obtainable conventional methods. In recent years, a municipal wastewater analysis has become a new and very promising way of collecting updated information on the use of psychoactive substances and medicines. It seems that this kind of study may play an important role in the ongoing monitoring of drug and/or medicines use by selected groups of population (e.g., students, military, firemen, policemen, etc.). This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

[Optimization of measurement methods for a multi-frequency electromagnetic field from mobile phone base station using broadband EMF meter].

PubMed

Bieńkowski, Paweł; Cała, Paweł; Zubrzak, Bartłomiej

2015-01-01

This paper presents the characteristics of the mobile phone base station (BS) as an electromagnetic field (EMF) source. The most common system configurations with their construction are described. The parameters of radiated EMF in the context of the access to methods and other parameters of the radio transmission are discussed. Attention was also paid to antennas that are used in this technology. The influence of individual components of a multi-frequency EMF, most commonly found in the BS surroundings, on the resultant EMF strength value indicated by popular broadband EMF meters was analyzed. The examples of metrological characteristics of the most common EMF probes and 2 measurement scenarios of the multisystem base station, with and without microwave relays, are shown. The presented method for measuring the multi-frequency EMF using 2 broadband probes allows for the significant minimization of measurement uncertainty. Equations and formulas that can be used to calculate the actual EMF intensity from multi-frequency sources are shown. They have been verified in the laboratory conditions on a specific standard setup as well as in real conditions in a survey of the existing base station with microwave relays. Presented measurement methodology of multi-frequency EMF from BS with microwave relays, validated both in laboratory and real conditions. It has been proven that the described measurement methodology is the optimal approach to the evaluation of EMF exposure in BS surrounding. Alternative approaches with much greater uncertainty (precaution method) or more complex measuring procedure (sources exclusion method) are also presented). This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.

50 CFR 660.319 - Open access fishery gear identification and marking.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Open access fishery gear identification and marking. 660.319 Section 660.319 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT... law, the vessel's number, the commercial fishing license number, or buoy brand number; or (ii) The...

A Practice-Oriented Review of Learning Objects

ERIC Educational Resources Information Center

Sinclair, J.; Joy, M.; Yau, J. Y.-K.; Hagan, S.

2013-01-01

Reusable learning objects support packaging of educational materials allowing their discovery and reuse. Open educational resources emphasize the need for open licensing and promote sharing and community involvement. For both teachers and learners, finding appropriate tried and tested resources on a topic of interest and being able to incorporate…

Principal visual word discovery for automatic license plate detection.

PubMed

Zhou, Wengang; Li, Houqiang; Lu, Yijuan; Tian, Qi

2012-09-01

License plates detection is widely considered a solved problem, with many systems already in operation. However, the existing algorithms or systems work well only under some controlled conditions. There are still many challenges for license plate detection in an open environment, such as various observation angles, background clutter, scale changes, multiple plates, uneven illumination, and so on. In this paper, we propose a novel scheme to automatically locate license plates by principal visual word (PVW), discovery and local feature matching. Observing that characters in different license plates are duplicates of each other, we bring in the idea of using the bag-of-words (BoW) model popularly applied in partial-duplicate image search. Unlike the classic BoW model, for each plate character, we automatically discover the PVW characterized with geometric context. Given a new image, the license plates are extracted by matching local features with PVW. Besides license plate detection, our approach can also be extended to the detection of logos and trademarks. Due to the invariance virtue of scale-invariant feature transform feature, our method can adaptively deal with various changes in the license plates, such as rotation, scaling, illumination, etc. Promising results of the proposed approach are demonstrated with an experimental study in license plate detection.

On the scaling of multicrystal data sets collected at high-intensity X-ray and electron sources

DOE PAGES

Coppens, Philip; Fournier, Bertrand

2015-11-11

Here, the need for data-scaling has become increasingly evident as time-resolved pump-probe photocrystallography is rapidly developing at high intensity X-ray sources. Several aspects of the scaling of data sets collected at synchrotrons, XFELs (X-ray Free Electron Lasers) and high-intensity pulsed electron sources are discussed. They include laser-ON/laser-OFF data scaling, inter- and intra-data set scaling. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License.

Field validation of secondary data sources for enumerating retail tobacco outlets in a state without tobacco outlet licensing.

PubMed

D'Angelo, Heather; Fleischhacker, Sheila; Rose, Shyanika W; Ribisl, Kurt M

2014-07-01

Identifying tobacco retail outlets for U.S. FDA compliance checks or calculating tobacco outlet density is difficult in the 13 States without tobacco retail licensing or where licensing lists are unavailable for research. This study uses primary data collection to identify tobacco outlets in three counties in a non-licensing state and validate two commercial secondary data sources. We calculated sensitivity and positive predictive values (PPV) to examine the evidence of validity for two secondary data sources, and conducted a geospatial analysis to determine correct allocation to census tract. ReferenceUSA had almost perfect sensitivity (0.82) while Dun & Bradstreet (D&B) had substantial sensitivity (0.69) for identifying tobacco outlets; combined, sensitivity improved to 0.89. D&B identified fewer "false positives" with a PPV of 0.82 compared to 0.71 for ReferenceUSA. More than 90% of the outlets identified by ReferenceUSA were geocoded to the correct census tract. Combining two commercial data sources resulted in enumeration of nearly 90% of tobacco outlets in a three county area. Commercial databases appear to provide a reasonably accurate way to identify tobacco outlets for enforcement operations and density estimation. Copyright © 2014 Elsevier Ltd. All rights reserved.

MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

PubMed

Englitz, B; David, S V; Sorenson, M D; Shamma, S A

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

MANTA—an open-source, high density electrophysiology recording suite for MATLAB

PubMed Central

Englitz, B.; David, S. V.; Sorenson, M. D.; Shamma, S. A.

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

A robust scientific workflow for assessing fire danger levels using open-source software

NASA Astrophysics Data System (ADS)

Vitolo, Claudia; Di Giuseppe, Francesca; Smith, Paul

2017-04-01

Modelling forest fires is theoretically and computationally challenging because it involves the use of a wide variety of information, in large volumes and affected by high uncertainties. In-situ observations of wildfire, for instance, are highly sparse and need to be complemented by remotely sensed data measuring biomass burning to achieve homogeneous coverage at global scale. Fire models use weather reanalysis products to measure energy release and rate of spread but can only assess the potential predictability of fire danger as the actual ignition is due to human behaviour and, therefore, very unpredictable. Lastly, fire forecasting systems rely on weather forecasts to extend the advance warning but are currently calibrated using fire danger thresholds that are defined at global scale and do not take into account the spatial variability of fuel availability. As a consequence, uncertainties sharply increase cascading from the observational to the modelling stage and they might be further inflated by non-reproducible analyses. Although uncertainties in observations will only decrease with technological advances over the next decades, the other uncertainties (i.e. generated during modelling and post-processing) can already be addressed by developing transparent and reproducible analysis workflows, even more if implemented within open-source initiatives. This is because reproducible workflows aim to streamline the processing task as they present ready-made solutions to handle and manipulate complex and heterogeneous datasets. Also, opening the code to the scrutiny of other experts increases the chances to implement more robust solutions and avoids duplication of efforts. In this work we present our contribution to the forest fire modelling community: an open-source tool called "caliver" for the calibration and verification of forest fire model results. This tool is developed in the R programming language and publicly available under an open license. We will present the caliver R package, illustrate the main functionalities and show the results of our preliminary experiments calculating fire danger thresholds for various regions on Earth. We will compare these with the existing global thresholds and, lastly, demonstrate how these newly-calculated regional thresholds can lead to improved calibration of fire forecast models in an operational setting.

Advancing climate justice and the right to health through procedural rights.

PubMed

Hall, Margaux J

2014-06-14

Scholars have increasingly recognized the ways in which climate change threatens the human rights of people around the world, with a disproportionate burden on the rights of already vulnerable persons. At particular risk to these populations is the right to health, as well as to interconnected human rights. Yet, scholars have generally not provided a thorough assessment of precisely how human rights law can catalyze a response to climate change to effectively avert health harms. This article suggests that human rights law is better suited to guide procedural responses to climate change and its health harms than it is to guide substantive decision-making. This article describes the ways in which climate change implicates the right to health and then analyzes human rights law's response. While acknowledging the intrinsic value of human rights in prompting climate change action, the article focuses its analysis on human rights' instrumental value in this arena. Copyright © 2014 Hall. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Striking a balance: conscientious objection and reproductive health care from the Colombian perspective.

PubMed

Cabal, Luisa; Olaya, Monica Arango; Robledo, Valentina Montoya

2014-12-11

Conscientious Objection or conscientious refusal (CO) in access to reproductive health care is at the center of current legal debates worldwide. In countries such as the US and the UK, constitutional dilemmas surrounding CO in the context of reproductive health services reveal inadequate policy frameworks for balancing CO rights with women's rights to access contraception and abortion. The Colombian Constitutional Court's holistic jurisprudence regarding CO standards has applied international human rights norms so as to not only protect women's reproductive rights as fundamental rights, but to also introduce clear limits for the exercise of CO in health care settings. This paper reviews Latin American lines of regulation in Argentina, Uruguay, and Mexico City to argue that the Colombian Court's jurisprudence offers a strong guidance for future comprehensive policy approaches that aim to effectively balance tensions between CO and women's reproductive rights. Copyright © 2014 Cabal, Olaya, Robledo. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data-driven human rights: using the electronic health record to promote human rights in jail.

PubMed

Glowa-Kollisch, Sarah; Andrade, Kelly; Stazesky, Richard; Teixeira, Paul; Kaba, Fatos; Macdonald, Ross; Rosner, Zachary; Selling, Daniel; Parsons, Amanda; Venters, Homer

2014-06-14

The electronic health record (EHR) is a commonplace innovation designed to promote efficiency, quality, and continuity of health services. In the New York City jail system, we implemented an EHR across 12 jails between 2008 and 2011. During the same time, our work increasingly focused on the importance of human rights as an essential element to the provision of medical and mental health care for our patients. Consequently, we made major modifications to the EHR to allow for better surveillance of vulnerable populations and enable reporting and analysis of patterns of abuse, neglect, and other patient concerns related to human rights. These modifications have improved our ability to find and care for patients injured in jail and those with mental health exacerbations. More work is needed, however, to optimize the potential of the EHR as a tool to promote human rights among patients in jail. Copyright © 2014 Sheffield, Durante, Rahona, and Zarcadoolas. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Chikungunya, climate change, and human rights.

PubMed

Meason, Braden; Paterson, Ryan

2014-06-14

Chikungunya is a re-emerging arbovirus that causes significant morbidity and some mortality. Global climate change leading to warmer temperatures and changes in rainfall patterns allow mosquito vectors to thrive at altitudes and at locations where they previously have not, ultimately leading to a spread of mosquito-borne diseases. While mutations to the chikungunya virus are responsible for some portion of the re-emergence, chikungunya epidemiology is closely tied with weather patterns in Southeast Asia. Extrapolation of this regional pattern, combined with known climate factors impacting the spread of malaria and dengue, summate to a dark picture of climate change and the spread of this disease from south Asia and Africa into Europe and North America. This review describes chikungunya and collates current data regarding its spread in which climate change plays an important part. We also examine human rights obligations of States and others to protect against this disease. Copyright © 2014 Meason, Paterson. This is an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

Automated management of radioactive sources in Saudi Arabia

NASA Astrophysics Data System (ADS)

Al-Kheliewi, Abdullah S.; Jamil, M. F.; Basar, M. R.; Tuwaili, W. R.

2014-09-01

For usage of radioactive substances, any facility has to register and take license from relevant authority of the country in which such facility is operating. In the Kingdom of Saudi Arabia (KSA), the authority for managing radioactive sources and providing licenses to organizations for its usage is the National Center of Radiation Protection (NCRP). This paper describes the system that automates registration and licensing process of the National Center of Radiation Protection. To provide 24×7 accesses to all the customers of NCRP, system is developed as web-based application that provide facility to online register, request license, renew license, check request status, view historical data and reports etc. and other features are provided as Electronic Services that would be accessible to users via internet. The system also was designed to streamline and optimize internal operations of NCRP besides providing ease of access to its customers by implementing a defined workflow through which every registration and license request will be routed. In addition to manual payment option, the system would also be integrated with SADAD (online payment system) that will avoid lengthy and cumbersome procedures associated with manual payment mechanism. Using SADAD payment option license fee could be paid through internet/ATM machine or branch of any designated bank, Payment will be instantly notified to NCRP hence delay in funds transfer and verification of invoice could be avoided, SADAD integration is discussed later in the document.

Public Access and Open Access: Is There a Difference? | Poster

Cancer.gov

By Robin Meckley, Contributing Writer, and Tracie Frederick, Guest Writer Open access and public access—are they different concepts or are they the same? What do they mean for the researchers at NCI at Frederick? “Open-access (OA) literature is digital, online, free of charge, and free of most copyright and licensing restrictions. What makes it possible is the Internet and the consent of the author or copyright-holder,” according to an open access website maintained by Peter Suber, director, Harvard Open Access Project.

10 CFR 51.22 - Criterion for categorical exclusion; identification of licensing and regulatory actions eligible...

Code of Federal Regulations, 2010 CFR

2010-01-01

... requirements. (11) Issuance of amendments to licenses for fuel cycle plants and radioactive waste disposal... licensees, except processing of source material for extraction of rare earth and other metals. (xiv) Nuclear...

10 CFR 170.31 - Schedule of fees for materials licenses and other regulatory services, including inspections, and...

Code of Federal Regulations, 2010 CFR

2010-01-01

... material in sealed sources contained in devices used in industrial measuring systems, including x-ray... metals other than uranium or thorium, including licenses authorizing the possession of byproduct waste...

Chapter 5, "License Renewal and Aging Management for Continued Service

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

Naus, Dan J

As of August 2011, there were 104 commercial nuclear power reactors licensed to operate in 31 states in the United States. Initial operating licenses in the United States are granted for a period of 40 years. In order to help assure an adequate energy supply, the USNRC has established a timely license renewal process and clear requirements that are needed to ensure safe plant operation for an extended plant life. The principals of license renewal and the basic requirements that address license renewal are identified as well as additional sources of guidance that can be utilized as part of themore » license renewal process. Aging management program inspections and operating experience related to the concrete and steel containment structures are provided. Finally, several lessons learned are provided based on containment operating experience.« less

Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

NASA Astrophysics Data System (ADS)

Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

2009-12-01

This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.