OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia

PubMed Central

2012-01-01

Background The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. Results The following related ontologies have been developed for OpenTox: a) Toxicological ontology – listing the toxicological endpoints; b) Organs system and Effects ontology – addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology – representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology– representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink–ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology. OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources. The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). Availability The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/ PMID:22541598

OpenTox predictive toxicology framework: toxicological ontology and semantic media wiki-based OpenToxipedia.

PubMed

Tcheremenskaia, Olga; Benigni, Romualdo; Nikolova, Ivelina; Jeliazkova, Nina; Escher, Sylvia E; Batke, Monika; Baier, Thomas; Poroikov, Vladimir; Lagunin, Alexey; Rautenberg, Micha; Hardy, Barry

2012-04-24

The OpenTox Framework, developed by the partners in the OpenTox project (http://www.opentox.org), aims at providing a unified access to toxicity data, predictive models and validation procedures. Interoperability of resources is achieved using a common information model, based on the OpenTox ontologies, describing predictive algorithms, models and toxicity data. As toxicological data may come from different, heterogeneous sources, a deployed ontology, unifying the terminology and the resources, is critical for the rational and reliable organization of the data, and its automatic processing. The following related ontologies have been developed for OpenTox: a) Toxicological ontology - listing the toxicological endpoints; b) Organs system and Effects ontology - addressing organs, targets/examinations and effects observed in in vivo studies; c) ToxML ontology - representing semi-automatic conversion of the ToxML schema; d) OpenTox ontology- representation of OpenTox framework components: chemical compounds, datasets, types of algorithms, models and validation web services; e) ToxLink-ToxCast assays ontology and f) OpenToxipedia community knowledge resource on toxicology terminology.OpenTox components are made available through standardized REST web services, where every compound, data set, and predictive method has a unique resolvable address (URI), used to retrieve its Resource Description Framework (RDF) representation, or to initiate the associated calculations and generate new RDF-based resources.The services support the integration of toxicity and chemical data from various sources, the generation and validation of computer models for toxic effects, seamless integration of new algorithms and scientifically sound validation routines and provide a flexible framework, which allows building arbitrary number of applications, tailored to solving different problems by end users (e.g. toxicologists). The OpenTox toxicological ontology projects may be accessed via the OpenTox ontology development page http://www.opentox.org/dev/ontology; the OpenTox ontology is available as OWL at http://opentox.org/api/1 1/opentox.owl, the ToxML - OWL conversion utility is an open source resource available at http://ambit.svn.sourceforge.net/viewvc/ambit/branches/toxml-utils/

Deterministic Design Optimization of Structures in OpenMDAO Framework

NASA Technical Reports Server (NTRS)

Coroneos, Rula M.; Pai, Shantaram S.

2012-01-01

Nonlinear programming algorithms play an important role in structural design optimization. Several such algorithms have been implemented in OpenMDAO framework developed at NASA Glenn Research Center (GRC). OpenMDAO is an open source engineering analysis framework, written in Python, for analyzing and solving Multi-Disciplinary Analysis and Optimization (MDAO) problems. It provides a number of solvers and optimizers, referred to as components and drivers, which users can leverage to build new tools and processes quickly and efficiently. Users may download, use, modify, and distribute the OpenMDAO software at no cost. This paper summarizes the process involved in analyzing and optimizing structural components by utilizing the framework s structural solvers and several gradient based optimizers along with a multi-objective genetic algorithm. For comparison purposes, the same structural components were analyzed and optimized using CometBoards, a NASA GRC developed code. The reliability and efficiency of the OpenMDAO framework was compared and reported in this report.

OpenCluster: A Flexible Distributed Computing Framework for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Wei, Shoulin; Wang, Feng; Deng, Hui; Liu, Cuiyin; Dai, Wei; Liang, Bo; Mei, Ying; Shi, Congming; Liu, Yingbo; Wu, Jingping

2017-02-01

The volume of data generated by modern astronomical telescopes is extremely large and rapidly growing. However, current high-performance data processing architectures/frameworks are not well suited for astronomers because of their limitations and programming difficulties. In this paper, we therefore present OpenCluster, an open-source distributed computing framework to support rapidly developing high-performance processing pipelines of astronomical big data. We first detail the OpenCluster design principles and implementations and present the APIs facilitated by the framework. We then demonstrate a case in which OpenCluster is used to resolve complex data processing problems for developing a pipeline for the Mingantu Ultrawide Spectral Radioheliograph. Finally, we present our OpenCluster performance evaluation. Overall, OpenCluster provides not only high fault tolerance and simple programming interfaces, but also a flexible means of scaling up the number of interacting entities. OpenCluster thereby provides an easily integrated distributed computing framework for quickly developing a high-performance data processing system of astronomical telescopes and for significantly reducing software development expenses.

Comparison of Physics Frameworks for WebGL-Based Game Engine

NASA Astrophysics Data System (ADS)

Yogya, Resa; Kosala, Raymond

2014-03-01

Recently, a new technology called WebGL shows a lot of potentials for developing games. However since this technology is still new, there are still many potentials in the game development area that are not explored yet. This paper tries to uncover the potential of integrating physics frameworks with WebGL technology in a game engine for developing 2D or 3D games. Specifically we integrated three open source physics frameworks: Bullet, Cannon, and JigLib into a WebGL-based game engine. Using experiment, we assessed these frameworks in terms of their correctness or accuracy, performance, completeness and compatibility. The results show that it is possible to integrate open source physics frameworks into a WebGLbased game engine, and Bullet is the best physics framework to be integrated into the WebGL-based game engine.

Lowering the barrier to a decentralized NHIN using the open healthcare framework.

PubMed

Smith, Eishay; Kaufman, James H

2006-01-01

In this paper, we discuss two important elements to lowering the barrier to creation of a National Health Information Network. The first element is the adoption of standards that will enable interoperability while guarantee open interfaces (and preventing vendor lock-in). The second element is the role of open source. While adoption of open standards by large EMR vendors is critically important to enterprise healthcare providers and payors, the availability of inexpensive (or free) standardized Healthcare Information Technology for small physician practices is critical. By analogy to the emergence of the World Wide Web, a framework for creating inexpensive and open source applications for physicians will be as important to realizing a National Health Information Network as availability of free browser technology was to the growth of the internet.

OpenDrift v1.0: a generic framework for trajectory modelling

NASA Astrophysics Data System (ADS)

Dagestad, Knut-Frode; Röhrs, Johannes; Breivik, Øyvind; Ådlandsvik, Bjørn

2018-04-01

OpenDrift is an open-source Python-based framework for Lagrangian particle modelling under development at the Norwegian Meteorological Institute with contributions from the wider scientific community. The framework is highly generic and modular, and is designed to be used for any type of drift calculations in the ocean or atmosphere. A specific module within the OpenDrift framework corresponds to a Lagrangian particle model in the traditional sense. A number of modules have already been developed, including an oil drift module, a stochastic search-and-rescue module, a pelagic egg module, and a basic module for atmospheric drift. The framework allows for the ingestion of an unspecified number of forcing fields (scalar and vectorial) from various sources, including Eulerian ocean, atmosphere and wave models, but also measurements or a priori values for the same variables. A basic backtracking mechanism is inherent, using sign reversal of the total displacement vector and negative time stepping. OpenDrift is fast and simple to set up and use on Linux, Mac and Windows environments, and can be used with minimal or no Python experience. It is designed for flexibility, and researchers may easily adapt or write modules for their specific purpose. OpenDrift is also designed for performance, and simulations with millions of particles may be performed on a laptop. Further, OpenDrift is designed for robustness and is in daily operational use for emergency preparedness modelling (oil drift, search and rescue, and drifting ships) at the Norwegian Meteorological Institute.

OpenDrift - an open source framework for ocean trajectory modeling

NASA Astrophysics Data System (ADS)

Dagestad, Knut-Frode; Breivik, Øyvind; Ådlandsvik, Bjørn

2016-04-01

We will present a new, open source tool for modeling the trajectories and fate of particles or substances (Lagrangian Elements) drifting in the ocean, or even in the atmosphere. The software is named OpenDrift, and has been developed at Norwegian Meteorological Institute in cooperation with Institute of Marine Research. OpenDrift is a generic framework written in Python, and is openly available at https://github.com/knutfrode/opendrift/. The framework is modular with respect to three aspects: (1) obtaining input data, (2) the transport/morphological processes, and (3) exporting of results to file. Modularity is achieved through well defined interfaces between components, and use of a consistent vocabulary (CF conventions) for naming of variables. Modular input implies that it is not necessary to preprocess input data (e.g. currents, wind and waves from Eulerian models) to a particular file format. Instead "reader modules" can be written/used to obtain data directly from any original source, including files or through web based protocols (e.g. OPeNDAP/Thredds). Modularity of processes implies that a model developer may focus on the geophysical processes relevant for the application of interest, without needing to consider technical tasks such as reading, reprojecting, and colocating input data, rotation and scaling of vectors and model output. We will show a few example applications of using OpenDrift for predicting drifters, oil spills, and search and rescue objects.

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

Multi-Disciplinary Analysis and Optimization Frameworks

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2009-01-01

Since July 2008, the Multidisciplinary Analysis & Optimization Working Group (MDAO WG) of the Systems Analysis Design & Optimization (SAD&O) discipline in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project completed one major milestone, Define Architecture & Interfaces for Next Generation Open Source MDAO Framework Milestone (9/30/08), and is completing the Generation 1 Framework validation milestone, which is due December 2008. Included in the presentation are: details of progress on developing the Open MDAO framework, modeling and testing the Generation 1 Framework, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations

QuantumOptics.jl: A Julia framework for simulating open quantum systems

NASA Astrophysics Data System (ADS)

Krämer, Sebastian; Plankensteiner, David; Ostermann, Laurin; Ritsch, Helmut

2018-06-01

We present an open source computational framework geared towards the efficient numerical investigation of open quantum systems written in the Julia programming language. Built exclusively in Julia and based on standard quantum optics notation, the toolbox offers speed comparable to low-level statically typed languages, without compromising on the accessibility and code readability found in dynamic languages. After introducing the framework, we highlight its features and showcase implementations of generic quantum models. Finally, we compare its usability and performance to two well-established and widely used numerical quantum libraries.

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

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

Chatzidakis, Stylianos; Greulich, Christopher

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

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy.

PubMed

Barabas, Federico M; Masullo, Luciano A; Stefani, Fernando D

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

Note: Tormenta: An open source Python-powered control software for camera based optical microscopy

NASA Astrophysics Data System (ADS)

Barabas, Federico M.; Masullo, Luciano A.; Stefani, Fernando D.

2016-12-01

Until recently, PC control and synchronization of scientific instruments was only possible through closed-source expensive frameworks like National Instruments' LabVIEW. Nowadays, efficient cost-free alternatives are available in the context of a continuously growing community of open-source software developers. Here, we report on Tormenta, a modular open-source software for the control of camera-based optical microscopes. Tormenta is built on Python, works on multiple operating systems, and includes some key features for fluorescence nanoscopy based on single molecule localization.

An open-source job management framework for parameter-space exploration: OACIS

NASA Astrophysics Data System (ADS)

Murase, Y.; Uchitane, T.; Ito, N.

2017-11-01

We present an open-source software framework for parameter-space exporation, named OACIS, which is useful to manage vast amount of simulation jobs and results in a systematic way. Recent development of high-performance computers enabled us to explore parameter spaces comprehensively, however, in such cases, manual management of the workflow is practically impossible. OACIS is developed aiming at reducing the cost of these repetitive tasks when conducting simulations by automating job submissions and data management. In this article, an overview of OACIS as well as a getting started guide are presented.

An open data mining framework for the analysis of medical images: application on obstructive nephropathy microscopy images.

PubMed

Doukas, Charalampos; Goudas, Theodosis; Fischer, Simon; Mierswa, Ingo; Chatziioannou, Aristotle; Maglogiannis, Ilias

2010-01-01

This paper presents an open image-mining framework that provides access to tools and methods for the characterization of medical images. Several image processing and feature extraction operators have been implemented and exposed through Web Services. Rapid-Miner, an open source data mining system has been utilized for applying classification operators and creating the essential processing workflows. The proposed framework has been applied for the detection of salient objects in Obstructive Nephropathy microscopy images. Initial classification results are quite promising demonstrating the feasibility of automated characterization of kidney biopsy images.

Open-Source Integrated Design-Analysis Environment For Nuclear Energy Advanced Modeling & Simulation Final Scientific/Technical Report

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

O'Leary, Patrick

The framework created through the Open-Source Integrated Design-Analysis Environment (IDAE) for Nuclear Energy Advanced Modeling & Simulation grant has simplify and democratize advanced modeling and simulation in the nuclear energy industry that works on a range of nuclear engineering applications. It leverages millions of investment dollars from the Department of Energy's Office of Nuclear Energy for modeling and simulation of light water reactors and the Office of Nuclear Energy's research and development. The IDEA framework enhanced Kitware’s Computational Model Builder (CMB) while leveraging existing open-source toolkits and creating a graphical end-to-end umbrella guiding end-users and developers through the nuclear energymore » advanced modeling and simulation lifecycle. In addition, the work deliver strategic advancements in meshing and visualization for ensembles.« less

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

Lee, Seyong; Kim, Jungwon; Vetter, Jeffrey S

This paper presents a directive-based, high-level programming framework for high-performance reconfigurable computing. It takes a standard, portable OpenACC C program as input and generates a hardware configuration file for execution on FPGAs. We implemented this prototype system using our open-source OpenARC compiler; it performs source-to-source translation and optimization of the input OpenACC program into an OpenCL code, which is further compiled into a FPGA program by the backend Altera Offline OpenCL compiler. Internally, the design of OpenARC uses a high- level intermediate representation that separates concerns of program representation from underlying architectures, which facilitates portability of OpenARC. In fact, thismore » design allowed us to create the OpenACC-to-FPGA translation framework with minimal extensions to our existing system. In addition, we show that our proposed FPGA-specific compiler optimizations and novel OpenACC pragma extensions assist the compiler in generating more efficient FPGA hardware configuration files. Our empirical evaluation on an Altera Stratix V FPGA with eight OpenACC benchmarks demonstrate the benefits of our strategy. To demonstrate the portability of OpenARC, we show results for the same benchmarks executing on other heterogeneous platforms, including NVIDIA GPUs, AMD GPUs, and Intel Xeon Phis. This initial evidence helps support the goal of using a directive-based, high-level programming strategy for performance portability across heterogeneous HPC architectures.« less

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.

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

NASA Astrophysics Data System (ADS)

Udell, C.; Selker, J. S.

2017-12-01

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

Open source and open content: A framework for global collaboration in social-ecological research

Treesearch

Charles Schweik; Tom Evans; J. Morgan Grove

2005-01-01

This paper discusses opportunities for alternative collaborative approaches for social-ecological research in general and, in this context, for modeling land-use/land-cover change. In this field, the rate of progress in academic research is steady but perhaps not as rapid or efficient as might be possible with alternative organizational frameworks. The convergence of...

Critical Analysis on Open Source LMSs Using FCA

ERIC Educational Resources Information Center

Sumangali, K.; Kumar, Ch. Aswani

2013-01-01

The objective of this paper is to apply Formal Concept Analysis (FCA) to identify the best open source Learning Management System (LMS) for an E-learning environment. FCA is a mathematical framework that represents knowledge derived from a formal context. In constructing the formal context, LMSs are treated as objects and their features as…

Modular Object-Oriented Dynamic Learning Environment: What Open Source Has to Offer

ERIC Educational Resources Information Center

Antonenko, Pavlo; Toy, Serkan; Niederhauser, Dale

2004-01-01

Open source online learning environments have emerged and developed over the past 10 years. In this paper we will analyze the underlying philosophy and features of MOODLE based on the theoretical framework developed by Hannafin and Land (2000). Psychological, pedagogical, technological, cultural, and pragmatic foundations comprise the framework…

Open-source Framework for Storing and Manipulation of Plasma Chemical Reaction Data

NASA Astrophysics Data System (ADS)

Jenkins, T. G.; Averkin, S. N.; Cary, J. R.; Kruger, S. E.

2017-10-01

We present a new open-source framework for storage and manipulation of plasma chemical reaction data that has emerged from our in-house project MUNCHKIN. This framework consists of python scripts and C + + programs. It stores data in an SQL data base for fast retrieval and manipulation. For example, it is possible to fit cross-section data into most widely used analytical expressions, calculate reaction rates for Maxwellian distribution functions of colliding particles, and fit them into different analytical expressions. Another important feature of this framework is the ability to calculate transport properties based on the cross-section data and supplied distribution functions. In addition, this framework allows the export of chemical reaction descriptions in LaTeX format for ease of inclusion in scientific papers. With the help of this framework it is possible to generate corresponding VSim (Particle-In-Cell simulation code) and USim (unstructured multi-fluid code) input blocks with appropriate cross-sections.

GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.

PubMed

Madec, Morgan; Pecheux, François; Gendrault, Yves; Rosati, Elise; Lallement, Christophe; Haiech, Jacques

2016-10-01

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.

Distributed chemical computing using ChemStar: an open source java remote method invocation architecture applied to large scale molecular data from PubChem.

PubMed

Karthikeyan, M; Krishnan, S; Pandey, Anil Kumar; Bender, Andreas; Tropsha, Alexander

2008-04-01

We present the application of a Java remote method invocation (RMI) based open source architecture to distributed chemical computing. This architecture was previously employed for distributed data harvesting of chemical information from the Internet via the Google application programming interface (API; ChemXtreme). Due to its open source character and its flexibility, the underlying server/client framework can be quickly adopted to virtually every computational task that can be parallelized. Here, we present the server/client communication framework as well as an application to distributed computing of chemical properties on a large scale (currently the size of PubChem; about 18 million compounds), using both the Marvin toolkit as well as the open source JOELib package. As an application, for this set of compounds, the agreement of log P and TPSA between the packages was compared. Outliers were found to be mostly non-druglike compounds and differences could usually be explained by differences in the underlying algorithms. ChemStar is the first open source distributed chemical computing environment built on Java RMI, which is also easily adaptable to user demands due to its "plug-in architecture". The complete source codes as well as calculated properties along with links to PubChem resources are available on the Internet via a graphical user interface at http://moltable.ncl.res.in/chemstar/.

[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.

The successes and challenges of open-source biopharmaceutical innovation.

PubMed

Allarakhia, Minna

2014-05-01

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

Bioclipse: an open source workbench for chemo- and bioinformatics.

PubMed

Spjuth, Ola; Helmus, Tobias; Willighagen, Egon L; Kuhn, Stefan; Eklund, Martin; Wagener, Johannes; Murray-Rust, Peter; Steinbeck, Christoph; Wikberg, Jarl E S

2007-02-22

There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.

Open source Modeling and optimization tools for Planning

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

Peles, S.

Open source modeling and optimization tools for planning The existing tools and software used for planning and analysis in California are either expensive, difficult to use, or not generally accessible to a large number of participants. These limitations restrict the availability of participants for larger scale energy and grid studies in the state. The proposed initiative would build upon federal and state investments in open source software, and create and improve open source tools for use in the state planning and analysis activities. Computational analysis and simulation frameworks in development at national labs and universities can be brought forward tomore » complement existing tools. An open source platform would provide a path for novel techniques and strategies to be brought into the larger community and reviewed by a broad set of stakeholders.« less

OpenLMD, multimodal monitoring and control of LMD processing

NASA Astrophysics Data System (ADS)

Rodríguez-Araújo, Jorge; García-Díaz, Antón

2017-02-01

This paper presents OpenLMD, a novel open-source solution for on-line multimodal monitoring of Laser Metal Deposition (LMD). The solution is also applicable to a wider range of laser-based applications that require on-line control (e.g. laser welding). OpenLMD is a middleware that enables the orchestration and virtualization of a LMD robot cell, using several open-source frameworks (e.g. ROS, OpenCV, PCL). The solution also allows reconfiguration by easy integration of multiple sensors and processing equipment. As a result, OpenLMD delivers significant advantages over existing monitoring and control approaches, such as improved scalability, and multimodal monitoring and data sharing capabilities.

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

EPA Science Inventory

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

OpenDA-WFLOW framework for improving hydrologic predictions using distributed hydrologic models

NASA Astrophysics Data System (ADS)

Weerts, Albrecht; Schellekens, Jaap; Kockx, Arno; Hummel, Stef

2017-04-01

Data assimilation (DA) holds considerable potential for improving hydrologic predictions (Liu et al., 2012) and increase the potential for early warning and/or smart water management. However, advances in hydrologic DA research have not yet been adequately or timely implemented in operational forecast systems to improve the skill of forecasts for better informed real-world decision making. The objective of this work is to highlight the development of a generic linkage of the open source OpenDA package and the open source community hydrologic modeling framework Openstreams/WFLOW and its application in operational hydrological forecasting on various spatial scales. The coupling between OpenDA and Openstreams/wflow framework is based on the emerging standard Basic Model Interface (BMI) as advocated by CSDMS using cross-platform webservices (i.e. Apache Thrift) developed by Hut et al. (2016). The potential application of the OpenDA-WFLOW for operational hydrologic forecasting including its integration with Delft-FEWS (used by more than 40 operational forecast centers around the world (Werner et al., 2013)) is demonstrated by the presented case studies. We will also highlight the possibility to give real-time insight into the working of the DA methods applied for supporting the forecaster as mentioned as one of the burning issues by Liu et al., (2012).

A Framework for the Systematic Collection of Open Source Intelligence

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

Pouchard, Line Catherine; Trien, Joseph P; Dobson, Jonathan D

2009-01-01

Following legislative directions, the Intelligence Community has been mandated to make greater use of Open Source Intelligence (OSINT). Efforts are underway to increase the use of OSINT but there are many obstacles. One of these obstacles is the lack of tools helping to manage the volume of available data and ascertain its credibility. We propose a unique system for selecting, collecting and storing Open Source data from the Web and the Open Source Center. Some data management tasks are automated, document source is retained, and metadata containing geographical coordinates are added to the documents. Analysts are thus empowered to search,more » view, store, and analyze Web data within a single tool. We present ORCAT I and ORCAT II, two implementations of the system.« less

The RAVE/VERTIGO vertex reconstruction toolkit and framework

NASA Astrophysics Data System (ADS)

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

2008-07-01

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

Key Considerations of Community, Scalability, Supportability, Security, and Functionality in Selecting Open-Source Software in California Universities as Perceived by Technology Leaders

ERIC Educational Resources Information Center

Britton, Todd Alan

2014-01-01

Purpose: The purpose of this study was to examine the key considerations of community, scalability, supportability, security, and functionality for selecting open-source software in California universities as perceived by technology leaders. Methods: After a review of the cogent literature, the key conceptual framework categories were identified…

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

PubMed

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

2011-09-28

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

OpenSeesPy: Python library for the OpenSees finite element framework

NASA Astrophysics Data System (ADS)

Zhu, Minjie; McKenna, Frank; Scott, Michael H.

2018-01-01

OpenSees, an open source finite element software framework, has been used broadly in the earthquake engineering community for simulating the seismic response of structural and geotechnical systems. The framework allows users to perform finite element analysis with a scripting language and for developers to create both serial and parallel finite element computer applications as interpreters. For the last 15 years, Tcl has been the primary scripting language to which the model building and analysis modules of OpenSees are linked. To provide users with different scripting language options, particularly Python, the OpenSees interpreter interface was refactored to provide multi-interpreter capabilities. This refactoring, resulting in the creation of OpenSeesPy as a Python module, is accomplished through an abstract interface for interpreter calls with concrete implementations for different scripting languages. Through this approach, users are able to develop applications that utilize the unique features of several scripting languages while taking advantage of advanced finite element analysis models and algorithms.

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

PubMed Central

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

2013-01-01

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

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

PubMed

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

2013-01-01

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

A Numerical Modeling Framework for Cohesive Sediment Transport Driven by Waves and Tidal Currents

DTIC Science & Technology

2012-09-30

for sediment transport. The successful extension to multi-dimensions is benefited from an open-source CFD package, OpenFOAM (www.openfoam.org). This...linz.at/Drupal/), which couples the fluid solver OpenFOAM with the Discrete Element Model (DEM) solver LIGGGHTS (an improved LAMMPS for granular flow

Open-Source, Web-Based Dashboard Components for DICOM Connectivity.

PubMed

Bustamante, Catalina; Pineda, Julian; Rascovsky, Simon; Arango, Andres

2016-08-01

The administration of a DICOM network within an imaging healthcare institution requires tools that allow for monitoring of connectivity and availability for adequate uptime measurements and help guide technology management strategies. We present the implementation of an open-source widget for the Dashing framework that provides basic dashboard functionality allowing for monitoring of a DICOM network using network "ping" and DICOM "C-ECHO" operations.

Hybrid Optimization Parallel Search PACKage

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

2009-11-10

HOPSPACK is open source software for solving optimization problems without derivatives. Application problems may have a fully nonlinear objective function, bound constraints, and linear and nonlinear constraints. Problem variables may be continuous, integer-valued, or a mixture of both. The software provides a framework that supports any derivative-free type of solver algorithm. Through the framework, solvers request parallel function evaluation, which may use MPI (multiple machines) or multithreading (multiple processors/cores on one machine). The framework provides a Cache and Pending Cache of saved evaluations that reduces execution time and facilitates restarts. Solvers can dynamically create other algorithms to solve subproblems, amore » useful technique for handling multiple start points and integer-valued variables. HOPSPACK ships with the Generating Set Search (GSS) algorithm, developed at Sandia as part of the APPSPACK open source software project.« less

Instrumentino: An Open-Source Software for Scientific Instruments.

PubMed

Koenka, Israel Joel; Sáiz, Jorge; Hauser, Peter C

2015-01-01

Scientists often need to build dedicated computer-controlled experimental systems. For this purpose, it is becoming common to employ open-source microcontroller platforms, such as the Arduino. These boards and associated integrated software development environments provide affordable yet powerful solutions for the implementation of hardware control of transducers and acquisition of signals from detectors and sensors. It is, however, a challenge to write programs that allow interactive use of such arrangements from a personal computer. This task is particularly complex if some of the included hardware components are connected directly to the computer and not via the microcontroller. A graphical user interface framework, Instrumentino, was therefore developed to allow the creation of control programs for complex systems with minimal programming effort. By writing a single code file, a powerful custom user interface is generated, which enables the automatic running of elaborate operation sequences and observation of acquired experimental data in real time. The framework, which is written in Python, allows extension by users, and is made available as an open source project.

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

PubMed

Barre, Arnaud; Armand, Stéphane

2014-04-01

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

Coalescent: an open-source and scalable framework for exact calculations in coalescent theory

PubMed Central

2012-01-01

Background Currently, there is no open-source, cross-platform and scalable framework for coalescent analysis in population genetics. There is no scalable GUI based user application either. Such a framework and application would not only drive the creation of more complex and realistic models but also make them truly accessible. Results As a first attempt, we built a framework and user application for the domain of exact calculations in coalescent analysis. The framework provides an API with the concepts of model, data, statistic, phylogeny, gene tree and recursion. Infinite-alleles and infinite-sites models are considered. It defines pluggable computations such as counting and listing all the ancestral configurations and genealogies and computing the exact probability of data. It can visualize a gene tree, trace and visualize the internals of the recursion algorithm for further improvement and attach dynamically a number of output processors. The user application defines jobs in a plug-in like manner so that they can be activated, deactivated, installed or uninstalled on demand. Multiple jobs can be run and their inputs edited. Job inputs are persisted across restarts and running jobs can be cancelled where applicable. Conclusions Coalescent theory plays an increasingly important role in analysing molecular population genetic data. Models involved are mathematically difficult and computationally challenging. An open-source, scalable framework that lets users immediately take advantage of the progress made by others will enable exploration of yet more difficult and realistic models. As models become more complex and mathematically less tractable, the need for an integrated computational approach is obvious. Object oriented designs, though has upfront costs, are practical now and can provide such an integrated approach. PMID:23033878

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

PubMed Central

2011-01-01

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

Generalized Intelligent Framework for Tutoring (GIFT) Cloud/Virtual Open Campus Quick Start Guide (Revision 1)

DTIC Science & Technology

2017-06-01

for GIFT Cloud, the web -based application version of the Generalized Intelligent Framework for Tutoring (GIFT). GIFT is a modular, open-source...external applications. GIFT is available to users with a GIFT Account at no cost. GIFT Cloud is an implementation of GIFT. This web -based application...section. Approved for public release; distribution is unlimited. 3 3. Requirements for GIFT Cloud GIFT Cloud is accessed via a web browser

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

NASA Astrophysics Data System (ADS)

Konnik, Mikhail V.; Welsh, James

2012-09-01

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

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

NASA Astrophysics Data System (ADS)

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

2015-04-01

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

Open Source Clinical NLP - More than Any Single System.

PubMed

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

2014-01-01

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

OpenElectrophy: An Electrophysiological Data- and Analysis-Sharing Framework

PubMed Central

Garcia, Samuel; Fourcaud-Trocmé, Nicolas

2008-01-01

Progress in experimental tools and design is allowing the acquisition of increasingly large datasets. Storage, manipulation and efficient analyses of such large amounts of data is now a primary issue. We present OpenElectrophy, an electrophysiological data- and analysis-sharing framework developed to fill this niche. It stores all experiment data and meta-data in a single central MySQL database, and provides a graphic user interface to visualize and explore the data, and a library of functions for user analysis scripting in Python. It implements multiple spike-sorting methods, and oscillation detection based on the ridge extraction methods due to Roux et al. (2007). OpenElectrophy is open source and is freely available for download at http://neuralensemble.org/trac/OpenElectrophy. PMID:19521545

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

DTIC Science & Technology

2008-03-01

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

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

None

Assessing the impact of energy efficiency technologies at a district or city scale is of great interest to local governments, real estate developers, utility companies, and policymakers. This paper describes a flexible framework that can be used to create and run district and city scale building energy simulations. The framework is built around the new OpenStudio City Database (CityDB). Building footprints, building height, building type, and other data can be imported from public records or other sources. Missing data can be inferred or assigned from a statistical sampling of other datasets. Once all required data is available, OpenStudio Measures aremore » used to create starting point energy models and to model energy efficiency measures for each building. Together this framework allows a user to pose several scenarios such as 'what if 30% of the commercial retail buildings added rooftop solar' or 'what if all elementary schools converted to ground source heat pumps' and then visualize the impacts at a district or city scale. This paper focuses on modeling existing building stock using public records. However, the framework is capable of supporting the evaluation of new construction, district systems, and the use of proprietary data sources.« less

SCIFIO: an extensible framework to support scientific image formats.

PubMed

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

2016-12-07

No gold standard exists in the world of scientific image acquisition; a proliferation of instruments each with its own proprietary data format has made out-of-the-box sharing of that data nearly impossible. In the field of light microscopy, the Bio-Formats library was designed to translate such proprietary data formats to a common, open-source schema, enabling sharing and reproduction of scientific results. While Bio-Formats has proved successful for microscopy images, the greater scientific community was lacking a domain-independent framework for format translation. SCIFIO (SCientific Image Format Input and Output) is presented as a freely available, open-source library unifying the mechanisms of reading and writing image data. The core of SCIFIO is its modular definition of formats, the design of which clearly outlines the components of image I/O to encourage extensibility, facilitated by the dynamic discovery of the SciJava plugin framework. SCIFIO is structured to support coexistence of multiple domain-specific open exchange formats, such as Bio-Formats' OME-TIFF, within a unified environment. SCIFIO is a freely available software library developed to standardize the process of reading and writing scientific image formats.

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!

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.

PaaS for web applications with OpenShift Origin

NASA Astrophysics Data System (ADS)

Lossent, A.; Rodriguez Peon, A.; Wagner, A.

2017-10-01

The CERN Web Frameworks team has deployed OpenShift Origin to facilitate deployment of web applications and to improving efficiency in terms of computing resource usage. OpenShift leverages Docker containers and Kubernetes orchestration to provide a Platform-as-a-service solution oriented for web applications. We will review use cases and how OpenShift was integrated with other services such as source control, web site management and authentication services.

OpCost: an open-source system for estimating costs of stand-level forest operations

Treesearch

Conor K. Bell; Robert F. Keefe; Jeremy S. Fried

2017-01-01

This report describes and documents the OpCost forest operations cost model, a key component of the BioSum analysis framework. OpCost is available in two editions: as a callable module for use with BioSum, and in a stand-alone edition that can be run directly from R. OpCost model logic and assumptions for this open-source tool are explained, references to the...

Frameworks Coordinate Scientific Data Management

NASA Technical Reports Server (NTRS)

2012-01-01

Jet Propulsion Laboratory computer scientists developed a unique software framework to help NASA manage its massive amounts of science data. Through a partnership with the Apache Software Foundation of Forest Hill, Maryland, the technology is now available as an open-source solution and is in use by cancer researchers and pediatric hospitals.

gadfly: A pandas-based Framework for Analyzing GADGET Simulation Data

NASA Astrophysics Data System (ADS)

Hummel, Jacob A.

2016-11-01

We present the first public release (v0.1) of the open-source gadget Dataframe Library: gadfly. The aim of this package is to leverage the capabilities of the broader python scientific computing ecosystem by providing tools for analyzing simulation data from the astrophysical simulation codes gadget and gizmo using pandas, a thoroughly documented, open-source library providing high-performance, easy-to-use data structures that is quickly becoming the standard for data analysis in python. Gadfly is a framework for analyzing particle-based simulation data stored in the HDF5 format using pandas DataFrames. The package enables efficient memory management, includes utilities for unit handling, coordinate transformations, and parallel batch processing, and provides highly optimized routines for visualizing smoothed-particle hydrodynamics data sets.

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.

Generalizable open source urban water portfolio simulation framework demonstrated using a multi-objective risk-based planning benchmark problem.

NASA Astrophysics Data System (ADS)

Trindade, B. C.; Reed, P. M.

2017-12-01

The growing access and reduced cost for computing power in recent years has promoted rapid development and application of multi-objective water supply portfolio planning. As this trend continues there is a pressing need for flexible risk-based simulation frameworks and improved algorithm benchmarking for emerging classes of water supply planning and management problems. This work contributes the Water Utilities Management and Planning (WUMP) model: a generalizable and open source simulation framework designed to capture how water utilities can minimize operational and financial risks by regionally coordinating planning and management choices, i.e. making more efficient and coordinated use of restrictions, water transfers and financial hedging combined with possible construction of new infrastructure. We introduce the WUMP simulation framework as part of a new multi-objective benchmark problem for planning and management of regionally integrated water utility companies. In this problem, a group of fictitious water utilities seek to balance the use of the mentioned reliability driven actions (e.g., restrictions, water transfers and infrastructure pathways) and their inherent financial risks. Several traits of this problem make it ideal for a benchmark problem, namely the presence of (1) strong non-linearities and discontinuities in the Pareto front caused by the step-wise nature of the decision making formulation and by the abrupt addition of storage through infrastructure construction, (2) noise due to the stochastic nature of the streamflows and water demands, and (3) non-separability resulting from the cooperative formulation of the problem, in which decisions made by stakeholder may substantially impact others. Both the open source WUMP simulation framework and its demonstration in a challenging benchmarking example hold value for promoting broader advances in urban water supply portfolio planning for regions confronting change.

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.

Crossing the Virtual World Barrier with OpenAvatar

NASA Technical Reports Server (NTRS)

Joy, Bruce; Kavle, Lori; Tan, Ian

2012-01-01

There are multiple standards and formats for 3D models in virtual environments. The problem is that there is no open source platform for generating models out of discrete parts; this results in the process of having to "reinvent the wheel" when new games, virtual worlds and simulations want to enable their users to create their own avatars or easily customize in-world objects. OpenAvatar is designed to provide a framework to allow artists and programmers to create reusable assets which can be used by end users to generate vast numbers of complete models that are unique and functional. OpenAvatar serves as a framework which facilitates the modularization of 3D models allowing parts to be interchanged within a set of logical constraints.

Collaborative development of predictive toxicology applications

PubMed Central

2010-01-01

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals. The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation. Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way. PMID:20807436

Collaborative development of predictive toxicology applications.

PubMed

Hardy, Barry; Douglas, Nicki; Helma, Christoph; Rautenberg, Micha; Jeliazkova, Nina; Jeliazkov, Vedrin; Nikolova, Ivelina; Benigni, Romualdo; Tcheremenskaia, Olga; Kramer, Stefan; Girschick, Tobias; Buchwald, Fabian; Wicker, Joerg; Karwath, Andreas; Gütlein, Martin; Maunz, Andreas; Sarimveis, Haralambos; Melagraki, Georgia; Afantitis, Antreas; Sopasakis, Pantelis; Gallagher, David; Poroikov, Vladimir; Filimonov, Dmitry; Zakharov, Alexey; Lagunin, Alexey; Gloriozova, Tatyana; Novikov, Sergey; Skvortsova, Natalia; Druzhilovsky, Dmitry; Chawla, Sunil; Ghosh, Indira; Ray, Surajit; Patel, Hitesh; Escher, Sylvia

2010-08-31

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

Distributed GIS Systems, Open Specifications and Interoperability: How do They Relate to the Sustainable Management of Natural Resources?

Treesearch

Rafael Moreno-Sanchez

2006-01-01

The aim of this is paper is to provide a conceptual framework for the session: “The role of web-based Geographic Information Systems in supporting sustainable management.” The concepts of sustainability, sustainable forest management, Web Services, Distributed Geographic Information Systems, interoperability, Open Specifications, and Open Source Software are defined...

Direct simulation Monte Carlo method for gas flows in micro-channels with bends with added curvature

NASA Astrophysics Data System (ADS)

Tisovský, Tomáš; Vít, Tomáš

Gas flows in micro-channels are simulated using an open source Direct Simulation Monte Carlo (DSMC) code dsmcFOAM for general application to rarefied gas flow written within the framework of the open source C++ toolbox called OpenFOAM. Aim of this paper is to investigate the flow in micro-channel with bend with added curvature. Results are compared with flows in channel without added curvature and equivalent straight channel. Effects of micro-channel bend was already thoroughly investigated by White et al. Geometry proposed by White is also used here for refference.

Open Source Clinical NLP – More than Any Single System

PubMed Central

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

2014-01-01

The number of Natural Language Processing (NLP) tools and systems for processing clinical free-text has grown as interest and processing capability have surged. Unfortunately any two systems typically cannot simply interoperate, even when both are built upon a framework designed to facilitate the creation of pluggable components. We present two ongoing activities promoting open source clinical NLP. The Open Health Natural Language Processing (OHNLP) Consortium was originally founded to foster a collaborative community around clinical NLP, releasing UIMA-based open source software. OHNLP’s mission currently includes maintaining a catalog of clinical NLP software and providing interfaces to simplify the interaction of NLP systems. Meanwhile, Apache cTAKES aims to integrate best-of-breed annotators, providing a world-class NLP system for accessing clinical information within free-text. These two activities are complementary. OHNLP promotes open source clinical NLP activities in the research community and Apache cTAKES bridges research to the health information technology (HIT) practice. PMID:25954581

Rapid development of entity-based data models for bioinformatics with persistence object-oriented design and structured interfaces.

PubMed

Ezra Tsur, Elishai

2017-01-01

Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of specialized databases is an ever-growing challenge due to the introduction of new data sources and the emergence of new relational connections between established datasets. Here, an open-source framework for the curation of specialized databases is proposed. The framework supports user-designed models of data encapsulation, objects persistency and structured interfaces to local and external data sources such as MalaCards, Biomodels and the National Centre for Biotechnology Information (NCBI) databases. The proposed framework was implemented using Java as the development environment, EclipseLink as the data persistency agent and Apache Derby as the database manager. Syntactic analysis was based on J3D, jsoup, Apache Commons and w3c.dom open libraries. Finally, a construction of a specialized database for aneurysms associated vascular diseases is demonstrated. This database contains 3-dimensional geometries of aneurysms, patient's clinical information, articles, biological models, related diseases and our recently published model of aneurysms' risk of rapture. Framework is available in: http://nbel-lab.com.

syris: a flexible and efficient framework for X-ray imaging experiments simulation.

PubMed

Faragó, Tomáš; Mikulík, Petr; Ershov, Alexey; Vogelgesang, Matthias; Hänschke, Daniel; Baumbach, Tilo

2017-11-01

An open-source framework for conducting a broad range of virtual X-ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time-dependent, which enables simulations of dynamic experiments, e.g. four-dimensional time-resolved tomography and laminography. The high-level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high-speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.

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

PubMed

Paton, C; Karopka, T

2017-08-01

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

The Experiment Factory: Standardizing Behavioral Experiments.

PubMed

Sochat, Vanessa V; Eisenberg, Ian W; Enkavi, A Zeynep; Li, Jamie; Bissett, Patrick G; Poldrack, Russell A

2016-01-01

The administration of behavioral and experimental paradigms for psychology research is hindered by lack of a coordinated effort to develop and deploy standardized paradigms. While several frameworks (Mason and Suri, 2011; McDonnell et al., 2012; de Leeuw, 2015; Lange et al., 2015) have provided infrastructure and methods for individual research groups to develop paradigms, missing is a coordinated effort to develop paradigms linked with a system to easily deploy them. This disorganization leads to redundancy in development, divergent implementations of conceptually identical tasks, disorganized and error-prone code lacking documentation, and difficulty in replication. The ongoing reproducibility crisis in psychology and neuroscience research (Baker, 2015; Open Science Collaboration, 2015) highlights the urgency of this challenge: reproducible research in behavioral psychology is conditional on deployment of equivalent experiments. A large, accessible repository of experiments for researchers to develop collaboratively is most efficiently accomplished through an open source framework. Here we present the Experiment Factory, an open source framework for the development and deployment of web-based experiments. The modular infrastructure includes experiments, virtual machines for local or cloud deployment, and an application to drive these components and provide developers with functions and tools for further extension. We release this infrastructure with a deployment (http://www.expfactory.org) that researchers are currently using to run a set of over 80 standardized web-based experiments on Amazon Mechanical Turk. By providing open source tools for both deployment and development, this novel infrastructure holds promise to bring reproducibility to the administration of experiments, and accelerate scientific progress by providing a shared community resource of psychological paradigms.

The Experiment Factory: Standardizing Behavioral Experiments

PubMed Central

Sochat, Vanessa V.; Eisenberg, Ian W.; Enkavi, A. Zeynep; Li, Jamie; Bissett, Patrick G.; Poldrack, Russell A.

2016-01-01

The administration of behavioral and experimental paradigms for psychology research is hindered by lack of a coordinated effort to develop and deploy standardized paradigms. While several frameworks (Mason and Suri, 2011; McDonnell et al., 2012; de Leeuw, 2015; Lange et al., 2015) have provided infrastructure and methods for individual research groups to develop paradigms, missing is a coordinated effort to develop paradigms linked with a system to easily deploy them. This disorganization leads to redundancy in development, divergent implementations of conceptually identical tasks, disorganized and error-prone code lacking documentation, and difficulty in replication. The ongoing reproducibility crisis in psychology and neuroscience research (Baker, 2015; Open Science Collaboration, 2015) highlights the urgency of this challenge: reproducible research in behavioral psychology is conditional on deployment of equivalent experiments. A large, accessible repository of experiments for researchers to develop collaboratively is most efficiently accomplished through an open source framework. Here we present the Experiment Factory, an open source framework for the development and deployment of web-based experiments. The modular infrastructure includes experiments, virtual machines for local or cloud deployment, and an application to drive these components and provide developers with functions and tools for further extension. We release this infrastructure with a deployment (http://www.expfactory.org) that researchers are currently using to run a set of over 80 standardized web-based experiments on Amazon Mechanical Turk. By providing open source tools for both deployment and development, this novel infrastructure holds promise to bring reproducibility to the administration of experiments, and accelerate scientific progress by providing a shared community resource of psychological paradigms. PMID:27199843

Sustainability of Open-Source Software Organizations as Underpinning for Sustainable Interoperability on Large Scales

NASA Astrophysics Data System (ADS)

Fulker, D. W.; Gallagher, J. H. R.

2015-12-01

OPeNDAP's Hyrax data server is an open-source framework fostering interoperability via easily-deployed Web services. Compatible with solutions listed in the (PA001) session description—federation, rigid standards and brokering/mediation—the framework can support tight or loose coupling, even with dependence on community-contributed software. Hyrax is a Web-services framework with a middleware-like design and a handler-style architecture that together reduce the interoperability challenge (for N datatypes and M user contexts) to an O(N+M) problem, similar to brokering. Combined with an open-source ethos, this reduction makes Hyrax a community tool for gaining interoperability. E.g., in its response to the Big Earth Data Initiative (BEDI), NASA references OPeNDAP-based interoperability. Assuming its suitability, the question becomes: how sustainable is OPeNDAP, a small not-for-profit that produces open-source software, i.e., has no software-sales? In other words, if geoscience interoperability depends on OPeNDAP and similar organizations, are those entities in turn sustainable? Jim Collins (in Good to Great) highlights three questions that successful companies can answer (paraphrased here): What is your passion? Where is your world-class excellence? What drives your economic engine? We attempt to shed light on OPeNDAP sustainability by examining these. Passion: OPeNDAP has a focused passion for improving the effectiveness of scientific data sharing and use, as deeply-cooperative community endeavors. Excellence: OPeNDAP has few peers in remote, scientific data access. Skills include computer science with experience in data science, (operational, secure) Web services, and software design (for servers and clients, where the latter vary from Web pages to standalone apps and end-user programs). Economic Engine: OPeNDAP is an engineering services organization more than a product company, despite software being key to OPeNDAP's reputation. In essence, provision of engineering expertise, via contracts and grants, is the economic engine. Hence sustainability, as needed to address global grand challenges in geoscience, depends on agencies' and others' abilities and willingness to offer grants and let contracts for continually upgrading open-source software from OPeNDAP and others.

MARVIN: a medical research application framework based on open source software.

PubMed

Rudolph, Tobias; Puls, Marc; Anderegg, Christoph; Ebert, Lars; Broehan, Martina; Rudin, Adrian; Kowal, Jens

2008-08-01

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

The Trick Simulation Toolkit: A NASA/Open source Framework for Running Time Based Physics Models

NASA Technical Reports Server (NTRS)

Penn, John M.; Lin, Alexander S.

2016-01-01

This paper describes the design and use at of the Trick Simulation Toolkit, a simulation development environment for creating high fidelity training and engineering simulations at the NASA Johnson Space Center and many other NASA facilities. It describes Trick's design goals and how the development environment attempts to achieve those goals. It describes how Trick is used in some of the many training and engineering simulations at NASA. Finally it describes the Trick NASA/Open source project on Github.

Time Resolved Phonon Spectroscopy, Version 1.0

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

Goett, Johnny; Zhu, Brian

TRPS code was developed for the project "Time Resolved Phonon Spectroscopy". Routines contained in this piece of software were specially created to model phonon generation and tracking within materials that interact with ionizing radiation, particularly applicable to the modeling of cryogenic radiation detectors for dark matter and neutrino research. These routines were created to link seamlessly with the open source Geant4 framework for the modeling of radiation transport in matter, with the explicit intent of open sourcing them for eventual integration into that code base.

ADEpedia: a scalable and standardized knowledge base of Adverse Drug Events using semantic web technology.

PubMed

Jiang, Guoqian; Solbrig, Harold R; Chute, Christopher G

2011-01-01

A source of semantically coded Adverse Drug Event (ADE) data can be useful for identifying common phenotypes related to ADEs. We proposed a comprehensive framework for building a standardized ADE knowledge base (called ADEpedia) through combining ontology-based approach with semantic web technology. The framework comprises four primary modules: 1) an XML2RDF transformation module; 2) a data normalization module based on NCBO Open Biomedical Annotator; 3) a RDF store based persistence module; and 4) a front-end module based on a Semantic Wiki for the review and curation. A prototype is successfully implemented to demonstrate the capability of the system to integrate multiple drug data and ontology resources and open web services for the ADE data standardization. A preliminary evaluation is performed to demonstrate the usefulness of the system, including the performance of the NCBO annotator. In conclusion, the semantic web technology provides a highly scalable framework for ADE data source integration and standard query service.

Exploring the Role of Value Networks for Software Innovation

NASA Astrophysics Data System (ADS)

Morgan, Lorraine; Conboy, Kieran

This paper describes a research-in-progress that aims to explore the applicability and implications of open innovation practices in two firms - one that employs agile development methods and another that utilizes open source software. The open innovation paradigm has a lot in common with open source and agile development methodologies. A particular strength of agile approaches is that they move away from 'introverted' development, involving only the development personnel, and intimately involves the customer in all areas of software creation, supposedly leading to the development of a more innovative and hence more valuable information system. Open source software (OSS) development also shares two key elements of the open innovation model, namely the collaborative development of the technology and shared rights to the use of the technology. However, one shortfall with agile development in particular is the narrow focus on a single customer representative. In response to this, we argue that current thinking regarding innovation needs to be extended to include multiple stakeholders both across and outside the organization. Additionally, for firms utilizing open source, it has been found that their position in a network of potential complementors determines the amount of superior value they create for their customers. Thus, this paper aims to get a better understanding of the applicability and implications of open innovation practices in firms that employ open source and agile development methodologies. In particular, a conceptual framework is derived for further testing.

Full open-framework batteries for stationary energy storage

NASA Astrophysics Data System (ADS)

Pasta, Mauro; Wessells, Colin D.; Liu, Nian; Nelson, Johanna; McDowell, Matthew T.; Huggins, Robert A.; Toney, Michael F.; Cui, Yi

2014-01-01

New types of energy storage are needed in conjunction with the deployment of renewable energy sources and their integration with the electrical grid. We have recently introduced a family of cathodes involving the reversible insertion of cations into materials with the Prussian Blue open-framework crystal structure. Here we report a newly developed manganese hexacyanomanganate open-framework anode that has the same crystal structure. By combining it with the previously reported copper hexacyanoferrate cathode we demonstrate a safe, fast, inexpensive, long-cycle life aqueous electrolyte battery, which involves the insertion of sodium ions. This high rate, high efficiency cell shows a 96.7% round trip energy efficiency when cycled at a 5C rate and an 84.2% energy efficiency at a 50C rate. There is no measurable capacity loss after 1,000 deep-discharge cycles. Bulk quantities of the electrode materials can be produced by a room temperature chemical synthesis from earth-abundant precursors.

Full open-framework batteries for stationary energy storage.

PubMed

Pasta, Mauro; Wessells, Colin D; Liu, Nian; Nelson, Johanna; McDowell, Matthew T; Huggins, Robert A; Toney, Michael F; Cui, Yi

2014-01-01

New types of energy storage are needed in conjunction with the deployment of renewable energy sources and their integration with the electrical grid. We have recently introduced a family of cathodes involving the reversible insertion of cations into materials with the Prussian Blue open-framework crystal structure. Here we report a newly developed manganese hexacyanomanganate open-framework anode that has the same crystal structure. By combining it with the previously reported copper hexacyanoferrate cathode we demonstrate a safe, fast, inexpensive, long-cycle life aqueous electrolyte battery, which involves the insertion of sodium ions. This high rate, high efficiency cell shows a 96.7% round trip energy efficiency when cycled at a 5C rate and an 84.2% energy efficiency at a 50C rate. There is no measurable capacity loss after 1,000 deep-discharge cycles. Bulk quantities of the electrode materials can be produced by a room temperature chemical synthesis from earth-abundant precursors.

A framework for air quality monitoring based on free public data and open source tools

NASA Astrophysics Data System (ADS)

Nikolov, Hristo; Borisova, Denitsa

2014-10-01

In the recent years more and more widely accepted by the Space agencies (e.g. NASA, ESA) is the policy toward provision of Earth observation (EO) data and end products concerning air quality especially in large urban areas without cost to researchers and SMEs. Those EO data are complemented by increasing amount of in-situ data also provided at no cost either from national authorities or having crowdsourced origin. This accessibility together with the increased processing capabilities of the free and open source software is a prerequisite for creation of solid framework for air modeling in support of decision making at medium and large scale. Essential part of this framework is web-based GIS mapping tool responsible for dissemination of the output generated. In this research an attempt is made to establish a running framework based solely on openly accessible data on air quality and on set of freely available software tools for processing and modeling taking into account the present status quo in Bulgaria. Among the primary sources of data, especially for bigger urban areas, for different types of gases and dust particles, noted should be the National Institute of Meteorology and Hydrology of Bulgaria (NIMH) and National System for Environmental Monitoring managed by Bulgarian Executive Environmental Agency (ExEA). Both authorities provide data for concentration of several gases just to mention CO, CO2, NO2, SO2, and fine suspended dust (PM10, PM2.5) on monthly (for some data on daily) basis. In the framework proposed these data will complement the data from satellite-based sensors such as OMI instrument aboard EOS-Aura satellite and from TROPOMI instrument payload for future ESA Sentinel-5P mission. Integral part of the framework is the modern map for the land use/land cover which is provided from EEA by initiative GIO Land CORINE. This map is also a product from EO data distributed at European level. First and above all, our effort is focused on provision to the wider public living in urbanized areas with one reliable source of information on the present conditions concerning the air quality. Also this information might be used as indicator for presence of acid rains in agriculture areas close to industrial or electricity plants. Its availability at regular basis makes such information valuable source in case of manmade industrial disasters or incidents such as forest fires. Key issue in developing this framework is to ensure the delivery of reliable data products related to air quality at larger scale that those available at the moment.

Agent-based Large-Scale Emergency Evacuation Using Real-Time Open Government Data

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

Lu, Wei; Liu, Cheng; Bhaduri, Budhendra L

The open government initiatives have provided tremendous data resources for the transportation system and emergency services in urban areas. This paper proposes a traffic simulation framework using high temporal resolution demographic data and real time open government data for evacuation planning and operation. A comparison study using real-world data in Seattle, Washington is conducted to evaluate the framework accuracy and evacuation efficiency. The successful simulations of selected area prove the concept to take advantage open government data, open source data, and high resolution demographic data in emergency management domain. There are two aspects of parameters considered in this study: usermore » equilibrium (UE) conditions of traffic assignment model (simple Non-UE vs. iterative UE) and data temporal resolution (Daytime vs. Nighttime). Evacuation arrival rate, average travel time, and computation time are adopted as Measure of Effectiveness (MOE) for evacuation performance analysis. The temporal resolution of demographic data has significant impacts on urban transportation dynamics during evacuation scenarios. Better evacuation performance estimation can be approached by integrating both Non-UE and UE scenarios. The new framework shows flexibility in implementing different evacuation strategies and accuracy in evacuation performance. The use of this framework can be explored to day-to-day traffic assignment to support daily traffic operations.« less

Governance Structures for Open Innovation: A Preliminary Framework

NASA Astrophysics Data System (ADS)

Feller, Joseph; Finnegan, Patrick; Hayes, Jeremy; O'Reilly, Philip

This research-in-progress paper presents a preliminary framework of four open innovation governance structures. The study seeks to describe four distinct ways in which firms utilize hierarchical relationships, organizational intermediaries, and the market system to supply and acquire intellectual property and/or innovation capabilities from sources external to the firm. This paper reports on phase one of the study, which involved an analysis of six open innovation exemplars based on public data. This phase of the study reveals that governance structures for open innovation can be categorized based on whether they (1) are mediated or direct or (2) seek to acquire intellectual property or innovation capability. We analyze the differences in four governance structures along seven dimensions, and reveal the importance of knowledge dispersion and uncertainty to the use of open innovation hierarchies, brokerages, and markets. The paper concludes by examining the implications of the findings and outlining the next phase of the study.

pyOpenMS: a Python-based interface to the OpenMS mass-spectrometry algorithm library.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2014-01-01

pyOpenMS is an open-source, Python-based interface to the C++ OpenMS library, providing facile access to a feature-rich, open-source algorithm library for MS-based proteomics analysis. It contains Python bindings that allow raw access to the data structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping, and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ, and SWATH analysis tools). pyOpenMS thus allows fast prototyping and efficient workflow development in a fully interactive manner (using the interactive Python interpreter) and is also ideally suited for researchers not proficient in C++. In addition, our code to wrap a complex C++ library is completely open-source, allowing other projects to create similar bindings with ease. The pyOpenMS framework is freely available at https://pypi.python.org/pypi/pyopenms while the autowrap tool to create Cython code automatically is available at https://pypi.python.org/pypi/autowrap (both released under the 3-clause BSD licence). © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Maintaining Quality and Confidence in Open-Source, Evolving Software: Lessons Learned with PFLOTRAN

NASA Astrophysics Data System (ADS)

Frederick, J. M.; Hammond, G. E.

2017-12-01

Software evolution in an open-source framework poses a major challenge to a geoscientific simulator, but when properly managed, the pay-off can be enormous for both the developers and the community at large. Developers must juggle implementing new scientific process models, adopting increasingly efficient numerical methods and programming paradigms, changing funding sources (or total lack of funding), while also ensuring that legacy code remains functional and reported bugs are fixed in a timely manner. With robust software engineering and a plan for long-term maintenance, a simulator can evolve over time incorporating and leveraging many advances in the computational and domain sciences. In this positive light, what practices in software engineering and code maintenance can be employed within open-source development to maximize the positive aspects of software evolution and community contributions while minimizing its negative side effects? This presentation will discusses steps taken in the development of PFLOTRAN (www.pflotran.org), an open source, massively parallel subsurface simulator for multiphase, multicomponent, and multiscale reactive flow and transport processes in porous media. As PFLOTRAN's user base and development team continues to grow, it has become increasingly important to implement strategies which ensure sustainable software development while maintaining software quality and community confidence. In this presentation, we will share our experiences and "lessons learned" within the context of our open-source development framework and community engagement efforts. Topics discussed will include how we've leveraged both standard software engineering principles, such as coding standards, version control, and automated testing, as well unique advantages of object-oriented design in process model coupling, to ensure software quality and confidence. We will also be prepared to discuss the major challenges faced by most open-source software teams, such as on-boarding new developers or one-time contributions, dealing with competitors or lookie-loos, and other downsides of complete transparency, as well as our approach to community engagement, including a user group email list, hosting short courses and workshops for new users, and maintaining a website. SAND2017-8174A

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR.

PubMed

Pfiffner, Pascal B; Pinyol, Isaac; Natter, Marc D; Mandl, Kenneth D

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR).

Open source libraries and frameworks for mass spectrometry based proteomics: A developer's perspective☆

PubMed Central

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. PMID:23467006

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR

PubMed Central

Pfiffner, Pascal B.; Pinyol, Isaac; Natter, Marc D.; Mandl, Kenneth D.

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR). PMID:27031856

Open source libraries and frameworks for mass spectrometry based proteomics: a developer's perspective.

PubMed

Perez-Riverol, Yasset; Wang, Rui; Hermjakob, Henning; Müller, Markus; Vesada, Vladimir; Vizcaíno, Juan Antonio

2014-01-01

Data processing, management and visualization are central and critical components of a state of the art high-throughput mass spectrometry (MS)-based proteomics experiment, and are often some of the most time-consuming steps, especially for labs without much bioinformatics support. The growing interest in the field of proteomics has triggered an increase in the development of new software libraries, including freely available and open-source software. From database search analysis to post-processing of the identification results, even though the objectives of these libraries and packages can vary significantly, they usually share a number of features. Common use cases include the handling of protein and peptide sequences, the parsing of results from various proteomics search engines output files, and the visualization of MS-related information (including mass spectra and chromatograms). In this review, we provide an overview of the existing software libraries, open-source frameworks and also, we give information on some of the freely available applications which make use of them. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. Copyright © 2013 Elsevier B.V. All rights reserved.

Sirepo for Synchrotron Radiation Workshop

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

Nagler, Robert; Moeller, Paul; Rakitin, Maksim

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jinja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is the Synchrotron Radiation Workshop (SRW). SRW computes synchrotron radiation from relativistic electrons in arbitrary magnetic fields and propagates the radiation wavefronts through optical beamlines. SRW is open source and is primarily supported by Dr. Oleg Chubar of NSLS-II at Brookhaven National Laboratory.« less

RAVE—a Detector-independent vertex reconstruction toolkit

NASA Astrophysics Data System (ADS)

Waltenberger, Wolfgang; Mitaroff, Winfried; Moser, Fabian

2007-10-01

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

Nektar++: An open-source spectral/ hp element framework

NASA Astrophysics Data System (ADS)

Cantwell, C. D.; Moxey, D.; Comerford, A.; Bolis, A.; Rocco, G.; Mengaldo, G.; De Grazia, D.; Yakovlev, S.; Lombard, J.-E.; Ekelschot, D.; Jordi, B.; Xu, H.; Mohamied, Y.; Eskilsson, C.; Nelson, B.; Vos, P.; Biotto, C.; Kirby, R. M.; Sherwin, S. J.

2015-07-01

Nektar++ is an open-source software framework designed to support the development of high-performance scalable solvers for partial differential equations using the spectral/ hp element method. High-order methods are gaining prominence in several engineering and biomedical applications due to their improved accuracy over low-order techniques at reduced computational cost for a given number of degrees of freedom. However, their proliferation is often limited by their complexity, which makes these methods challenging to implement and use. Nektar++ is an initiative to overcome this limitation by encapsulating the mathematical complexities of the underlying method within an efficient C++ framework, making the techniques more accessible to the broader scientific and industrial communities. The software supports a variety of discretisation techniques and implementation strategies, supporting methods research as well as application-focused computation, and the multi-layered structure of the framework allows the user to embrace as much or as little of the complexity as they need. The libraries capture the mathematical constructs of spectral/ hp element methods, while the associated collection of pre-written PDE solvers provides out-of-the-box application-level functionality and a template for users who wish to develop solutions for addressing questions in their own scientific domains.

pyomo.dae: a modeling and automatic discretization framework for optimization with differential and algebraic equations

DOE PAGES

Nicholson, Bethany; Siirola, John D.; Watson, Jean-Paul; ...

2017-12-20

We describe pyomo.dae, an open source Python-based modeling framework that enables high-level abstract specification of optimization problems with differential and algebraic equations. The pyomo.dae framework is integrated with the Pyomo open source algebraic modeling language, and is available at http://www.pyomo.org. One key feature of pyomo.dae is that it does not restrict users to standard, predefined forms of differential equations, providing a high degree of modeling flexibility and the ability to express constraints that cannot be easily specified in other modeling frameworks. Other key features of pyomo.dae are the ability to specify optimization problems with high-order differential equations and partial differentialmore » equations, defined on restricted domain types, and the ability to automatically transform high-level abstract models into finite-dimensional algebraic problems that can be solved with off-the-shelf solvers. Moreover, pyomo.dae users can leverage existing capabilities of Pyomo to embed differential equation models within stochastic and integer programming models and mathematical programs with equilibrium constraint formulations. Collectively, these features enable the exploration of new modeling concepts, discretization schemes, and the benchmarking of state-of-the-art optimization solvers.« less

pyomo.dae: a modeling and automatic discretization framework for optimization with differential and algebraic equations

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

Nicholson, Bethany; Siirola, John D.; Watson, Jean-Paul

We describe pyomo.dae, an open source Python-based modeling framework that enables high-level abstract specification of optimization problems with differential and algebraic equations. The pyomo.dae framework is integrated with the Pyomo open source algebraic modeling language, and is available at http://www.pyomo.org. One key feature of pyomo.dae is that it does not restrict users to standard, predefined forms of differential equations, providing a high degree of modeling flexibility and the ability to express constraints that cannot be easily specified in other modeling frameworks. Other key features of pyomo.dae are the ability to specify optimization problems with high-order differential equations and partial differentialmore » equations, defined on restricted domain types, and the ability to automatically transform high-level abstract models into finite-dimensional algebraic problems that can be solved with off-the-shelf solvers. Moreover, pyomo.dae users can leverage existing capabilities of Pyomo to embed differential equation models within stochastic and integer programming models and mathematical programs with equilibrium constraint formulations. Collectively, these features enable the exploration of new modeling concepts, discretization schemes, and the benchmarking of state-of-the-art optimization solvers.« less

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

Advanced Computational Framework for Environmental Management ZEM, Version 1.x

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

Vesselinov, Velimir V.; O'Malley, Daniel; Pandey, Sachin

2016-11-04

Typically environmental management problems require analysis of large and complex data sets originating from concurrent data streams with different data collection frequencies and pedigree. These big data sets require on-the-fly integration into a series of models with different complexity for various types of model analyses where the data are applied as soft and hard model constraints. This is needed to provide fast iterative model analyses based on the latest available data to guide decision-making. Furthermore, the data and model are associated with uncertainties. The uncertainties are probabilistic (e.g. measurement errors) and non-probabilistic (unknowns, e.g. alternative conceptual models characterizing site conditions).more » To address all of these issues, we have developed an integrated framework for real-time data and model analyses for environmental decision-making called ZEM. The framework allows for seamless and on-the-fly integration of data and modeling results for robust and scientifically-defensible decision-making applying advanced decision analyses tools such as Bayesian- Information-Gap Decision Theory (BIG-DT). The framework also includes advanced methods for optimization that are capable of dealing with a large number of unknown model parameters, and surrogate (reduced order) modeling capabilities based on support vector regression techniques. The framework is coded in Julia, a state-of-the-art high-performance programing language (http://julialang.org). The ZEM framework is open-source and can be applied to any environmental management site. The framework will be open-source and released under GPL V3 license.« less

Global Health Innovation Technology Models.

PubMed

Harding, Kimberly

2016-01-01

Chronic technology and business process disparities between High Income, Low Middle Income and Low Income (HIC, LMIC, LIC) research collaborators directly prevent the growth of sustainable Global Health innovation for infectious and rare diseases. There is a need for an Open Source-Open Science Architecture Framework to bridge this divide. We are proposing such a framework for consideration by the Global Health community, by utilizing a hybrid approach of integrating agnostic Open Source technology and healthcare interoperability standards and Total Quality Management principles. We will validate this architecture framework through our programme called Project Orchid. Project Orchid is a conceptual Clinical Intelligence Exchange and Virtual Innovation platform utilizing this approach to support clinical innovation efforts for multi-national collaboration that can be locally sustainable for LIC and LMIC research cohorts. The goal is to enable LIC and LMIC research organizations to accelerate their clinical trial process maturity in the field of drug discovery, population health innovation initiatives and public domain knowledge networks. When sponsored, this concept will be tested by 12 confirmed clinical research and public health organizations in six countries. The potential impact of this platform is reduced drug discovery and public health innovation lag time and improved clinical trial interventions, due to reliable clinical intelligence and bio-surveillance across all phases of the clinical innovation process.

Global Health Innovation Technology Models

PubMed Central

Harding, Kimberly

2016-01-01

Chronic technology and business process disparities between High Income, Low Middle Income and Low Income (HIC, LMIC, LIC) research collaborators directly prevent the growth of sustainable Global Health innovation for infectious and rare diseases. There is a need for an Open Source-Open Science Architecture Framework to bridge this divide. We are proposing such a framework for consideration by the Global Health community, by utilizing a hybrid approach of integrating agnostic Open Source technology and healthcare interoperability standards and Total Quality Management principles. We will validate this architecture framework through our programme called Project Orchid. Project Orchid is a conceptual Clinical Intelligence Exchange and Virtual Innovation platform utilizing this approach to support clinical innovation efforts for multi-national collaboration that can be locally sustainable for LIC and LMIC research cohorts. The goal is to enable LIC and LMIC research organizations to accelerate their clinical trial process maturity in the field of drug discovery, population health innovation initiatives and public domain knowledge networks. When sponsored, this concept will be tested by 12 confirmed clinical research and public health organizations in six countries. The potential impact of this platform is reduced drug discovery and public health innovation lag time and improved clinical trial interventions, due to reliable clinical intelligence and bio-surveillance across all phases of the clinical innovation process.

Noninvasive Fetal ECG: the PhysioNet/Computing in Cardiology Challenge 2013.

PubMed

Silva, Ikaro; Behar, Joachim; Sameni, Reza; Zhu, Tingting; Oster, Julien; Clifford, Gari D; Moody, George B

2013-03-01

The PhysioNet/CinC 2013 Challenge aimed to stimulate rapid development and improvement of software for estimating fetal heart rate (FHR), fetal interbeat intervals (FRR), and fetal QT intervals (FQT), from multichannel recordings made using electrodes placed on the mother's abdomen. For the challenge, five data collections from a variety of sources were used to compile a large standardized database, which was divided into training, open test, and hidden test subsets. Gold-standard fetal QRS and QT interval annotations were developed using a novel crowd-sourcing framework. The challenge organizers used the hidden test subset to evaluate 91 open-source software entries submitted by 53 international teams of participants in three challenge events, estimating FHR, FRR, and FQT using the hidden test subset, which was not available for study by participants. Two additional events required only user-submitted QRS annotations to evaluate FHR and FRR estimation accuracy using the open test subset available to participants. The challenge yielded a total of 91 open-source software entries. The best of these achieved average estimation errors of 187bpm 2 for FHR, 20.9 ms for FRR, and 152.7 ms for FQT. The open data sets, scoring software, and open-source entries are available at PhysioNet for researchers interested on working on these problems.

Development of an Analysis and Design Optimization Framework for Marine Propellers

NASA Astrophysics Data System (ADS)

Tamhane, Ashish C.

In this thesis, a framework for the analysis and design optimization of ship propellers is developed. This framework can be utilized as an efficient synthesis tool in order to determine the main geometric characteristics of the propeller but also to provide the designer with the capability to optimize the shape of the blade sections based on their specific criteria. A hybrid lifting-line method with lifting-surface corrections to account for the three-dimensional flow effects has been developed. The prediction of the correction factors is achieved using Artificial Neural Networks and Support Vector Regression. This approach results in increased approximation accuracy compared to existing methods and allows for extrapolation of the correction factor values. The effect of viscosity is implemented in the framework via the coupling of the lifting line method with the open-source RANSE solver OpenFOAM for the calculation of lift, drag and pressure distribution on the blade sections using a transition kappa-o SST turbulence model. Case studies of benchmark high-speed propulsors are utilized in order to validate the proposed framework for propeller operation in open-water conditions but also in a ship's wake.

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…

Use of Open Standards and Technologies at the Lunar Mapping and Modeling Project

NASA Astrophysics Data System (ADS)

Law, E.; Malhotra, S.; Bui, B.; Chang, G.; Goodale, C. E.; Ramirez, P.; Kim, R. M.; Sadaqathulla, S.; Rodriguez, L.

2011-12-01

The Lunar Mapping and Modeling Project (LMMP), led by the Marshall Space Flight center (MSFC), is tasked by NASA. The project is responsible for the development of an information system to support lunar exploration activities. It provides lunar explorers a set of tools and lunar map and model products that are predominantly derived from present lunar missions (e.g., the Lunar Reconnaissance Orbiter (LRO)) and from historical missions (e.g., Apollo). At Jet Propulsion Laboratory (JPL), we have built the LMMP interoperable geospatial information system's underlying infrastructure and a single point of entry - the LMMP Portal by employing a number of open standards and technologies. The Portal exposes a set of services to users to allow search, visualization, subset, and download of lunar data managed by the system. Users also have access to a set of tools that visualize, analyze and annotate the data. The infrastructure and Portal are based on web service oriented architecture. We designed the system to support solar system bodies in general including asteroids, earth and planets. We employed a combination of custom software, commercial and open-source components, off-the-shelf hardware and pay-by-use cloud computing services. The use of open standards and web service interfaces facilitate platform and application independent access to the services and data, offering for instances, iPad and Android mobile applications and large screen multi-touch with 3-D terrain viewing functions, for a rich browsing and analysis experience from a variety of platforms. The web services made use of open standards including: Representational State Transfer (REST); and Open Geospatial Consortium (OGC)'s Web Map Service (WMS), Web Coverage Service (WCS), Web Feature Service (WFS). Its data management services have been built on top of a set of open technologies including: Object Oriented Data Technology (OODT) - open source data catalog, archive, file management, data grid framework; openSSO - open source access management and federation platform; solr - open source enterprise search platform; redmine - open source project collaboration and management framework; GDAL - open source geospatial data abstraction library; and others. Its data products are compliant with Federal Geographic Data Committee (FGDC) metadata standard. This standardization allows users to access the data products via custom written applications or off-the-shelf applications such as GoogleEarth. We will demonstrate this ready-to-use system for data discovery and visualization by walking through the data services provided through the portal such as browse, search, and other tools. We will further demonstrate image viewing and layering of lunar map images from the Internet, via mobile devices such as Apple's iPad.

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

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

NASA Astrophysics Data System (ADS)

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

2015-08-01

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

Global OpenSearch

NASA Astrophysics Data System (ADS)

Newman, D. J.; Mitchell, A. E.

2015-12-01

At AGU 2014, NASA EOSDIS demonstrated a case-study of an OpenSearch framework for Earth science data discovery. That framework leverages the IDN and CWIC OpenSearch API implementations to provide seamless discovery of data through the 'two-step' discovery process as outlined by the Federation for Earth Sciences (ESIP) OpenSearch Best Practices. But how would an Earth Scientist leverage this framework and what are the benefits? Using a client that understands the OpenSearch specification and, for further clarity, the various best practices and extensions, a scientist can discovery a plethora of data not normally accessible either by traditional methods (NASA Earth Data Search, Reverb, etc) or direct methods (going to the source of the data) We will demonstrate, via the CWICSmart web client, how an earth scientist can access regional data on a regional phenomena in a uniform and aggregated manner. We will demonstrate how an earth scientist can 'globalize' their discovery. You want to find local data on 'sea surface temperature of the Indian Ocean'? We can help you with that. 'European meteorological data'? Yes. 'Brazilian rainforest satellite imagery'? That too. CWIC allows you to get earth science data in a uniform fashion from a large number of disparate, world-wide agencies. This is what we mean by Global OpenSearch.

Information Foraging Theory: A Framework for Intelligence Analysis

DTIC Science & Technology

2014-11-01

oceanographic information, human intelligence (HUMINT), open-source intelligence ( OSINT ), and information provided by other governmental departments [1][5...Human Intelligence IFT Information Foraging Theory LSA Latent Semantic Similarity MVT Marginal Value Theorem OFT Optimal Foraging Theory OSINT

The Matsu Wheel: A Cloud-Based Framework for Efficient Analysis and Reanalysis of Earth Satellite Imagery

NASA Technical Reports Server (NTRS)

Patterson, Maria T.; Anderson, Nicholas; Bennett, Collin; Bruggemann, Jacob; Grossman, Robert L.; Handy, Matthew; Ly, Vuong; Mandl, Daniel J.; Pederson, Shane; Pivarski, James;

Description of the U.S. Geological Survey Geo Data Portal data integration framework

USGS Publications Warehouse

Blodgett, David L.; Booth, Nathaniel L.; Kunicki, Thomas C.; Walker, Jordan I.; Lucido, Jessica M.

2012-01-01

The U.S. Geological Survey has developed an open-standard data integration framework for working efficiently and effectively with large collections of climate and other geoscience data. A web interface accesses catalog datasets to find data services. Data resources can then be rendered for mapping and dataset metadata are derived directly from these web services. Algorithm configuration and information needed to retrieve data for processing are passed to a server where all large-volume data access and manipulation takes place. The data integration strategy described here was implemented by leveraging existing free and open source software. Details of the software used are omitted; rather, emphasis is placed on how open-standard web services and data encodings can be used in an architecture that integrates common geographic and atmospheric data.

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation

PubMed Central

Portales-Casamar, Elodie; Kirov, Stefan; Lim, Jonathan; Lithwick, Stuart; Swanson, Magdalena I; Ticoll, Amy; Snoddy, Jay; Wasserman, Wyeth W

2007-01-01

PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. Curated boutique data collections can be maintained and disseminated through the unified schema of the mall-like PAZAR repository. The Pleiades Promoter Project collection of brain-linked regulatory sequences is introduced to demonstrate the depth of annotation possible within PAZAR. PAZAR, located at , is open for business. PMID:17916232

PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation.

PubMed

Portales-Casamar, Elodie; Kirov, Stefan; Lim, Jonathan; Lithwick, Stuart; Swanson, Magdalena I; Ticoll, Amy; Snoddy, Jay; Wasserman, Wyeth W

2007-01-01

PAZAR is an open-access and open-source database of transcription factor and regulatory sequence annotation with associated web interface and programming tools for data submission and extraction. Curated boutique data collections can be maintained and disseminated through the unified schema of the mall-like PAZAR repository. The Pleiades Promoter Project collection of brain-linked regulatory sequences is introduced to demonstrate the depth of annotation possible within PAZAR. PAZAR, located at http://www.pazar.info, is open for business.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders.

PubMed

Drouin, Simon; Collins, D Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel.

PRISM: An open source framework for the interactive design of GPU volume rendering shaders

PubMed Central

Collins, D. Louis

2018-01-01

Direct volume rendering has become an essential tool to explore and analyse 3D medical images. Despite several advances in the field, it remains a challenge to produce an image that highlights the anatomy of interest, avoids occlusion of important structures, provides an intuitive perception of shape and depth while retaining sufficient contextual information. Although the computer graphics community has proposed several solutions to address specific visualization problems, the medical imaging community still lacks a general volume rendering implementation that can address a wide variety of visualization use cases while avoiding complexity. In this paper, we propose a new open source framework called the Programmable Ray Integration Shading Model, or PRISM, that implements a complete GPU ray-casting solution where critical parts of the ray integration algorithm can be replaced to produce new volume rendering effects. A graphical user interface allows clinical users to easily experiment with pre-existing rendering effect building blocks drawn from an open database. For programmers, the interface enables real-time editing of the code inside the blocks. We show that in its default mode, the PRISM framework produces images very similar to those produced by a widely-adopted direct volume rendering implementation in VTK at comparable frame rates. More importantly, we demonstrate the flexibility of the framework by showing how several volume rendering techniques can be implemented in PRISM with no more than a few lines of code. Finally, we demonstrate the simplicity of our system in a usability study with 5 medical imaging expert subjects who have none or little experience with volume rendering. The PRISM framework has the potential to greatly accelerate development of volume rendering for medical applications by promoting sharing and enabling faster development iterations and easier collaboration between engineers and clinical personnel. PMID:29534069

Sirepo - Warp

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

Nagler, Robert; Moeller, Paul

Sirepo is an open source framework for cloud computing. The graphical user interface (GUI) for Sirepo, also known as the client, executes in any HTML5 compliant web browser on any computing platform, including tablets. The client is built in JavaScript, making use of the following open source libraries: Bootstrap, which is fundamental for cross-platform web applications; AngularJS, which provides a model–view–controller (MVC) architecture and GUI components; and D3.js, which provides interactive plots and data-driven transformations. The Sirepo server is built on the following Python technologies: Flask, which is a lightweight framework for web development; Jin-ja, which is a secure andmore » widely used templating language; and Werkzeug, a utility library that is compliant with the WSGI standard. We use Nginx as the HTTP server and proxy, which provides a scalable event-driven architecture. The physics codes supported by Sirepo execute inside a Docker container. One of the codes supported by Sirepo is Warp. Warp is a particle-in-cell (PIC) code de-signed to simulate high-intensity charged particle beams and plasmas in both the electrostatic and electromagnetic regimes, with a wide variety of integrated physics models and diagnostics. At pre-sent, Sirepo supports a small subset of Warp’s capabilities. Warp is open source and is part of the Berkeley Lab Accelerator Simulation Toolkit.« less

Modernizing the MagIC Paleomagnetic and Rock Magnetic Database Technology Stack to Encourage Code Reuse and Reproducible Science

NASA Astrophysics Data System (ADS)

Minnett, R.; Koppers, A. A. P.; Jarboe, N.; Jonestrask, L.; Tauxe, L.; Constable, C.

2016-12-01

The Magnetics Information Consortium (https://earthref.org/MagIC/) develops and maintains a database and web application for supporting the paleo-, geo-, and rock magnetic scientific community. Historically, this objective has been met with an Oracle database and a Perl web application at the San Diego Supercomputer Center (SDSC). The Oracle Enterprise Cluster at SDSC, however, was decommissioned in July of 2016 and the cost for MagIC to continue using Oracle became prohibitive. This provided MagIC with a unique opportunity to reexamine the entire technology stack and data model. MagIC has developed an open-source web application using the Meteor (http://meteor.com) framework and a MongoDB database. The simplicity of the open-source full-stack framework that Meteor provides has improved MagIC's development pace and the increased flexibility of the data schema in MongoDB encouraged the reorganization of the MagIC Data Model. As a result of incorporating actively developed open-source projects into the technology stack, MagIC has benefited from their vibrant software development communities. This has translated into a more modern web application that has significantly improved the user experience for the paleo-, geo-, and rock magnetic scientific community.

Proscene: A feature-rich framework for interactive environments

NASA Astrophysics Data System (ADS)

Charalambos, Jean Pierre

We introduce Proscene, a feature-rich, open-source framework for interactive environments. The design of Proscene comprises a three-layered onion-like software architecture, promoting different possible development scenarios. The framework innermost layer decouples user gesture parsing from user-defined actions. The in-between layer implements a feature-rich set of widely-used motion actions allowing the selection and manipulation of objects, including the scene viewpoint. The outermost layer exposes those features as a Processing library. The results have shown the feasibility of our approach together with the simplicity and flexibility of the Proscene framework API.

Evaluation metrics for bone segmentation in ultrasound

NASA Astrophysics Data System (ADS)

Lougheed, Matthew; Fichtinger, Gabor; Ungi, Tamas

2015-03-01

Tracked ultrasound is a safe alternative to X-ray for imaging bones. The interpretation of bony structures is challenging as ultrasound has no specific intensity characteristic of bones. Several image segmentation algorithms have been devised to identify bony structures. We propose an open-source framework that would aid in the development and comparison of such algorithms by quantitatively measuring segmentation performance in the ultrasound images. True-positive and false-negative metrics used in the framework quantify algorithm performance based on correctly segmented bone and correctly segmented boneless regions. Ground-truth for these metrics are defined manually and along with the corresponding automatically segmented image are used for the performance analysis. Manually created ground truth tests were generated to verify the accuracy of the analysis. Further evaluation metrics for determining average performance per slide and standard deviation are considered. The metrics provide a means of evaluating accuracy of frames along the length of a volume. This would aid in assessing the accuracy of the volume itself and the approach to image acquisition (positioning and frequency of frame). The framework was implemented as an open-source module of the 3D Slicer platform. The ground truth tests verified that the framework correctly calculates the implemented metrics. The developed framework provides a convenient way to evaluate bone segmentation algorithms. The implementation fits in a widely used application for segmentation algorithm prototyping. Future algorithm development will benefit by monitoring the effects of adjustments to an algorithm in a standard evaluation framework.

Moose: An Open-Source Framework to Enable Rapid Development of Collaborative, Multi-Scale, Multi-Physics Simulation Tools

NASA Astrophysics Data System (ADS)

Slaughter, A. E.; Permann, C.; Peterson, J. W.; Gaston, D.; Andrs, D.; Miller, J.

2014-12-01

The Idaho National Laboratory (INL)-developed Multiphysics Object Oriented Simulation Environment (MOOSE; www.mooseframework.org), is an open-source, parallel computational framework for enabling the solution of complex, fully implicit multiphysics systems. MOOSE provides a set of computational tools that scientists and engineers can use to create sophisticated multiphysics simulations. Applications built using MOOSE have computed solutions for chemical reaction and transport equations, computational fluid dynamics, solid mechanics, heat conduction, mesoscale materials modeling, geomechanics, and others. To facilitate the coupling of diverse and highly-coupled physical systems, MOOSE employs the Jacobian-free Newton-Krylov (JFNK) method when solving the coupled nonlinear systems of equations arising in multiphysics applications. The MOOSE framework is written in C++, and leverages other high-quality, open-source scientific software packages such as LibMesh, Hypre, and PETSc. MOOSE uses a "hybrid parallel" model which combines both shared memory (thread-based) and distributed memory (MPI-based) parallelism to ensure efficient resource utilization on a wide range of computational hardware. MOOSE-based applications are inherently modular, which allows for simulation expansion (via coupling of additional physics modules) and the creation of multi-scale simulations. Any application developed with MOOSE supports running (in parallel) any other MOOSE-based application. Each application can be developed independently, yet easily communicate with other applications (e.g., conductivity in a slope-scale model could be a constant input, or a complete phase-field micro-structure simulation) without additional code being written. This method of development has proven effective at INL and expedites the development of sophisticated, sustainable, and collaborative simulation tools.

Calibration of space instruments at the Metrology Light Source

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

Klein, R., E-mail: roman.klein@ptb.de; Fliegauf, R.; Gottwald, A.

2016-07-27

PTB has more than 20 years of experience in the calibration of space-based instruments using synchrotron radiation to cover the UV, VUV and X-ray spectral range. New instrumentation at the electron storage ring Metrology Light Source (MLS) opens up extended calibration possibilities within this framework. In particular, the set-up of a large vacuum vessel that can accommodate entire space instruments opens up new prospects. Moreover, a new facility for the calibration of radiation transfer source standards with a considerably extended spectral range has been put into operation. Besides, characterization and calibration of single components like e.g. mirrors, filters, gratings, andmore » detectors is continued.« less

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

PubMed

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

2016-09-01

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

Identifying populations sensitive to environmental chemicals by simulating toxicokinetic variability

EPA Science Inventory

We incorporate inter-individual variability, including variability across demographic subgroups, into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of...

Lost Confidence and Potential: A Mixed Methods Study of Underachieving College Students' Sources of Self-Efficacy

ERIC Educational Resources Information Center

Fong, Carlton J.; Krause, Jaimie M.

2014-01-01

This study investigated the sources of self-efficacy of college students enrolled in a learning frameworks course, whom we identified as underachievers. Through weekly journal entries, the group of underachievers (n = 13) cited the factors that made them feel confident or not confident. Students' responses to open-ended prompts were coded…

Introducing FNCS: Framework for Network Co-Simulation

ScienceCinema

None

2018-06-07

This video provides a basic overview of the PNNL Future Power Grid Initiative-developed Framework for Network Co-Simulation (FNCS). It discusses the increasing amounts of data coming from the power grid, and the need for a tool like FNCS that brings together data, transmission and distribution simulators. Included is a description of the FNCS architecture, and the advantages this new open source tool can bring to grid research and development efforts.

Bootstrapping Development of a Cloud-Based Spoken Dialog System in the Educational Domain from Scratch Using Crowdsourced Data. Research Report. ETS RR-16-16

ERIC Educational Resources Information Center

Ramanarayanan, Vikram; Suendermann-Oeft, David; Lange, Patrick; Ivanov, Alexei V.; Evanini, Keelan; Yu, Zhou; Tsuprun, Eugene; Qian, Yao

2016-01-01

We propose a crowdsourcing-based framework to iteratively and rapidly bootstrap a dialog system from scratch for a new domain. We leverage the open-source modular HALEF dialog system to deploy dialog applications. We illustrate the usefulness of this framework using four different prototype dialog items with applications in the educational domain…

Introducing FNCS: Framework for Network Co-Simulation

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

None

2014-10-23

This video provides a basic overview of the PNNL Future Power Grid Initiative-developed Framework for Network Co-Simulation (FNCS). It discusses the increasing amounts of data coming from the power grid, and the need for a tool like FNCS that brings together data, transmission and distribution simulators. Included is a description of the FNCS architecture, and the advantages this new open source tool can bring to grid research and development efforts.

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,

Open Source Tools for Seismicity Analysis

NASA Astrophysics Data System (ADS)

Powers, P.

2010-12-01

The spatio-temporal analysis of seismicity plays an important role in earthquake forecasting and is integral to research on earthquake interactions and triggering. For instance, the third version of the Uniform California Earthquake Rupture Forecast (UCERF), currently under development, will use Epidemic Type Aftershock Sequences (ETAS) as a model for earthquake triggering. UCERF will be a "living" model and therefore requires robust, tested, and well-documented ETAS algorithms to ensure transparency and reproducibility. Likewise, as earthquake aftershock sequences unfold, real-time access to high quality hypocenter data makes it possible to monitor the temporal variability of statistical properties such as the parameters of the Omori Law and the Gutenberg Richter b-value. Such statistical properties are valuable as they provide a measure of how much a particular sequence deviates from expected behavior and can be used when assigning probabilities of aftershock occurrence. To address these demands and provide public access to standard methods employed in statistical seismology, we present well-documented, open-source JavaScript and Java software libraries for the on- and off-line analysis of seismicity. The Javascript classes facilitate web-based asynchronous access to earthquake catalog data and provide a framework for in-browser display, analysis, and manipulation of catalog statistics; implementations of this framework will be made available on the USGS Earthquake Hazards website. The Java classes, in addition to providing tools for seismicity analysis, provide tools for modeling seismicity and generating synthetic catalogs. These tools are extensible and will be released as part of the open-source OpenSHA Commons library.

Status and future plans for open source QuickPIC

NASA Astrophysics Data System (ADS)

An, Weiming; Decyk, Viktor; Mori, Warren

2017-10-01

QuickPIC is a three dimensional (3D) quasi-static particle-in-cell (PIC) code developed based on the UPIC framework. It can be used for efficiently modeling plasma based accelerator (PBA) problems. With quasi-static approximation, QuickPIC can use different time scales for calculating the beam (or laser) evolution and the plasma response, and a 3D plasma wake field can be simulated using a two-dimensional (2D) PIC code where the time variable is ξ = ct - z and z is the beam propagation direction. QuickPIC can be thousand times faster than the normal PIC code when simulating the PBA. It uses an MPI/OpenMP hybrid parallel algorithm, which can be run on either a laptop or the largest supercomputer. The open source QuickPIC is an object-oriented program with high level classes written in Fortran 2003. It can be found at https://github.com/UCLA-Plasma-Simulation-Group/QuickPIC-OpenSource.git

msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies*

PubMed Central

Hoekman, Berend; Breitling, Rainer; Suits, Frank; Bischoff, Rainer; Horvatovich, Peter

2012-01-01

Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare and evaluate various publicly available open source label-free data processing workflows, we developed msCompare, a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a novel scoring method to evaluate their overall performance. We used msCompare to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and our in-house developed modules on peptide-spiked urine and trypsin-digested cerebrospinal fluid (CSF) samples. We found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. Our scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is open source software (https://trac.nbic.nl/mscompare), and we provide a web-based data processing service for our framework by integration into the Galaxy server of the Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) to allow scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets. PMID:22318370

A Standard Platform for Testing and Comparison of MDAO Architectures

NASA Technical Reports Server (NTRS)

Gray, Justin S.; Moore, Kenneth T.; Hearn, Tristan A.; Naylor, Bret A.

2012-01-01

The Multidisciplinary Design Analysis and Optimization (MDAO) community has developed a multitude of algorithms and techniques, called architectures, for performing optimizations on complex engineering systems which involve coupling between multiple discipline analyses. These architectures seek to efficiently handle optimizations with computationally expensive analyses including multiple disciplines. We propose a new testing procedure that can provide a quantitative and qualitative means of comparison among architectures. The proposed test procedure is implemented within the open source framework, OpenMDAO, and comparative results are presented for five well-known architectures: MDF, IDF, CO, BLISS, and BLISS-2000. We also demonstrate how using open source soft- ware development methods can allow the MDAO community to submit new problems and architectures to keep the test suite relevant.

Virtual shelves in a digital library: a framework for access to networked information sources.

PubMed

Patrick, T B; Springer, G K; Mitchell, J A; Sievert, M E

1995-01-01

Develop a framework for collections-based access to networked information sources that addresses the problem of location-dependent access to information sources. This framework uses a metaphor of a virtual shelf. A virtual shelf is a general-purpose server that is dedicated to a particular information subject class. The identifier of one of these servers identifies its subject class. Location-independent call numbers are assigned to information sources. Call numbers are based on standard vocabulary codes. The call numbers are first mapped to the location-independent identifiers of virtual shelves. When access to an information resource is required, a location directory provides a second mapping of these location-independent server identifiers to actual network locations. The framework has been implemented in two different systems. One system is based on the Open System Foundation/Distributed Computing Environment and the other is based on the World Wide Web. This framework applies in new ways traditional methods of library classification and cataloging. It is compatible with two traditional styles of selecting information searching and browsing. Traditional methods may be combined with new paradigms of information searching that will be able to take advantage of the special properties of digital information. Cooperation between the library-informational science community and the informatics community can provide a means for a continuing application of the knowledge and techniques of library science to the new problems of networked information sources.

On the implicit density based OpenFOAM solver for turbulent compressible flows

NASA Astrophysics Data System (ADS)

Fürst, Jiří

The contribution deals with the development of coupled implicit density based solver for compressible flows in the framework of open source package OpenFOAM. However the standard distribution of OpenFOAM contains several ready-made segregated solvers for compressible flows, the performance of those solvers is rather week in the case of transonic flows. Therefore we extend the work of Shen [15] and we develop an implicit semi-coupled solver. The main flow field variables are updated using lower-upper symmetric Gauss-Seidel method (LU-SGS) whereas the turbulence model variables are updated using implicit Euler method.

openBIS: a flexible framework for managing and analyzing complex data in biology research

PubMed Central

2011-01-01

Background Modern data generation techniques used in distributed systems biology research projects often create datasets of enormous size and diversity. We argue that in order to overcome the challenge of managing those large quantitative datasets and maximise the biological information extracted from them, a sound information system is required. Ease of integration with data analysis pipelines and other computational tools is a key requirement for it. Results We have developed openBIS, an open source software framework for constructing user-friendly, scalable and powerful information systems for data and metadata acquired in biological experiments. openBIS enables users to collect, integrate, share, publish data and to connect to data processing pipelines. This framework can be extended and has been customized for different data types acquired by a range of technologies. Conclusions openBIS is currently being used by several SystemsX.ch and EU projects applying mass spectrometric measurements of metabolites and proteins, High Content Screening, or Next Generation Sequencing technologies. The attributes that make it interesting to a large research community involved in systems biology projects include versatility, simplicity in deployment, scalability to very large data, flexibility to handle any biological data type and extensibility to the needs of any research domain. PMID:22151573

GRASS GIS: The first Open Source Temporal GIS

NASA Astrophysics Data System (ADS)

Gebbert, Sören; Leppelt, Thomas

2015-04-01

GRASS GIS is a full featured, general purpose Open Source geographic information system (GIS) with raster, 3D raster and vector processing support[1]. Recently, time was introduced as a new dimension that transformed GRASS GIS into the first Open Source temporal GIS with comprehensive spatio-temporal analysis, processing and visualization capabilities[2]. New spatio-temporal data types were introduced in GRASS GIS version 7, to manage raster, 3D raster and vector time series. These new data types are called space time datasets. They are designed to efficiently handle hundreds of thousands of time stamped raster, 3D raster and vector map layers of any size. Time stamps can be defined as time intervals or time instances in Gregorian calendar time or relative time. Space time datasets are simplifying the processing and analysis of large time series in GRASS GIS, since these new data types are used as input and output parameter in temporal modules. The handling of space time datasets is therefore equal to the handling of raster, 3D raster and vector map layers in GRASS GIS. A new dedicated Python library, the GRASS GIS Temporal Framework, was designed to implement the spatio-temporal data types and their management. The framework provides the functionality to efficiently handle hundreds of thousands of time stamped map layers and their spatio-temporal topological relations. The framework supports reasoning based on the temporal granularity of space time datasets as well as their temporal topology. It was designed in conjunction with the PyGRASS [3] library to support parallel processing of large datasets, that has a long tradition in GRASS GIS [4,5]. We will present a subset of more than 40 temporal modules that were implemented based on the GRASS GIS Temporal Framework, PyGRASS and the GRASS GIS Python scripting library. These modules provide a comprehensive temporal GIS tool set. The functionality range from space time dataset and time stamped map layer management over temporal aggregation, temporal accumulation, spatio-temporal statistics, spatio-temporal sampling, temporal algebra, temporal topology analysis, time series animation and temporal topology visualization to time series import and export capabilities with support for NetCDF and VTK data formats. We will present several temporal modules that support parallel processing of raster and 3D raster time series. [1] GRASS GIS Open Source Approaches in Spatial Data Handling In Open Source Approaches in Spatial Data Handling, Vol. 2 (2008), pp. 171-199, doi:10.1007/978-3-540-74831-19 by M. Neteler, D. Beaudette, P. Cavallini, L. Lami, J. Cepicky edited by G. Brent Hall, Michael G. Leahy [2] Gebbert, S., Pebesma, E., 2014. A temporal GIS for field based environmental modeling. Environ. Model. Softw. 53, 1-12. [3] Zambelli, P., Gebbert, S., Ciolli, M., 2013. Pygrass: An Object Oriented Python Application Programming Interface (API) for Geographic Resources Analysis Support System (GRASS) Geographic Information System (GIS). ISPRS Intl Journal of Geo-Information 2, 201-219. [4] Löwe, P., Klump, J., Thaler, J. (2012): The FOSS GIS Workbench on the GFZ Load Sharing Facility compute cluster, (Geophysical Research Abstracts Vol. 14, EGU2012-4491, 2012), General Assembly European Geosciences Union (Vienna, Austria 2012). [5] Akhter, S., Aida, K., Chemin, Y., 2010. "GRASS GIS on High Performance Computing with MPI, OpenMP and Ninf-G Programming Framework". ISPRS Conference, Kyoto, 9-12 August 2010

Web accessibility and open source software.

PubMed

Obrenović, Zeljko

2009-07-01

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

Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

PubMed

Echegaray, Sebastian; Bakr, Shaimaa; Rubin, Daniel L; Napel, Sandy

2017-10-06

The aim of this study was to develop an open-source, modular, locally run or server-based system for 3D radiomics feature computation that can be used on any computer system and included in existing workflows for understanding associations and building predictive models between image features and clinical data, such as survival. The QIFE exploits various levels of parallelization for use on multiprocessor systems. It consists of a managing framework and four stages: input, pre-processing, feature computation, and output. Each stage contains one or more swappable components, allowing run-time customization. We benchmarked the engine using various levels of parallelization on a cohort of CT scans presenting 108 lung tumors. Two versions of the QIFE have been released: (1) the open-source MATLAB code posted to Github, (2) a compiled version loaded in a Docker container, posted to DockerHub, which can be easily deployed on any computer. The QIFE processed 108 objects (tumors) in 2:12 (h/mm) using 1 core, and 1:04 (h/mm) hours using four cores with object-level parallelization. We developed the Quantitative Image Feature Engine (QIFE), an open-source feature-extraction framework that focuses on modularity, standards, parallelism, provenance, and integration. Researchers can easily integrate it with their existing segmentation and imaging workflows by creating input and output components that implement their existing interfaces. Computational efficiency can be improved by parallelizing execution at the cost of memory usage. Different parallelization levels provide different trade-offs, and the optimal setting will depend on the size and composition of the dataset to be processed.

Evaluation of a Framework to Implement Electronic Health Record Systems Based on the openEHR Standard

NASA Astrophysics Data System (ADS)

Orellana, Diego A.; Salas, Alberto A.; Solarz, Pablo F.; Medina Ruiz, Luis; Rotger, Viviana I.

2016-04-01

The production of clinical information about each patient is constantly increasing, and it is noteworthy that the information is created in different formats and at diverse points of care, resulting in fragmented, incomplete, inaccurate and isolated, health information. The use of health information technology has been promoted as having a decisive impact to improve the efficiency, cost-effectiveness, quality and safety of medical care delivery. However in developing countries the utilization of health information technology is insufficient and lacking of standards among other situations. In the present work we evaluate the framework EHRGen, based on the openEHR standard, as mean to reach generation and availability of patient centered information. The framework has been evaluated through the provided tools for final users, that is, without intervention of computer experts. It makes easier to adopt the openEHR ideas and provides an open source basis with a set of services, although some limitations in its current state conspire against interoperability and usability. However, despite the described limitations respect to usability and semantic interoperability, EHRGen is, at least regionally, a considerable step toward EHR adoption and interoperability, so that it should be supported from academic and administrative institutions.

JACOB: an enterprise framework for computational chemistry.

PubMed

Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

2013-06-15

Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

Integrating Distributed Interactive Simulations With the Project Darkstar Open-Source Massively Multiplayer Online Game (MMOG) Middleware

DTIC Science & Technology

2009-09-01

be complete MMOG solutions such as Multiverse are not within the scope of this thesis, though it is recommended that readers compare this type of...software to the middleware described here ( Multiverse , 2009). 1. University of Munster: Real-Time Framework The Real-Time Framework (RTF) project is...10, 2009, from http://wiki.secondlife.com/wiki/MMOX Multiverse . (2009). Multiverse platform architecture. Retrieved September 9, 2009, from http

Pika: A snow science simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.; Johnson, M.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase-field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture and crack propagation (via the extended finite-element method), flow in porous media, and others. The heat conduction, tensor mechanics, and phase-field modules, in particular, are well-suited for snow science problems. Pika--an open-source MOOSE-based application--is capable of simulating both 3D, coupled nonlinear continuum heat transfer and large-deformation mechanics applications (such as settlement) and phase-field based micro-structure applications. Additionally, these types of problems may be coupled tightly in a single solve or across length and time scales using a loosely coupled Picard iteration approach. In addition to the wide range of physics capabilities, MOOSE-based applications also inherit an extensible testing framework, graphical user interface, and documentation system; tools that allow MOOSE and other applications to adhere to nuclear software quality standards. The snow science community can learn from the nuclear industry and harness the existing effort to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The snow science community should build on existing tools to enable collaboration between researchers and practitioners throughout the world, and advance the state-of-the-art in line with other scientific research efforts.

Inter-Individual Variability in High-Throughput Risk Prioritization of Environmental Chemicals (Sot)

EPA Science Inventory

We incorporate realistic human variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which have...

Inter-individual variability in high-throughput risk prioritization of environmental chemicals (IVIVE)

EPA Science Inventory

We incorporate inter-individual variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which hav...

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.

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

PubMed Central

Degenhart, Alan D.; Kelly, John W.; Ashmore, Robin C.; Collinger, Jennifer L.; Tyler-Kabara, Elizabeth C.; Weber, Douglas J.; Wang, Wei

2011-01-01

This paper presents “Craniux,” an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development. PMID:21687575

Craniux: a LabVIEW-based modular software framework for brain-machine interface research.

PubMed

Degenhart, Alan D; Kelly, John W; Ashmore, Robin C; Collinger, Jennifer L; Tyler-Kabara, Elizabeth C; Weber, Douglas J; Wang, Wei

2011-01-01

This paper presents "Craniux," an open-access, open-source software framework for brain-machine interface (BMI) research. Developed in LabVIEW, a high-level graphical programming environment, Craniux offers both out-of-the-box functionality and a modular BMI software framework that is easily extendable. Specifically, it allows researchers to take advantage of multiple features inherent to the LabVIEW environment for on-the-fly data visualization, parallel processing, multithreading, and data saving. This paper introduces the basic features and system architecture of Craniux and describes the validation of the system under real-time BMI operation using simulated and real electrocorticographic (ECoG) signals. Our results indicate that Craniux is able to operate consistently in real time, enabling a seamless work flow to achieve brain control of cursor movement. The Craniux software framework is made available to the scientific research community to provide a LabVIEW-based BMI software platform for future BMI research and development.

Open source libraries and frameworks for biological data visualisation: a guide for developers.

PubMed

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-04-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. © 2014 The Authors. PROTEOMICS published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Open source libraries and frameworks for biological data visualisation: A guide for developers

PubMed Central

Wang, Rui; Perez-Riverol, Yasset; Hermjakob, Henning; Vizcaíno, Juan Antonio

2015-01-01

Recent advances in high-throughput experimental techniques have led to an exponential increase in both the size and the complexity of the data sets commonly studied in biology. Data visualisation is increasingly used as the key to unlock this data, going from hypothesis generation to model evaluation and tool implementation. It is becoming more and more the heart of bioinformatics workflows, enabling scientists to reason and communicate more effectively. In parallel, there has been a corresponding trend towards the development of related software, which has triggered the maturation of different visualisation libraries and frameworks. For bioinformaticians, scientific programmers and software developers, the main challenge is to pick out the most fitting one(s) to create clear, meaningful and integrated data visualisation for their particular use cases. In this review, we introduce a collection of open source or free to use libraries and frameworks for creating data visualisation, covering the generation of a wide variety of charts and graphs. We will focus on software written in Java, JavaScript or Python. We truly believe this software offers the potential to turn tedious data into exciting visual stories. PMID:25475079

Open-source software platform for medical image segmentation applications

NASA Astrophysics Data System (ADS)

Namías, R.; D'Amato, J. P.; del Fresno, M.

2017-11-01

Segmenting 2D and 3D images is a crucial and challenging problem in medical image analysis. Although several image segmentation algorithms have been proposed for different applications, no universal method currently exists. Moreover, their use is usually limited when detection of complex and multiple adjacent objects of interest is needed. In addition, the continually increasing volumes of medical imaging scans require more efficient segmentation software design and highly usable applications. In this context, we present an extension of our previous segmentation framework which allows the combination of existing explicit deformable models in an efficient and transparent way, handling simultaneously different segmentation strategies and interacting with a graphic user interface (GUI). We present the object-oriented design and the general architecture which consist of two layers: the GUI at the top layer, and the processing core filters at the bottom layer. We apply the framework for segmenting different real-case medical image scenarios on public available datasets including bladder and prostate segmentation from 2D MRI, and heart segmentation in 3D CT. Our experiments on these concrete problems show that this framework facilitates complex and multi-object segmentation goals while providing a fast prototyping open-source segmentation tool.

Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording

NASA Astrophysics Data System (ADS)

Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

2017-06-01

Objective. Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Approach. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. Main results. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Significance. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

Open Ephys electroencephalography (Open Ephys  +  EEG): a modular, low-cost, open-source solution to human neural recording.

PubMed

Black, Christopher; Voigts, Jakob; Agrawal, Uday; Ladow, Max; Santoyo, Juan; Moore, Christopher; Jones, Stephanie

2017-06-01

Electroencephalography (EEG) offers a unique opportunity to study human neural activity non-invasively with millisecond resolution using minimal equipment in or outside of a lab setting. EEG can be combined with a number of techniques for closed-loop experiments, where external devices are driven by specific neural signals. However, reliable, commercially available EEG systems are expensive, often making them impractical for individual use and research development. Moreover, by design, a majority of these systems cannot be easily altered to the specification needed by the end user. We focused on mitigating these issues by implementing open-source tools to develop a new EEG platform to drive down research costs and promote collaboration and innovation. Here, we present methods to expand the open-source electrophysiology system, Open Ephys (www.openephys.org), to include human EEG recordings. We describe the equipment and protocol necessary to interface various EEG caps with the Open Ephys acquisition board, and detail methods for processing data. We present applications of Open Ephys  +  EEG as a research tool and discuss how this innovative EEG technology lays a framework for improved closed-loop paradigms and novel brain-computer interface experiments. The Open Ephys  +  EEG system can record reliable human EEG data, as well as human EMG data. A side-by-side comparison of eyes closed 8-14 Hz activity between the Open Ephys  +  EEG system and the Brainvision ActiCHamp EEG system showed similar average power and signal to noise. Open Ephys  +  EEG enables users to acquire high-quality human EEG data comparable to that of commercially available systems, while maintaining the price point and extensibility inherent to open-source systems.

Explicit B-spline regularization in diffeomorphic image registration

PubMed Central

Tustison, Nicholas J.; Avants, Brian B.

2013-01-01

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

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.

Open Source Live Distributions for Computer Forensics

NASA Astrophysics Data System (ADS)

Giustini, Giancarlo; Andreolini, Mauro; Colajanni, Michele

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

Trends and New Directions in Software Architecture

DTIC Science & Technology

2014-10-10

frameworks  Open source  Cloud strategies  NoSQL  Machine Learning  MDD  Incremental approaches  Dashboards  Distributed development...complexity grows  NoSQL Models are not created equal 2014 Our Current Research  Lightweight Evaluation and Architecture Prototyping for Big Data

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures

Human variability in high-throughput risk prioritization of environmental chemicals (Texas AM U. webinar)

EPA Science Inventory

We incorporate inter-individual variability into an open-source high-throughput (HT) toxicokinetics (TK) modeling framework for use in a next-generation risk prioritization approach. Risk prioritization involves rapid triage of thousands of environmental chemicals, most which hav...

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS

PubMed Central

Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2016-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optimizations1 to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor a , an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions. PMID:27896971

RABIX: AN OPEN-SOURCE WORKFLOW EXECUTOR SUPPORTING RECOMPUTABILITY AND INTEROPERABILITY OF WORKFLOW DESCRIPTIONS.

PubMed

Kaushik, Gaurav; Ivkovic, Sinisa; Simonovic, Janko; Tijanic, Nebojsa; Davis-Dusenbery, Brandi; Kural, Deniz

2017-01-01

As biomedical data has become increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. Reproducible and reusable methods are required to learn from large volumes of data reliably. To address this issue, numerous groups have developed workflow specifications or execution engines, which provide a framework with which to perform a sequence of analyses. One such specification is the Common Workflow Language, an emerging standard which provides a robust and flexible framework for describing data analysis tools and workflows. In addition, reproducibility can be furthered by executors or workflow engines which interpret the specification and enable additional features, such as error logging, file organization, optim1izations to computation and job scheduling, and allow for easy computing on large volumes of data. To this end, we have developed the Rabix Executor, an open-source workflow engine for the purposes of improving reproducibility through reusability and interoperability of workflow descriptions.

HERAFitter: Open source QCD fit project

DOE PAGES

Alekhin, S.; Behnke, O.; Belov, P.; ...

2015-07-01

HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from a wide range of experimental measurements in lepton-proton deep inelastic scattering and proton-proton (proton-antiproton) collisions at hadron colliders. These are complemented with a variety of theoretical options for calculating PDF-dependent cross section predictions corresponding to the measurements. The framework covers a large number of the existing methods and schemes used for PDF determination. The data and theoretical predictions are brought together through numerous methodologicalmore » options for carrying out PDF fits and plotting tools to help visualise the results. While primarily based on the approach of collinear factorisation, HERAFitter also provides facilities for fits of dipole models and transverse-momentum dependent PDFs. The package can be used to study the impact of new precise measurements from hadron colliders. This paper describes the general structure of HERAFitter and its wide choice of options.« less

openSE: a Systems Engineering Framework Particularly Suited to Particle Accelerator Studies and Development Projects

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

Bonnal, P.; Féral, B.; Kershaw, K.

Particle accelerator projects share many characteristics with industrial projects. However, experience has shown that best practice of industrial project management is not always well suited to particle accelerator projects. Major differences include the number and complexity of technologies involved, the importance of collaborative work, development phases that can last more than a decade, and the importance of telerobotics and remote handling to address future preventive and corrective maintenance requirements due to induced radioactivity, to cite just a few. The openSE framework it is a systems engineering and project management framework specifically designed for scientific facilities’ systems and equipment studies andmore » development projects. Best practices in project management, in systems and requirements engineering, in telerobotics and remote handling and in radiation safety management were used as sources of inspiration, together with analysis of current practices surveyed at CERN, GSI and ESS.« less

Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data.

PubMed

2017-03-07

Integrating multiple sources of pharmacovigilance evidence has the potential to advance the science of safety signal detection and evaluation. In this regard, there is a need for more research on how to integrate multiple disparate evidence sources while making the evidence computable from a knowledge representation perspective (i.e., semantic enrichment). Existing frameworks suggest well-promising outcomes for such integration but employ a rather limited number of sources. In particular, none have been specifically designed to support both regulatory and clinical use cases, nor have any been designed to add new resources and use cases through an open architecture. This paper discusses the architecture and functionality of a system called Large-scale Adverse Effects Related to Treatment Evidence Standardization (LAERTES) that aims to address these shortcomings. LAERTES provides a standardized, open, and scalable architecture for linking evidence sources relevant to the association of drugs with health outcomes of interest (HOIs). Standard terminologies are used to represent different entities. For example, drugs and HOIs are represented in RxNorm and Systematized Nomenclature of Medicine -- Clinical Terms respectively. At the time of this writing, six evidence sources have been loaded into the LAERTES evidence base and are accessible through prototype evidence exploration user interface and a set of Web application programming interface services. This system operates within a larger software stack provided by the Observational Health Data Sciences and Informatics clinical research framework, including the relational Common Data Model for observational patient data created by the Observational Medical Outcomes Partnership. Elements of the Linked Data paradigm facilitate the systematic and scalable integration of relevant evidence sources. The prototype LAERTES system provides useful functionality while creating opportunities for further research. Future work will involve improving the method for normalizing drug and HOI concepts across the integrated sources, aggregated evidence at different levels of a hierarchy of HOI concepts, and developing more advanced user interface for drug-HOI investigations.

Open Scenario Study, Phase I. Volume 3. Questionnaire Response

DTIC Science & Technology

2008-03-01

a conceptual framework to assist users to grasp new ideas. As the concepts are used by a broad community and internationally, classified scenarios are...framework to assist users to grasp new ideas. As the concepts are used by a broad community and internationally, classified scenarios are not necessary for...from other sources Comment: Normally have an old version that we can update. Occasionally we’ve had to develop new scenarios - the SSSP for example - we

A Bayesian Machine Learning Model for Estimating Building Occupancy from Open Source Data

DOE PAGES

Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.; ...

2016-01-01

Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the artmore » by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian model and informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000 ft 2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.« less

Virtual shelves in a digital library: a framework for access to networked information sources.

PubMed Central

Patrick, T B; Springer, G K; Mitchell, J A; Sievert, M E

1995-01-01

OBJECTIVE: Develop a framework for collections-based access to networked information sources that addresses the problem of location-dependent access to information sources. DESIGN: This framework uses a metaphor of a virtual shelf. A virtual shelf is a general-purpose server that is dedicated to a particular information subject class. The identifier of one of these servers identifies its subject class. Location-independent call numbers are assigned to information sources. Call numbers are based on standard vocabulary codes. The call numbers are first mapped to the location-independent identifiers of virtual shelves. When access to an information resource is required, a location directory provides a second mapping of these location-independent server identifiers to actual network locations. RESULTS: The framework has been implemented in two different systems. One system is based on the Open System Foundation/Distributed Computing Environment and the other is based on the World Wide Web. CONCLUSIONS: This framework applies in new ways traditional methods of library classification and cataloging. It is compatible with two traditional styles of selecting information searching and browsing. Traditional methods may be combined with new paradigms of information searching that will be able to take advantage of the special properties of digital information. Cooperation between the library-informational science community and the informatics community can provide a means for a continuing application of the knowledge and techniques of library science to the new problems of networked information sources. PMID:8581554

A computational framework for automation of point defect calculations

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

Goyal, Anuj; Gorai, Prashun; Peng, Haowei

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

Human-assisted sound event recognition for home service robots.

PubMed

Do, Ha Manh; Sheng, Weihua; Liu, Meiqin

This paper proposes and implements an open framework of active auditory learning for a home service robot to serve the elderly living alone at home. The framework was developed to realize the various auditory perception capabilities while enabling a remote human operator to involve in the sound event recognition process for elderly care. The home service robot is able to estimate the sound source position and collaborate with the human operator in sound event recognition while protecting the privacy of the elderly. Our experimental results validated the proposed framework and evaluated auditory perception capabilities and human-robot collaboration in sound event recognition.

A computational framework for automation of point defect calculations

DOE PAGES

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; ...

2017-01-13

We have developed a complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory. Furthermore, the framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. This package provides the capability to compute widely-accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3 as test examples, we demonstrate the package capabilities and validate the methodology.

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.

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

NASA Astrophysics Data System (ADS)

Engel, P.; Schweimler, B.

2016-04-01

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

Computational toxicology using the OpenTox application programming interface and Bioclipse

PubMed Central

2011-01-01

Background Toxicity is a complex phenomenon involving the potential adverse effect on a range of biological functions. Predicting toxicity involves using a combination of experimental data (endpoints) and computational methods to generate a set of predictive models. Such models rely strongly on being able to integrate information from many sources. The required integration of biological and chemical information sources requires, however, a common language to express our knowledge ontologically, and interoperating services to build reliable predictive toxicology applications. Findings This article describes progress in extending the integrative bio- and cheminformatics platform Bioclipse to interoperate with OpenTox, a semantic web framework which supports open data exchange and toxicology model building. The Bioclipse workbench environment enables functionality from OpenTox web services and easy access to OpenTox resources for evaluating toxicity properties of query molecules. Relevant cases and interfaces based on ten neurotoxins are described to demonstrate the capabilities provided to the user. The integration takes advantage of semantic web technologies, thereby providing an open and simplifying communication standard. Additionally, the use of ontologies ensures proper interoperation and reliable integration of toxicity information from both experimental and computational sources. Conclusions A novel computational toxicity assessment platform was generated from integration of two open science platforms related to toxicology: Bioclipse, that combines a rich scriptable and graphical workbench environment for integration of diverse sets of information sources, and OpenTox, a platform for interoperable toxicology data and computational services. The combination provides improved reliability and operability for handling large data sets by the use of the Open Standards from the OpenTox Application Programming Interface. This enables simultaneous access to a variety of distributed predictive toxicology databases, and algorithm and model resources, taking advantage of the Bioclipse workbench handling the technical layers. PMID:22075173

Framework for Assessing Biogenic CO2 Emissions from ...

EPA Pesticide Factsheets

This revision of the 2011 report, Accounting Framework for Biogenic CO2 Emissions from Stationary Sources, evaluates biogenic CO2 emissions from stationary sources, including a detailed study of the scientific and technical issues associated with assessing biogenic carbon dioxide emissions from stationary sources. EPA developed the revised report, Framework for Assessing Biogenic CO2 Emissions from Stationary Sources, to present a methodological framework for assessing the extent to which the production, processing, and use of biogenic material at stationary sources for energy production results in a net atmospheric contribution of biogenic CO2 emissions. Biogenic carbon dioxide emissions are defined as CO2 emissions related to the natural carbon cycle, as well as those resulting from the production, harvest, combustion, digestion, decomposition, and processing of biologically-based materials. The EPA is continuing to refine its technical assessment of biogenic CO2 emissions through another round of targeted peer review of the revised study with the EPA Science Advisory Board (SAB). This study was submitted to the SAB's Biogenic Carbon Emissions Panel in February 2015. http://yosemite.epa.gov/sab/sabproduct.nsf/0/3235dac747c16fe985257da90053f252!OpenDocument&TableRow=2.2#2 The revised report will inform efforts by policymakers, academics, and other stakeholders to evaluate the technical aspects related to assessments of biogenic feedstocks used for energy at s

GMODWeb: a web framework for the generic model organism database

PubMed Central

O'Connor, Brian D; Day, Allen; Cain, Scott; Arnaiz, Olivier; Sperling, Linda; Stein, Lincoln D

2008-01-01

The Generic Model Organism Database (GMOD) initiative provides species-agnostic data models and software tools for representing curated model organism data. Here we describe GMODWeb, a GMOD project designed to speed the development of model organism database (MOD) websites. Sites created with GMODWeb provide integration with other GMOD tools and allow users to browse and search through a variety of data types. GMODWeb was built using the open source Turnkey web framework and is available from . PMID:18570664

Computation in Classical Mechanics with Easy Java Simulations (EJS)

NASA Astrophysics Data System (ADS)

Cox, Anne J.

2006-12-01

Let your students enjoy creating animations and incorporating some computational physics into your Classical Mechanics course. This talk will demonstrate the use of an Open Source Physics package, Easy Java Simulations (EJS), in an already existing sophomore/junior level Classical Mechanics course. EJS allows for incremental introduction of computational physics into existing courses because it is easy to use (for instructors and students alike) and it is open source. Students can use this tool for numerical solutions to problems (as they can with commercial systems: Mathcad and Mathematica), but they can also generate their own animations. For example, students in Classical Mechanics use Lagrangian mechanics to solve a problem, and then use EJS not only to numerically solve the differential equations, but to show the associated motion (and check their answers). EJS, developed by Francisco Esquembre (http://fem.um.es/Ejs/), is built on the OpenSource Physics framework (http://www.opensourcephysics.org/) supported through NSF DUE0442581.

AWIPS II+: An Open-Source SOA Solution Enabling Environmental Remote Sensing Integration, Analysis, and Decision Support

NASA Astrophysics Data System (ADS)

Ardanuy, P. E.; Hood, C. A.; Moran, S. G.; Ritchie, A. A.; Tarro, A. M.; Nappi, A. J.

2008-12-01

Our shared future demands a renewed focus on sound environment stewardship-on the GEOSS socioeconomic imperatives, as well as the interdisciplinary relationships interconnecting our environment, climate, ecosystems, energy, carbon, water-and national security. Data volumes are now measured in the many petabytes. An increasingly urgent and accelerated tempo of changing requirements and responsive solutions demands data exploitation, and transparent, seamless, effortless, bidirectional, and interdisciplinary interoperability across models and observations. There is today a robust working paradigm established with the Advanced Weather Interactive Processing System (AWIPS)-NOAA/NWS's information integration and fusion capability. This process model extends vertically, and seamlessly, from environmental sensing through the direct delivery of societal benefit. NWS, via AWIPS, is the primary source of weather forecast and warning information in the nation. AWIPS is the tested and proven "the nerve center of operations" at all 122 NWS Weather Forecast Offices and 13 River Forecast Centers. Raytheon, in partnership with NOAA, has now evolved AWIPS into an open-source 2nd generation capability to satisfy climate, ecosystems, weather, and water mission goals. Just as AWIPS II supports NOAA decision- making, it is at the same time a platform funded by Raytheon IRAD and Government investment that can be cost-effectively leveraged across all of the GEOSS and IEOS societal benefit areas. The core principles in the AWIPS II evolution to a service-oriented architecture (SOA) were to minimize coupling, increase cohesion, minimize size of code base, maximize simplicity, and incorporate a pull-style data flow. We focused on "ilities" to drive the new AWIPS architecture-our shared architecture framework vision included six elements: - Create a new, low-cost framework for hosting a full range of environmental services, including thick-client visualization via virtual Earth's and GIS - Scale down framework to a small laptop and through workstations to clusters of enterprise servers without software change - "Plug-n-play"- plug-ins can be hot deployable, or system cycled to pick up new plug-ins - Base the framework on highly reusable design patterns that maximize reuse and have datatype independence and fast adaptability - Open Source leveraged to maximize reuse - "Gaming-style" interaction with the data This talk addresses the challenges that we meet to realize benefits in applications that couple environmental data from many disparate remote sensing and ancillary sources and disciplines. By leveraging the existing AWIPS II weather, water, ecosystems, and climate functionality and these six elements, along with well- thought-out displays with the end user's specific needs in mind, we demonstrate an easily adapted, extremely powerful, open-source remote sensing software tool that will help non-geospatial-experts make better use of these remote sensing resources to enhance environmental mapping and analysis and help guide environmental decision making at the national, regional, local and citizen levels.

Framework for Analytic Cognition (FAC): A Guide for Doing All-Source Intelligence Analysis

DTIC Science & Technology

2011-12-01

humans as rational decision makers has been thoroughly discounted in the last decade. Recent research in neuroscience and cognitive psychology has...Intelligence and Counterintelligence, Vol. 18, No. 2, 2005, p. 206. 60 Moore, D.T. & Krizan, L. "Intelligence Analysis: Does NSA have what it Takes...SIGINT NSA Online TS/SCI Online Digital Yes COMINT Internet None N/A Unclassified Online Digital Yes Open Source STRATFOR Local information

Unified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms

PubMed Central

Joshi, Alark; Scheinost, Dustin; Okuda, Hirohito; Belhachemi, Dominique; Murphy, Isabella; Staib, Lawrence H.; Papademetris, Xenophon

2011-01-01

Developing both graphical and command-line user interfaces for neuroimaging algorithms requires considerable effort. Neuroimaging algorithms can meet their potential only if they can be easily and frequently used by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires consistency of user interface controls, consistent results across various platforms and thorough testing. We present the design and implementation of a novel object-oriented framework that allows for rapid development of complex image analysis algorithms with many reusable components and the ability to easily add graphical user interface controls. Our framework also allows for simplified yet robust nightly testing of the algorithms to ensure stability and cross platform interoperability. All of the functionality is encapsulated into a software object requiring no separate source code for user interfaces, testing or deployment. This formulation makes our framework ideal for developing novel, stable and easy-to-use algorithms for medical image analysis and computer assisted interventions. The framework has been both deployed at Yale and released for public use in the open source multi-platform image analysis software—BioImage Suite (bioimagesuite.org). PMID:21249532

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

A modelling framework to simulate foliar fungal epidemics using functional–structural plant models

PubMed Central

Garin, Guillaume; Fournier, Christian; Andrieu, Bruno; Houlès, Vianney; Robert, Corinne; Pradal, Christophe

2014-01-01

Background and Aims Sustainable agriculture requires the identification of new, environmentally responsible strategies of crop protection. Modelling of pathosystems can allow a better understanding of the major interactions inside these dynamic systems and may lead to innovative protection strategies. In particular, functional–structural plant models (FSPMs) have been identified as a means to optimize the use of architecture-related traits. A current limitation lies in the inherent complexity of this type of modelling, and thus the purpose of this paper is to provide a framework to both extend and simplify the modelling of pathosystems using FSPMs. Methods Different entities and interactions occurring in pathosystems were formalized in a conceptual model. A framework based on these concepts was then implemented within the open-source OpenAlea modelling platform, using the platform's general strategy of modelling plant–environment interactions and extending it to handle plant interactions with pathogens. New developments include a generic data structure for representing lesions and dispersal units, and a series of generic protocols to communicate with objects representing the canopy and its microenvironment in the OpenAlea platform. Another development is the addition of a library of elementary models involved in pathosystem modelling. Several plant and physical models are already available in OpenAlea and can be combined in models of pathosystems using this framework approach. Key Results Two contrasting pathosystems are implemented using the framework and illustrate its generic utility. Simulations demonstrate the framework's ability to simulate multiscaled interactions within pathosystems, and also show that models are modular components within the framework and can be extended. This is illustrated by testing the impact of canopy architectural traits on fungal dispersal. Conclusions This study provides a framework for modelling a large number of pathosystems using FSPMs. This structure can accommodate both previously developed models for individual aspects of pathosystems and new ones. Complex models are deconstructed into separate ‘knowledge sources’ originating from different specialist areas of expertise and these can be shared and reassembled into multidisciplinary models. The framework thus provides a beneficial tool for a potential diverse and dynamic research community. PMID:24925323

Architecture for autonomy

NASA Astrophysics Data System (ADS)

Broten, Gregory S.; Monckton, Simon P.; Collier, Jack; Giesbrecht, Jared

2006-05-01

In 2002 Defence R&D Canada changed research direction from pure tele-operated land vehicles to general autonomy for land, air, and sea craft. The unique constraints of the military environment coupled with the complexity of autonomous systems drove DRDC to carefully plan a research and development infrastructure that would provide state of the art tools without restricting research scope. DRDC's long term objectives for its autonomy program address disparate unmanned ground vehicle (UGV), unattended ground sensor (UGS), air (UAV), and subsea and surface (UUV and USV) vehicles operating together with minimal human oversight. Individually, these systems will range in complexity from simple reconnaissance mini-UAVs streaming video to sophisticated autonomous combat UGVs exploiting embedded and remote sensing. Together, these systems can provide low risk, long endurance, battlefield services assuming they can communicate and cooperate with manned and unmanned systems. A key enabling technology for this new research is a software architecture capable of meeting both DRDC's current and future requirements. DRDC built upon recent advances in the computing science field while developing its software architecture know as the Architecture for Autonomy (AFA). Although a well established practice in computing science, frameworks have only recently entered common use by unmanned vehicles. For industry and government, the complexity, cost, and time to re-implement stable systems often exceeds the perceived benefits of adopting a modern software infrastructure. Thus, most persevere with legacy software, adapting and modifying software when and wherever possible or necessary -- adopting strategic software frameworks only when no justifiable legacy exists. Conversely, academic programs with short one or two year projects frequently exploit strategic software frameworks but with little enduring impact. The open-source movement radically changes this picture. Academic frameworks, open to public scrutiny and modification, now rival commercial frameworks in both quality and economic impact. Further, industry now realizes that open source frameworks can reduce cost and risk of systems engineering. This paper describes the Architecture for Autonomy implemented by DRDC and how this architecture meets DRDC's current needs. It also presents an argument for why this architecture should also satisfy DRDC's future requirements as well.

Advancing global marine biogeography research with open-source GIS software and cloud-computing

USGS Publications Warehouse

Fujioka, Ei; Vanden Berghe, Edward; Donnelly, Ben; Castillo, Julio; Cleary, Jesse; Holmes, Chris; McKnight, Sean; Halpin, patrick

2012-01-01

Across many scientific domains, the ability to aggregate disparate datasets enables more meaningful global analyses. Within marine biology, the Census of Marine Life served as the catalyst for such a global data aggregation effort. Under the Census framework, the Ocean Biogeographic Information System was established to coordinate an unprecedented aggregation of global marine biogeography data. The OBIS data system now contains 31.3 million observations, freely accessible through a geospatial portal. The challenges of storing, querying, disseminating, and mapping a global data collection of this complexity and magnitude are significant. In the face of declining performance and expanding feature requests, a redevelopment of the OBIS data system was undertaken. Following an Open Source philosophy, the OBIS technology stack was rebuilt using PostgreSQL, PostGIS, GeoServer and OpenLayers. This approach has markedly improved the performance and online user experience while maintaining a standards-compliant and interoperable framework. Due to the distributed nature of the project and increasing needs for storage, scalability and deployment flexibility, the entire hardware and software stack was built on a Cloud Computing environment. The flexibility of the platform, combined with the power of the application stack, enabled rapid re-development of the OBIS infrastructure, and ensured complete standards-compliance.

IMAGINE: Interstellar MAGnetic field INference Engine

NASA Astrophysics Data System (ADS)

Steininger, Theo

2018-03-01

IMAGINE (Interstellar MAGnetic field INference Engine) performs inference on generic parametric models of the Galaxy. The modular open source framework uses highly optimized tools and technology such as the MultiNest sampler (ascl:1109.006) and the information field theory framework NIFTy (ascl:1302.013) to create an instance of the Milky Way based on a set of parameters for physical observables, using Bayesian statistics to judge the mismatch between measured data and model prediction. The flexibility of the IMAGINE framework allows for simple refitting for newly available data sets and makes state-of-the-art Bayesian methods easily accessible particularly for random components of the Galactic magnetic field.

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

PubMed

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

2018-06-01

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

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.

A Clustering-Based Approach to Enriching Code Foraging Environment.

PubMed

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

2016-09-01

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

A Generic Software Architecture For Prognostics

NASA Technical Reports Server (NTRS)

Teubert, Christopher; Daigle, Matthew J.; Sankararaman, Shankar; Goebel, Kai; Watkins, Jason

2017-01-01

Prognostics is a systems engineering discipline focused on predicting end-of-life of components and systems. As a relatively new and emerging technology, there are few fielded implementations of prognostics, due in part to practitioners perceiving a large hurdle in developing the models, algorithms, architecture, and integration pieces. As a result, no open software frameworks for applying prognostics currently exist. This paper introduces the Generic Software Architecture for Prognostics (GSAP), an open-source, cross-platform, object-oriented software framework and support library for creating prognostics applications. GSAP was designed to make prognostics more accessible and enable faster adoption and implementation by industry, by reducing the effort and investment required to develop, test, and deploy prognostics. This paper describes the requirements, design, and testing of GSAP. Additionally, a detailed case study involving battery prognostics demonstrates its use.

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.

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

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

Liao, C; Quinlan, D; Panas, T

2010-01-25

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

An Open Source Framework for Coupled Hydro-Hydrogeo-Chemical Systems in Catchment Research

NASA Astrophysics Data System (ADS)

Delfs, J.; Sachse, A.; Gayler, S.; Grathwohl, P.; He, W.; Jang, E.; Kalbacher, T.; Klein, C.; Kolditz, O.; Maier, U.; Priesack, E.; Rink, K.; Selle, B.; Shao, H.; Singh, A. K.; Streck, T.; Sun, Y.; Wang, W.; Walther, M.

2013-12-01

This poster presents an open-source framework designed to assist water scientists in the study of catchment hydraulic functions with associated chemical processes, e.g. contaminant degradation, plant nutrient turnover. The model successfully calculates the feedbacks between surface water, subsurface water and air in standard benchmarks. In specific model applications to heterogeneous catchments, subsurface water is driven by density variations and runs through double porous media. Software codes of water science are tightly coupled by iteration, namely the Storm Water Management Model (SWMM) for urban runoff, Expert-N for simulating water fluxes and nutrient turnover in agricultural and forested soils, and OpenGeoSys (OGS) for groundwater. The coupled model calculates flow of hydrostatic shallow water over the land surface with finite volume and difference methods. The flow equations for water in the porous subsurface are discretized in space with finite elements. Chemical components are transferred through 1D, 2D or 3D watershed representations with advection-dispersion solvers or, as an alternative, random walk particle tracking. A transport solver can be in sequence with a chemical solver, e.g. PHREEQ-C, BRNS, additionally. Besides coupled partial differential equations, the concept of hydrological response units is employed in simulations at regional scale with scarce data availability. In this case, a conceptual hydrological model, specifically the Jena Adaptable Modeling System (JAMS), passes groundwater recharge through a software interface into OGS, which solves the partial differential equations of groundwater flow. Most components of the modeling framework are open source and can be modified for individual purposes. Applications range from temperate climate regions in Germany (Ammer catchment and Hessian Ried) to arid regions in the Middle East (Oman and Dead See). Some of the presented examples originate from intensively monitored research sites of the WESS research centre and the monitoring initiative TERENO. Other examples originate from the IWAS project on integrated water resources management. The model applications are primarily concerned with groundwater resources, which are endangered by overexploitation, intrusion of saltwater, and nitrate loads.

Craniux: A LabVIEW-Based Modular Software Framework for Brain-Machine Interface Research

DTIC Science & Technology

2011-01-01

open-source BMI software solu- tions are currently available, we feel that the Craniux software package fills a specific need in the realm of BMI...data, such as cortical source imaging using EEG or MEG recordings. It is with these characteristics in mind that we feel the Craniux software package...S. Adee, “Dean Kamen’s ‘luke arm’ prosthesis readies for clinical trials,” IEEE Spectrum, February 2008, http://spectrum .ieee.org/biomedical

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

USGS Publications Warehouse

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

2015-09-18

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

FRED 2: an immunoinformatics framework for Python

PubMed Central

Schubert, Benjamin; Walzer, Mathias; Brachvogel, Hans-Philipp; Szolek, András; Mohr, Christopher; Kohlbacher, Oliver

2016-01-01

Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. Availability and implementation: FRED 2 is available at http://fred-2.github.io Contact: schubert@informatik.uni-tuebingen.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27153717

FRED 2: an immunoinformatics framework for Python.

PubMed

Schubert, Benjamin; Walzer, Mathias; Brachvogel, Hans-Philipp; Szolek, András; Mohr, Christopher; Kohlbacher, Oliver

2016-07-01

Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications. FRED 2 is available at http://fred-2.github.io schubert@informatik.uni-tuebingen.de Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Holonomic quantum computation in the presence of decoherence.

PubMed

Fuentes-Guridi, I; Girelli, F; Livine, E

2005-01-21

We present a scheme to study non-Abelian adiabatic holonomies for open Markovian systems. As an application of our framework, we analyze the robustness of holonomic quantum computation against decoherence. We pinpoint the sources of error that must be corrected to achieve a geometric implementation of quantum computation completely resilient to Markovian decoherence.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications.

PubMed

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu.

Harvest: an open platform for developing web-based biomedical data discovery and reporting applications

PubMed Central

Pennington, Jeffrey W; Ruth, Byron; Italia, Michael J; Miller, Jeffrey; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; White, Peter S

2014-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible as they seek inherent relationships between attributes in disparate data types. Data discovery in this context is limited by a lack of query systems that efficiently show relationships between individual variables, but without the need to navigate underlying data models. We have addressed this need by developing Harvest, an open-source framework of modular components, and using it for the rapid development and deployment of custom data discovery software applications. Harvest incorporates visualizations of highly dimensional data in a web-based interface that promotes rapid exploration and export of any type of biomedical information, without exposing researchers to underlying data models. We evaluated Harvest with two cases: clinical data from pediatric cardiology and demonstration data from the OpenMRS project. Harvest's architecture and public open-source code offer a set of rapid application development tools to build data discovery applications for domain-specific biomedical data repositories. All resources, including the OpenMRS demonstration, can be found at http://harvest.research.chop.edu PMID:24131510

An Open Source Extensible Smart Energy Framework

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

Rankin, Linda

Aggregated distributed energy resources are the subject of much interest in the energy industry and are expected to play an important role in meeting our future energy needs by changing how we use, distribute and generate electricity. This energy future includes an increased amount of energy from renewable resources, load management techniques to improve resiliency and reliability, and distributed energy storage and generation capabilities that can be managed to meet the needs of the grid as well as individual customers. These energy assets are commonly referred to as Distributed Energy Resources (DER). DERs rely on a means to communicate informationmore » between an energy provider and multitudes of devices. Today DER control systems are typically vendor-specific, using custom hardware and software solutions. As a result, customers are locked into communication transport protocols, applications, tools, and data formats. Today’s systems are often difficult to extend to meet new application requirements, resulting in stranded assets when business requirements or energy management models evolve. By partnering with industry advisors and researchers, an implementation DER research platform was developed called the Smart Energy Framework (SEF). The hypothesis of this research was that an open source Internet of Things (IoT) framework could play a role in creating a commodity-based eco-system for DER assets that would reduce costs and provide interoperable products. SEF is based on the AllJoynTM IoT open source framework. The demonstration system incorporated DER assets, specifically batteries and smart water heaters. To verify the behavior of the distributed system, models of water heaters and batteries were also developed. An IoT interface for communicating between the assets and a control server was defined. This interface supports a series of “events” and telemetry reporting, similar to those defined by current smart grid communication standards. The results of this effort demonstrated the feasibility and application potential of using IoT frameworks for the creation of commodity-based DER systems. All of the identified commodity-based system requirements were met by the AllJoyn framework. By having commodity solutions, small vendors can enter the market and the cost of implementation for all parties is reduced. Utilities and aggregators can choose from multiple interoperable products reducing the risk of stranded assets. Based on this research it is recommended that interfaces based on existing smart grid communication protocol standards be created for these emerging IoT frameworks. These interfaces should be standardized as part of the IoT framework allowing for interoperability testing and certification. Similarly, IoT frameworks are introducing application level security. This type of security is needed for protecting application and platforms and will be important moving forward. Recommendations are that along with DER-based data model interfaces, platform and application security requirements also be prescribed when IoT devices support DER applications.« less

The Pixhawk Open-Source Computer Vision Framework for Mavs

NASA Astrophysics Data System (ADS)

Meier, L.; Tanskanen, P.; Fraundorfer, F.; Pollefeys, M.

2011-09-01

Unmanned aerial vehicles (UAV) and micro air vehicles (MAV) are already intensively used in geodetic applications. State of the art autonomous systems are however geared towards the application area in safe and obstacle-free altitudes greater than 30 meters. Applications at lower altitudes still require a human pilot. A new application field will be the reconstruction of structures and buildings, including the facades and roofs, with semi-autonomous MAVs. Ongoing research in the MAV robotics field is focusing on enabling this system class to operate at lower altitudes in proximity to nearby obstacles and humans. PIXHAWK is an open source and open hardware toolkit for this purpose. The quadrotor design is optimized for onboard computer vision and can connect up to four cameras to its onboard computer. The validity of the system design is shown with a fully autonomous capture flight along a building.

Federated Space-Time Query for Earth Science Data Using OpenSearch Conventions

NASA Astrophysics Data System (ADS)

Lynnes, C.; Beaumont, B.; Duerr, R. E.; Hua, H.

2009-12-01

The past decade has seen a burgeoning of remote sensing and Earth science data providers, as evidenced in the growth of the Earth Science Information Partner (ESIP) federation. At the same time, the need to combine diverse data sets to enable understanding of the Earth as a system has also grown. While the expansion of data providers is in general a boon to such studies, the diversity presents a challenge to finding useful data for a given study. Locating all the data files with aerosol information for a particular volcanic eruption, for example, may involve learning and using several different search tools to execute the requisite space-time queries. To address this issue, the ESIP federation is developing a federated space-time query framework, based on the OpenSearch convention (www.opensearch.org), with Geo and Time extensions. In this framework, data providers publish OpenSearch Description Documents that describe in a machine-readable form how to execute queries against the provider. The novelty of OpenSearch is that the space-time query interface becomes both machine callable and easy enough to integrate into the web browser's search box. This flexibility, together with a simple REST (HTTP-get) interface, should allow a variety of data providers to participate in the federated search framework, from large institutional data centers to individual scientists. The simple interface enables trivial querying of multiple data sources and participation in recursive-like federated searches--all using the same common OpenSearch interface. This simplicity also makes the construction of clients easy, as does existing OpenSearch client libraries in a variety of languages. Moreover, a number of clients and aggregation services already exist and OpenSearch is already supported by a number of web browsers such as Firefox and Internet Explorer.

Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications

PubMed Central

Masanz, James J; Ogren, Philip V; Zheng, Jiaping; Sohn, Sunghwan; Kipper-Schuler, Karin C; Chute, Christopher G

2010-01-01

We aim to build and evaluate an open-source natural language processing system for information extraction from electronic medical record clinical free-text. We describe and evaluate our system, the clinical Text Analysis and Knowledge Extraction System (cTAKES), released open-source at http://www.ohnlp.org. The cTAKES builds on existing open-source technologies—the Unstructured Information Management Architecture framework and OpenNLP natural language processing toolkit. Its components, specifically trained for the clinical domain, create rich linguistic and semantic annotations. Performance of individual components: sentence boundary detector accuracy=0.949; tokenizer accuracy=0.949; part-of-speech tagger accuracy=0.936; shallow parser F-score=0.924; named entity recognizer and system-level evaluation F-score=0.715 for exact and 0.824 for overlapping spans, and accuracy for concept mapping, negation, and status attributes for exact and overlapping spans of 0.957, 0.943, 0.859, and 0.580, 0.939, and 0.839, respectively. Overall performance is discussed against five applications. The cTAKES annotations are the foundation for methods and modules for higher-level semantic processing of clinical free-text. PMID:20819853

FloorspaceJS - A New, Open Source, Web-Based Geometry Editor for Building Energy Modeling (BEM): Preprint

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

Macumber, Daniel L; Horowitz, Scott G; Schott, Marjorie

Across most industries, desktop applications are being rapidly migrated to web applications for a variety of reasons. Web applications are inherently cross platform, mobile, and easier to distribute than desktop applications. Fueling this trend are a wide range of free, open source libraries and frameworks that make it incredibly easy to develop powerful web applications. The building energy modeling community is just beginning to pick up on these larger trends, with a small but growing number of building energy modeling applications starting on or moving to the web. This paper presents a new, open source, web based geometry editor formore » Building Energy Modeling (BEM). The editor is written completely in JavaScript and runs in a modern web browser. The editor works on a custom JSON file format and is designed to be integrated into a variety of web and desktop applications. The web based editor is available to use as a standalone web application at: https://nrel.github.io/openstudio-geometry-editor/. An example integration is demonstrated with the OpenStudio desktop application. Finally, the editor can be easily integrated with a wide range of possible building energy modeling web applications.« less

Model-Based Reinforcement of Kinect Depth Data for Human Motion Capture Applications

PubMed Central

Calderita, Luis Vicente; Bandera, Juan Pedro; Bustos, Pablo; Skiadopoulos, Andreas

2013-01-01

Motion capture systems have recently experienced a strong evolution. New cheap depth sensors and open source frameworks, such as OpenNI, allow for perceiving human motion on-line without using invasive systems. However, these proposals do not evaluate the validity of the obtained poses. This paper addresses this issue using a model-based pose generator to complement the OpenNI human tracker. The proposed system enforces kinematics constraints, eliminates odd poses and filters sensor noise, while learning the real dimensions of the performer's body. The system is composed by a PrimeSense sensor, an OpenNI tracker and a kinematics-based filter and has been extensively tested. Experiments show that the proposed system improves pure OpenNI results at a very low computational cost. PMID:23845933

BioMart: a data federation framework for large collaborative projects.

PubMed

Zhang, Junjun; Haider, Syed; Baran, Joachim; Cros, Anthony; Guberman, Jonathan M; Hsu, Jack; Liang, Yong; Yao, Long; Kasprzyk, Arek

2011-01-01

BioMart is a freely available, open source, federated database system that provides a unified access to disparate, geographically distributed data sources. It is designed to be data agnostic and platform independent, such that existing databases can easily be incorporated into the BioMart framework. BioMart allows databases hosted on different servers to be presented seamlessly to users, facilitating collaborative projects between different research groups. BioMart contains several levels of query optimization to efficiently manage large data sets and offers a diverse selection of graphical user interfaces and application programming interfaces to ensure that queries can be performed in whatever manner is most convenient for the user. The software has now been adopted by a large number of different biological databases spanning a wide range of data types and providing a rich source of annotation available to bioinformaticians and biologists alike.

OpenSHMEM-UCX : Evaluation of UCX for implementing OpenSHMEM Programming Model

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

Baker, Matthew B; Gorentla Venkata, Manjunath; Aderholdt, William Ferrol

2016-01-01

The OpenSHMEM reference implementation was developed towards the goal of developing an open source and high-performing Open- SHMEM implementation. To achieve portability and performance across various networks, the OpenSHMEM reference implementation uses GAS- Net and UCCS for network operations. Recently, new network layers have emerged with the promise of providing high-performance, scalabil- ity, and portability for HPC applications. In this paper, we implement the OpenSHMEM reference implementation to use the UCX framework for network operations. Then, we evaluate its performance and scalabil- ity on Cray XK systems to understand UCX s suitability for developing the OpenSHMEM programming model. Further, wemore » develop a bench- mark called SHOMS for evaluating the OpenSHMEM implementation. Our experimental results show that OpenSHMEM-UCX outperforms the vendor supplied OpenSHMEM implementation in most cases on the Cray XK system by up to 40% with respect to message rate and up to 70% for the execution of application kernels.« less

Documentation for the MODFLOW 6 framework

USGS Publications Warehouse

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

2017-08-10

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

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.

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-01-01

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

Common Approach to Geoprocessing of Uav Data across Application Domains

NASA Astrophysics Data System (ADS)

Percivall, G. S.; Reichardt, M.; Taylor, T.

2015-08-01

UAVs are a disruptive technology bringing new geographic data and information to many application domains. UASs are similar to other geographic imagery systems so existing frameworks are applicable. But the diversity of UAVs as platforms along with the diversity of available sensors are presenting challenges in the processing and creation of geospatial products. Efficient processing and dissemination of the data is achieved using software and systems that implement open standards. The challenges identified point to the need for use of existing standards and extending standards. Results from the use of the OGC Sensor Web Enablement set of standards are presented. Next steps in the progress of UAVs and UASs may follow the path of open data, open source and open standards.

Assessment of Vision-Based Target Detection and Classification Solutions Using an Indoor Aerial Robot

DTIC Science & Technology

2014-09-01

college student alongside you, little sis! To Jes- xix sika Miller, Lauren Garcia and Caity White , my closest friends and confidants of ten years, who...arena corresponding coverage to the GUI is outlined in white 2.1.3 Challenges in the Model There are inherent challenges with any model that implements...source middleware originally maintained by Willow Garage [36] and now managed by the Open Source Robotics Foundation [37]. It provides a framework for

Software Toolbox Development for Rapid Earthquake Source Optimisation Combining InSAR Data and Seismic Waveforms

NASA Astrophysics Data System (ADS)

Isken, Marius P.; Sudhaus, Henriette; Heimann, Sebastian; Steinberg, Andreas; Bathke, Hannes M.

2017-04-01

We present a modular open-source software framework (pyrocko, kite, grond; http://pyrocko.org) for rapid InSAR data post-processing and modelling of tectonic and volcanic displacement fields derived from satellite data. Our aim is to ease and streamline the joint optimisation of earthquake observations from InSAR and GPS data together with seismological waveforms for an improved estimation of the ruptures' parameters. Through this approach we can provide finite models of earthquake ruptures and therefore contribute to a timely and better understanding of earthquake kinematics. The new kite module enables a fast processing of unwrapped InSAR scenes for source modelling: the spatial sub-sampling and data error/noise estimation for the interferogram is evaluated automatically and interactively. The rupture's near-field surface displacement data are then combined with seismic far-field waveforms and jointly modelled using the pyrocko.gf framwork, which allows for fast forward modelling based on pre-calculated elastodynamic and elastostatic Green's functions. Lastly the grond module supplies a bootstrap-based probabilistic (Monte Carlo) joint optimisation to estimate the parameters and uncertainties of a finite-source earthquake rupture model. We describe the developed and applied methods as an effort to establish a semi-automatic processing and modelling chain. The framework is applied to Sentinel-1 data from the 2016 Central Italy earthquake sequence, where we present the earthquake mechanism and rupture model from which we derive regions of increased coulomb stress. The open source software framework is developed at GFZ Potsdam and at the University of Kiel, Germany, it is written in Python and C programming languages. The toolbox architecture is modular and independent, and can be utilized flexibly for a variety of geophysical problems. This work is conducted within the BridGeS project (http://www.bridges.uni-kiel.de) funded by the German Research Foundation DFG through an Emmy-Noether grant.

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.

Robust, open-source removal of systematics in Kepler data

NASA Astrophysics Data System (ADS)

Aigrain, S.; Parviainen, H.; Roberts, S.; Reece, S.; Evans, T.

2017-10-01

We present ARC2 (Astrophysically Robust Correction 2), an open-source python-based systematics-correction pipeline, to correct for the Kepler prime mission long-cadence light curves. The ARC2 pipeline identifies and corrects any isolated discontinuities in the light curves and then removes trends common to many light curves. These trends are modelled using the publicly available co-trending basis vectors, within an (approximate) Bayesian framework with 'shrinkage' priors to minimize the risk of overfitting and the injection of any additional noise into the corrected light curves, while keeping any astrophysical signals intact. We show that the ARC2 pipeline's performance matches that of the standard Kepler PDC-MAP data products using standard noise metrics, and demonstrate its ability to preserve astrophysical signals using injection tests with simulated stellar rotation and planetary transit signals. Although it is not identical, the ARC2 pipeline can thus be used as an open-source alternative to PDC-MAP, whenever the ability to model the impact of the systematics removal process on other kinds of signal is important.

A Framework for Adopting LMS to Introduce e-Learning in a Traditional Course

ERIC Educational Resources Information Center

Georgouli, Katerina; Skalkidis, Ilias; Guerreiro, Pedro

2008-01-01

As more and more teachers in tertiary education experiment with technology, looking for new ways of enhancing their traditional ways of teaching, the need of flexible tools able to support well planned blended learning scenarios emerges. Learning Management Systems, especially those which are based on open source software, have shown to be very…

Molpher: a software framework for systematic chemical space exploration

PubMed Central

2014-01-01

Background Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. Results In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term ‘molecular morphing’, Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called ‘morphing operators’ that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Conclusions Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline. PMID:24655571

Plants in silico: why, why now and what?--an integrative platform for plant systems biology research.

PubMed

Zhu, Xin-Guang; Lynch, Jonathan P; LeBauer, David S; Millar, Andrew J; Stitt, Mark; Long, Stephen P

2016-05-01

A paradigm shift is needed and timely in moving plant modelling from largely isolated efforts to a connected community endeavour that can take full advantage of advances in computer science and in mechanistic understanding of plant processes. Plants in silico (Psi) envisions a digital representation of layered dynamic modules, linking from gene networks and metabolic pathways through to cellular organization, tissue, organ and whole plant development, together with resource capture and use efficiency in dynamic competitive environments, ultimately allowing a mechanistically rich simulation of the plant or of a community of plants in silico. The concept is to integrate models or modules from different layers of organization spanning from genome to phenome to ecosystem in a modular framework allowing the use of modules of varying mechanistic detail representing the same biological process. Developments in high-performance computing, functional knowledge of plants, the internet and open-source version controlled software make achieving the concept realistic. Open source will enhance collaboration and move towards testing and consensus on quantitative theoretical frameworks. Importantly, Psi provides a quantitative knowledge framework where the implications of a discovery at one level, for example, single gene function or developmental response, can be examined at the whole plant or even crop and natural ecosystem levels. © 2015 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

Molpher: a software framework for systematic chemical space exploration.

PubMed

Hoksza, David; Skoda, Petr; Voršilák, Milan; Svozil, Daniel

2014-03-21

Chemical space is virtual space occupied by all chemically meaningful organic compounds. It is an important concept in contemporary chemoinformatics research, and its systematic exploration is vital to the discovery of either novel drugs or new tools for chemical biology. In this paper, we describe Molpher, an open-source framework for the systematic exploration of chemical space. Through a process we term 'molecular morphing', Molpher produces a path of structurally-related compounds. This path is generated by the iterative application of so-called 'morphing operators' that represent simple structural changes, such as the addition or removal of an atom or a bond. Molpher incorporates an optimized parallel exploration algorithm, compound logging and a two-dimensional visualization of the exploration process. Its feature set can be easily extended by implementing additional morphing operators, chemical fingerprints, similarity measures and visualization methods. Molpher not only offers an intuitive graphical user interface, but also can be run in batch mode. This enables users to easily incorporate molecular morphing into their existing drug discovery pipelines. Molpher is an open-source software framework for the design of virtual chemical libraries focused on a particular mechanistic class of compounds. These libraries, represented by a morphing path and its surroundings, provide valuable starting data for future in silico and in vitro experiments. Molpher is highly extensible and can be easily incorporated into any existing computational drug design pipeline.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB.

PubMed

Lee, Leng-Feng; Umberger, Brian R

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1-2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility.

Generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB

PubMed Central

Lee, Leng-Feng

2016-01-01

Computer modeling, simulation and optimization are powerful tools that have seen increased use in biomechanics research. Dynamic optimizations can be categorized as either data-tracking or predictive problems. The data-tracking approach has been used extensively to address human movement problems of clinical relevance. The predictive approach also holds great promise, but has seen limited use in clinical applications. Enhanced software tools would facilitate the application of predictive musculoskeletal simulations to clinically-relevant research. The open-source software OpenSim provides tools for generating tracking simulations but not predictive simulations. However, OpenSim includes an extensive application programming interface that permits extending its capabilities with scripting languages such as MATLAB. In the work presented here, we combine the computational tools provided by MATLAB with the musculoskeletal modeling capabilities of OpenSim to create a framework for generating predictive simulations of musculoskeletal movement based on direct collocation optimal control techniques. In many cases, the direct collocation approach can be used to solve optimal control problems considerably faster than traditional shooting methods. Cyclical and discrete movement problems were solved using a simple 1 degree of freedom musculoskeletal model and a model of the human lower limb, respectively. The problems could be solved in reasonable amounts of time (several seconds to 1–2 hours) using the open-source IPOPT solver. The problems could also be solved using the fmincon solver that is included with MATLAB, but the computation times were excessively long for all but the smallest of problems. The performance advantage for IPOPT was derived primarily by exploiting sparsity in the constraints Jacobian. The framework presented here provides a powerful and flexible approach for generating optimal control simulations of musculoskeletal movement using OpenSim and MATLAB. This should allow researchers to more readily use predictive simulation as a tool to address clinical conditions that limit human mobility. PMID:26835184

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

A generic open-source software framework supporting scenario simulations in bioterrorist crises.

PubMed

Falenski, Alexander; Filter, Matthias; Thöns, Christian; Weiser, Armin A; Wigger, Jan-Frederik; Davis, Matthew; Douglas, Judith V; Edlund, Stefan; Hu, Kun; Kaufman, James H; Appel, Bernd; Käsbohrer, Annemarie

2013-09-01

Since the 2001 anthrax attack in the United States, awareness of threats originating from bioterrorism has grown. This led internationally to increased research efforts to improve knowledge of and approaches to protecting human and animal populations against the threat from such attacks. A collaborative effort in this context is the extension of the open-source Spatiotemporal Epidemiological Modeler (STEM) simulation and modeling software for agro- or bioterrorist crisis scenarios. STEM, originally designed to enable community-driven public health disease models and simulations, was extended with new features that enable integration of proprietary data as well as visualization of agent spread along supply and production chains. STEM now provides a fully developed open-source software infrastructure supporting critical modeling tasks such as ad hoc model generation, parameter estimation, simulation of scenario evolution, estimation of effects of mitigation or management measures, and documentation. This open-source software resource can be used free of charge. Additionally, STEM provides critical features like built-in worldwide data on administrative boundaries, transportation networks, or environmental conditions (eg, rainfall, temperature, elevation, vegetation). Users can easily combine their own confidential data with built-in public data to create customized models of desired resolution. STEM also supports collaborative and joint efforts in crisis situations by extended import and export functionalities. In this article we demonstrate specifically those new software features implemented to accomplish STEM application in agro- or bioterrorist crisis scenarios.

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.

pyGIMLi: An open-source library for modelling and inversion in geophysics

NASA Astrophysics Data System (ADS)

Rücker, Carsten; Günther, Thomas; Wagner, Florian M.

2017-12-01

Many tasks in applied geosciences cannot be solved by single measurements, but require the integration of geophysical, geotechnical and hydrological methods. Numerical simulation techniques are essential both for planning and interpretation, as well as for the process understanding of modern geophysical methods. These trends encourage open, simple, and modern software architectures aiming at a uniform interface for interdisciplinary and flexible modelling and inversion approaches. We present pyGIMLi (Python Library for Inversion and Modelling in Geophysics), an open-source framework that provides tools for modelling and inversion of various geophysical but also hydrological methods. The modelling component supplies discretization management and the numerical basis for finite-element and finite-volume solvers in 1D, 2D and 3D on arbitrarily structured meshes. The generalized inversion framework solves the minimization problem with a Gauss-Newton algorithm for any physical forward operator and provides opportunities for uncertainty and resolution analyses. More general requirements, such as flexible regularization strategies, time-lapse processing and different sorts of coupling individual methods are provided independently of the actual methods used. The usage of pyGIMLi is first demonstrated by solving the steady-state heat equation, followed by a demonstration of more complex capabilities for the combination of different geophysical data sets. A fully coupled hydrogeophysical inversion of electrical resistivity tomography (ERT) data of a simulated tracer experiment is presented that allows to directly reconstruct the underlying hydraulic conductivity distribution of the aquifer. Another example demonstrates the improvement of jointly inverting ERT and ultrasonic data with respect to saturation by a new approach that incorporates petrophysical relations in the inversion. Potential applications of the presented framework are manifold and include time-lapse, constrained, joint, and coupled inversions of various geophysical and hydrological data sets.

OpenHealth Platform for Interactive Contextualization of Population Health Open Data.

PubMed

Almeida, Jonas S; Hajagos, Janos; Crnosija, Ivan; Kurc, Tahsin; Saltz, Mary; Saltz, Joel

The financial incentives for data science applications leading to improved health outcomes, such as DSRIP (bit.ly/dsrip), are well-aligned with the broad adoption of Open Data by State and Federal agencies. This creates entirely novel opportunities for analytical applications that make exclusive use of the pervasive Web Computing platform. The framework described here explores this new avenue to contextualize Health data in a manner that relies exclusively on the native JavaScript interpreter and data processing resources of the ubiquitous Web Browser. The OpenHealth platform is made publicly available, and is publicly hosted with version control and open source, at https://github.com/mathbiol/openHealth. The different data/analytics workflow architectures explored are accompanied with live applications ranging from DSRIP, such as Hospital Inpatient Prevention Quality Indicators at http://bit.ly/pqiSuffolk, to The Cancer Genome Atlas (TCGA) as illustrated by http://bit.ly/tcgascopeGBM.

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

Implementation of highly parallel and large scale GW calculations within the OpenAtom software

NASA Astrophysics Data System (ADS)

Ismail-Beigi, Sohrab

The need to describe electronic excitations with better accuracy than provided by band structures produced by Density Functional Theory (DFT) has been a long-term enterprise for the computational condensed matter and materials theory communities. In some cases, appropriate theoretical frameworks have existed for some time but have been difficult to apply widely due to computational cost. For example, the GW approximation incorporates a great deal of important non-local and dynamical electronic interaction effects but has been too computationally expensive for routine use in large materials simulations. OpenAtom is an open source massively parallel ab initiodensity functional software package based on plane waves and pseudopotentials (http://charm.cs.uiuc.edu/OpenAtom/) that takes advantage of the Charm + + parallel framework. At present, it is developed via a three-way collaboration, funded by an NSF SI2-SSI grant (ACI-1339804), between Yale (Ismail-Beigi), IBM T. J. Watson (Glenn Martyna) and the University of Illinois at Urbana Champaign (Laxmikant Kale). We will describe the project and our current approach towards implementing large scale GW calculations with OpenAtom. Potential applications of large scale parallel GW software for problems involving electronic excitations in semiconductor and/or metal oxide systems will be also be pointed out.

The LSST metrics analysis framework (MAF)

NASA Astrophysics Data System (ADS)

Jones, R. L.; Yoachim, Peter; Chandrasekharan, Srinivasan; Connolly, Andrew J.; Cook, Kem H.; Ivezic, Željko; Krughoff, K. S.; Petry, Catherine; Ridgway, Stephen T.

2014-07-01

We describe the Metrics Analysis Framework (MAF), an open-source python framework developed to provide a user-friendly, customizable, easily-extensible set of tools for analyzing data sets. MAF is part of the Large Synoptic Survey Telescope (LSST) Simulations effort. Its initial goal is to provide a tool to evaluate LSST Operations Simulation (OpSim) simulated surveys to help understand the effects of telescope scheduling on survey performance, however MAF can be applied to a much wider range of datasets. The building blocks of the framework are Metrics (algorithms to analyze a given quantity of data), Slicers (subdividing the overall data set into smaller data slices as relevant for each Metric), and Database classes (to access the dataset and read data into memory). We describe how these building blocks work together, and provide an example of using MAF to evaluate different dithering strategies. We also outline how users can write their own custom Metrics and use these within the framework.

An efficient approach to the deployment of complex open source information systems

PubMed Central

Cong, Truong Van Chi; Groeneveld, Eildert

2011-01-01

Complex open source information systems are usually implemented as component-based software to inherit the available functionality of existing software packages developed by third parties. Consequently, the deployment of these systems not only requires the installation of operating system, application framework and the configuration of services but also needs to resolve the dependencies among components. The problem becomes more challenging when the application must be installed and used on different platforms such as Linux and Windows. To address this, an efficient approach using the virtualization technology is suggested and discussed in this paper. The approach has been applied in our project to deploy a web-based integrated information system in molecular genetics labs. It is a low-cost solution to benefit both software developers and end-users. PMID:22102770

Source-sink-storage relationships of conifers

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

Luxmoore, R.J.; Oren, R.; Sheriff, D.W.

1995-07-01

Irradiance, air temperature, saturation vapor pressure deficit, and soil temperature vary in association with Earth`s daily rotation, inducing significant hourly changes in the rates of plant physiological processes. These processes include carbon fixation in photosynthesis, sucrose translocation, and carbon utilization in growth, storage, and respiration. The sensitivity of these physiological processes to environmental factors such as temperature, soil water availability, and nutrient supply reveals differences that must be viewed as an interactive whole in order to comprehend whole-plant responses to the environment. Integrative frameworks for relationships between plant physiological processes are needed to provide syntheses of plant growth and development.more » Source-sink-storage relationships, addressed in this chapter, provide one framework for synthesis of whole-plant responses to external environmental variables. To address this issue, some examples of carbon assimilation and utilization responses of five conifer species to environmental factors from a range of field environments are first summarized. Next, the interactions between sources, sinks, and storages of carbon are examined at the leaf and tree scales, and finally, the review evaluates the proposition that processes involved with carbon utilization (sink activity) are more sensitive to the supply of water and nutrients (particularly nitrogen) than are the processes of carbon gain (source activity) and carbon storage. The terms {open_quotes}sink{close_quotes} and {open_quotes}source{close_quotes} refer to carbon utilization and carbon gain, respectively. The relative roles of stored carbon reserves and of current photosynthate in meeting sink demand are addressed. Discussions focus on source-sink-storage relationships within the diurnal, wetting-drying, and annual cycles of conifer growth and development, and some discussion of life cycle aspects is also presented.« less

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.

An Open Source modular platform for hydrological model implementation

NASA Astrophysics Data System (ADS)

Kolberg, Sjur; Bruland, Oddbjørn

2010-05-01

An implementation framework for setup and evaluation of spatio-temporal models is developed, forming a highly modularized distributed model system. The ENKI framework allows building space-time models for hydrological or other environmental purposes, from a suite of separately compiled subroutine modules. The approach makes it easy for students, researchers and other model developers to implement, exchange, and test single routines 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 hydropower forecasting or other water resource management. Written in C++, ENKI uses a plug-in structure to build a complete model from separately compiled subroutine implementations. These modules contain very little code apart from the core process simulation, and are compiled as dynamic-link libraries (dll). A narrow interface allows the main executable to recognise the number and type of the different variables in each routine. The framework then exposes these variables to the user within the proper context, ensuring that time series exist for input variables, initialisation for states, GIS data sets for static map data, manually or automatically calibrated values for parameters etc. ENKI is designed to meet three different levels of involvement in model construction: • Model application: Running and evaluating a given model. Regional calibration against arbitrary data using a rich suite of objective functions, including likelihood and Bayesian estimation. Uncertainty analysis directed towards input or parameter uncertainty. o Need not: Know the model's composition of subroutines, or the internal variables in the model, or the creation of method modules. • Model analysis: Link together different process methods, including parallel setup of alternative methods for solving the same task. Investigate the effect of different spatial discretization schemes. o Need not: Write or compile computer code, handle file IO for each modules, • Routine implementation and testing. Implementation of new process-simulating methods/equations, specialised objective functions or quality control routines, testing of these in an existing framework. o Need not: Implement user or model interface for the new routine, IO handling, administration of model setup and run, calibration and validation routines etc. From being developed for Norway's largest hydropower producer Statkraft, ENKI is now being turned into an Open Source project. At the time of writing, the licence and the project administration is not established. Also, it remains to port the application to other compilers and computer platforms. However, we hope that ENKI will prove useful for both academic and operational users.

Building an Open Source Framework for Integrated Catchment Modeling

NASA Astrophysics Data System (ADS)

Jagers, B.; Meijers, E.; Villars, M.

2015-12-01

In order to develop effective strategies and associated policies for environmental management, we need to understand the dynamics of the natural system as a whole and the human role therein. This understanding is gained by comparing our mental model of the world with observations from the field. However, to properly understand the system we should look at dynamics of water, sediments, water quality, and ecology throughout the whole system from catchment to coast both at the surface and in the subsurface. Numerical models are indispensable in helping us understand the interactions of the overall system, but we need to be able to update and adjust them to improve our understanding and test our hypotheses. To support researchers around the world with this challenging task we started a few years ago with the development of a new open source modeling environment DeltaShell that integrates distributed hydrological models with 1D, 2D, and 3D hydraulic models including generic components for the tracking of sediment, water quality, and ecological quantities throughout the hydrological cycle composed of the aforementioned components. The open source approach combined with a modular approach based on open standards, which allow for easy adjustment and expansion as demands and knowledge grow, provides an ideal starting point for addressing challenging integrated environmental questions.

The Open-Ended Approach Framework

ERIC Educational Resources Information Center

Munroe, Lloyd

2015-01-01

This paper describes a pedagogical framework that teachers can use to support students who are engaged in solving open-ended problems, by explaining how two Japanese expert teachers successfully apply open-ended problems in their mathematics class. The Open-Ended Approach (OPA) framework consists of two main sections: Understanding Mathematical…

Mimicking Nonequilibrium Steady States with Time-Periodic Driving (Open Source)

DTIC Science & Technology

2016-05-18

nonequilibrium steady states, and vice versa, within the theoretical framework of discrete-state stochastic thermodynamics . Nonequilibrium steady states...equilibrium [2], spontaneous relaxation towards equilibrium [3], nonequilibrium steady states generated by fixed thermodynamic forces [4], and stochastic pumps...paradigm, a system driven by fixed thermodynamic forces—such as temperature gradients or chemical potential differences— reaches a steady state in

Flexible configuration-interaction shell-model many-body solver

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

Johnson, Calvin W.; Ormand, W. Erich; McElvain, Kenneth S.

BIGSTICK Is a flexible configuration-Interaction open-source shell-model code for the many-fermion problem In a shell model (occupation representation) framework. BIGSTICK can generate energy spectra, static and transition one-body densities, and expectation values of scalar operators. Using the built-in Lanczos algorithm one can compute transition probabflity distributions and decompose wave functions into components defined by group theory.

Action Recommendation for Cyber Resilience

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

Choudhury, Sutanay; Rodriguez, Luke R.; Curtis, Darren S.

2015-09-01

This paper presents an unifying graph-based model for representing the infrastructure, behavior and missions of an enterprise. We describe how the model can be used to achieve resiliency against a wide class of failures and attacks. We introduce an algorithm for recommending resilience establishing actions based on dynamic updates to the models. Without loss of generality, we show the effectiveness of the algorithm for preserving latency based quality of service (QoS). Our models and the recommendation algorithms are implemented in a software framework that we seek to release as an open source framework for simulating resilient cyber systems.

Software for MR image overlay guided needle insertions: the clinical translation process

NASA Astrophysics Data System (ADS)

Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

2013-03-01

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

Identifying the Role of Terahertz Vibrations in Metal-Organic Frameworks: From Gate-Opening Phenomenon to Shear-Driven Structural Destabilization

NASA Astrophysics Data System (ADS)

Ryder, Matthew R.; Civalleri, Bartolomeo; Bennett, Thomas D.; Henke, Sebastian; Rudić, Svemir; Cinque, Gianfelice; Fernandez-Alonso, Felix; Tan, Jin-Chong

2014-11-01

We present an unambiguous identification of low-frequency terahertz vibrations in the archetypal imidazole-based metal-organic framework (MOF) materials: ZIF-4, ZIF-7, and ZIF-8, all of which adopt a zeolite-like nanoporous structure. Using inelastic neutron scattering and synchrotron radiation far-infrared absorption spectroscopy, in conjunction with density functional theory (DFT), we have pinpointed all major sources of vibrational modes. Ab initio DFT calculations revealed the complex nature of the collective THz modes, which enable us to establish detailed correlations with experiments. We discover that low-energy conformational dynamics offers multiple pathways to elucidate novel physical phenomena observed in MOFs. New evidence demonstrates that THz modes are intrinsically linked, not only to anomalous elasticity underpinning gate-opening and pore-breathing mechanisms, but also to shear-induced phase transitions and the onset of structural instability.

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.

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

The PO.DAAC Portal and its use of the Drupal Framework

NASA Astrophysics Data System (ADS)

Alarcon, C.; Huang, T.; Bingham, A.; Cosic, S.

2011-12-01

The Physical Oceanography Distributed Active Archive Center portal (http://podaac.jpl.nasa.gov) is the primary interface for discovering and accessing oceanographic datasets collected from the vantage point of space. In addition, it provides information about NASA's satellite missions and operational activities at the data center. Recently the portal underwent a major redesign and deployment utilizing the Drupal framework. The Drupal framework was chosen as the platform for the portal due to its flexibility, open source community, and modular infrastructure. The portal features efficient content addition and management, mailing lists, forums, role based access control, and a faceted dataset browse capability. The dataset browsing was built as a custom Drupal module and integrates with a SOLR search engine.

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.

Design and Implementation of a Modern Automatic Deformation Monitoring System

NASA Astrophysics Data System (ADS)

Engel, Philipp; Schweimler, Björn

2016-03-01

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

Urban Renewable Building And Neighborhood Optimization

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

URBANopt is a user interface for creating and running district and city scale building energy simulations. The framework is built around the OpenStudio Urban Measures which are part of the OpenStudio project. Building footprints, building height, building type, and other data can be imported from public records or other sources. Footprints and locations for new buildings and district systems can also be specified. OpenStudio Measures are used to create starting point energy models and to model energy design features and efficiency measures for each building. URBANopt allows a user to pose several scenarios such as “what if 30% of themore » commercial retail buildings added roof top solar” or “what if all elementary schools converted to ground source heat pumps” and then visualize the impacts at a district or city scale. URBANopt is capable of modeling existing buildings, new construction, and district energy systems. URBANopt can be used to explore options for achieving Zero Energy across a collection of buildings (e.g., Zero Energy Districts).« less

Global Dynamic Exposure and the OpenBuildingMap

NASA Astrophysics Data System (ADS)

Schorlemmer, D.; Beutin, T.; Hirata, N.; Hao, K. X.; Wyss, M.; Cotton, F.; Prehn, K.

2015-12-01

Detailed understanding of local risk factors regarding natural catastrophes requires in-depth characterization of the local exposure. Current exposure capture techniques have to find the balance between resolution and coverage. We aim at bridging this gap by employing a crowd-sourced approach to exposure capturing focusing on risk related to earthquake hazard. OpenStreetMap (OSM), the rich and constantly growing geographical database, is an ideal foundation for us. More than 2.5 billion geographical nodes, more than 150 million building footprints (growing by ~100'000 per day), and a plethora of information about school, hospital, and other critical facility locations allow us to exploit this dataset for risk-related computations. We will harvest this dataset by collecting exposure and vulnerability indicators from explicitly provided data (e.g. hospital locations), implicitly provided data (e.g. building shapes and positions), and semantically derived data, i.e. interpretation applying expert knowledge. With this approach, we can increase the resolution of existing exposure models from fragility classes distribution via block-by-block specifications to building-by-building vulnerability. To increase coverage, we will provide a framework for collecting building data by any person or community. We will implement a double crowd-sourced approach to bring together the interest and enthusiasm of communities with the knowledge of earthquake and engineering experts. The first crowd-sourced approach aims at collecting building properties in a community by local people and activists. This will be supported by tailored building capture tools for mobile devices for simple and fast building property capturing. The second crowd-sourced approach involves local experts in estimating building vulnerability that will provide building classification rules that translate building properties into vulnerability and exposure indicators as defined in the Building Taxonomy 2.0 developed by the Global Earthquake Model (GEM). These indicators will then be combined with a hazard model using the GEM OpenQuake engine to compute a risk model. The free/open framework we will provide can be used on commodity hardware for local to regional exposure capturing and for communities to understand their earthquake risk.

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.

Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya

PubMed Central

Tuti, Timothy; Bitok, Michael; Paton, Chris; Makone, Boniface; Malla, Lucas; Muinga, Naomi; Gathara, David; English, Mike

2016-01-01

Objective To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice. Materials and methods The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals’ pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals. Results In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use. Conclusion A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research. PMID:26063746

Innovating to enhance clinical data management using non-commercial and open source solutions across a multi-center network supporting inpatient pediatric care and research in Kenya.

PubMed

Tuti, Timothy; Bitok, Michael; Paton, Chris; Makone, Boniface; Malla, Lucas; Muinga, Naomi; Gathara, David; English, Mike

2016-01-01

To share approaches and innovations adopted to deliver a relatively inexpensive clinical data management (CDM) framework within a low-income setting that aims to deliver quality pediatric data useful for supporting research, strengthening the information culture and informing improvement efforts in local clinical practice. The authors implemented a CDM framework to support a Clinical Information Network (CIN) using Research Electronic Data Capture (REDCap), a noncommercial software solution designed for rapid development and deployment of electronic data capture tools. It was used for collection of standardized data from case records of multiple hospitals' pediatric wards. R, an open-source statistical language, was used for data quality enhancement, analysis, and report generation for the hospitals. In the first year of CIN, the authors have developed innovative solutions to support the implementation of a secure, rapid pediatric data collection system spanning 14 hospital sites with stringent data quality checks. Data have been collated on over 37 000 admission episodes, with considerable improvement in clinical documentation of admissions observed. Using meta-programming techniques in R, coupled with branching logic, randomization, data lookup, and Application Programming Interface (API) features offered by REDCap, CDM tasks were configured and automated to ensure quality data was delivered for clinical improvement and research use. A low-cost clinically focused but geographically dispersed quality CDM (Clinical Data Management) in a long-term, multi-site, and real world context can be achieved and sustained and challenges can be overcome through thoughtful design and implementation of open-source tools for handling data and supporting research. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

PLOCAN glider portal: a gateway for useful data management and visualization system

NASA Astrophysics Data System (ADS)

Morales, Tania; Lorenzo, Alvaro; Viera, Josue; Barrera, Carlos; José Rueda, María

2014-05-01

Nowadays monitoring ocean behavior and its characteristics involves a wide range of sources able to gather and provide a vast amount of data in spatio-temporal scales. Multiplatform infrastructures, like PLOCAN, hold a variety of autonomous Lagrangian and Eulerian devices addressed to collect information then transferred to land in near-real time. Managing all this data collection in an efficient way is a major issue. Advances in ocean observation technologies, where underwater autonomous gliders play a key role, has brought as a consequence an improvement of spatio-temporal resolution which offers a deeper understanding of the ocean but requires a bigger effort in the data management process. There are general requirements in terms of data management in that kind of environments, such as processing raw data at different levels to obtain valuable information, storing data coherently and providing accurate products to final users according to their specific needs. Managing large amount of data can be certainly tedious and complex without having right tools and operational procedures; hence automating these tasks through software applications saves time and reduces errors. Moreover, data distribution is highly relevant since scientist tent to assimilate different sources for comparison and validation. The use of web applications has boosted the necessary scientific dissemination. Within this argument, PLOCAN has implemented a set of independent but compatible applications to process, store and disseminate information gathered through different oceanographic platforms. These applications have been implemented using open standards, such as HTML and CSS, and open source software, like python as programming language and Django as framework web. More specifically, a glider application has been developed within the framework of FP7-GROOM project. Regarding data management, this project focuses on collecting and making available consistent and quality controlled datasets as well as fostering open access to glider data.

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

Stewart, Robert N.; Urban, Marie L.; Duchscherer, Samantha E.

Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the artmore » by introducing the Population Data Tables (PDT), a Bayesian based informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000ft2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.Understanding building occupancy is critical to a wide array of applications including natural hazards loss analysis, green building technologies, and population distribution modeling. Due to the expense of directly monitoring buildings, scientists rely in addition on a wide and disparate array of ancillary and open source information including subject matter expertise, survey data, and remote sensing information. These data are fused using data harmonization methods which refer to a loose collection of formal and informal techniques for fusing data together to create viable content for building occupancy estimation. In this paper, we add to the current state of the art by introducing the Population Data Tables (PDT), a Bayesian model and informatics system for systematically arranging data and harmonization techniques into a consistent, transparent, knowledge learning framework that retains in the final estimation uncertainty emerging from data, expert judgment, and model parameterization. PDT probabilistically estimates ambient occupancy in units of people/1000 ft 2 for over 50 building types at the national and sub-national level with the goal of providing global coverage. The challenge of global coverage led to the development of an interdisciplinary geospatial informatics system tool that provides the framework for capturing, storing, and managing open source data, handling subject matter expertise, carrying out Bayesian analytics as well as visualizing and exporting occupancy estimation results. We present the PDT project, situate the work within the larger community, and report on the progress of this multi-year project.« less

ABrowse--a customizable next-generation genome browser framework.

PubMed

Kong, Lei; Wang, Jun; Zhao, Shuqi; Gu, Xiaocheng; Luo, Jingchu; Gao, Ge

2012-01-05

With the rapid growth of genome sequencing projects, genome browser is becoming indispensable, not only as a visualization system but also as an interactive platform to support open data access and collaborative work. Thus a customizable genome browser framework with rich functions and flexible configuration is needed to facilitate various genome research projects. Based on next-generation web technologies, we have developed a general-purpose genome browser framework ABrowse which provides interactive browsing experience, open data access and collaborative work support. By supporting Google-map-like smooth navigation, ABrowse offers end users highly interactive browsing experience. To facilitate further data analysis, multiple data access approaches are supported for external platforms to retrieve data from ABrowse. To promote collaborative work, an online user-space is provided for end users to create, store and share comments, annotations and landmarks. For data providers, ABrowse is highly customizable and configurable. The framework provides a set of utilities to import annotation data conveniently. To build ABrowse on existing annotation databases, data providers could specify SQL statements according to database schema. And customized pages for detailed information display of annotation entries could be easily plugged in. For developers, new drawing strategies could be integrated into ABrowse for new types of annotation data. In addition, standard web service is provided for data retrieval remotely, providing underlying machine-oriented programming interface for open data access. ABrowse framework is valuable for end users, data providers and developers by providing rich user functions and flexible customization approaches. The source code is published under GNU Lesser General Public License v3.0 and is accessible at http://www.abrowse.org/. To demonstrate all the features of ABrowse, a live demo for Arabidopsis thaliana genome has been built at http://arabidopsis.cbi.edu.cn/.

Using Feedback from Data Consumers to Capture Quality Information on Environmental Research Data

NASA Astrophysics Data System (ADS)

Devaraju, A.; Klump, J. F.

2015-12-01

Data quality information is essential to facilitate reuse of Earth science data. Recorded quality information must be sufficient for other researchers to select suitable data sets for their analysis and confirm the results and conclusions. In the research data ecosystem, several entities are responsible for data quality. Data producers (researchers and agencies) play a major role in this aspect as they often include validation checks or data cleaning as part of their work. It is possible that the quality information is not supplied with published data sets; if it is available, the descriptions might be incomplete, ambiguous or address specific quality aspects. Data repositories have built infrastructures to share data, but not all of them assess data quality. They normally provide guidelines of documenting quality information. Some suggests that scholarly and data journals should take a role in ensuring data quality by involving reviewers to assess data sets used in articles, and incorporating data quality criteria in the author guidelines. However, this mechanism primarily addresses data sets submitted to journals. We believe that data consumers will complement existing entities to assess and document the quality of published data sets. This has been adopted in crowd-source platforms such as Zooniverse, OpenStreetMap, Wikipedia, Mechanical Turk and Tomnod. This paper presents a framework designed based on open source tools to capture and share data users' feedback on the application and assessment of research data. The framework comprises a browser plug-in, a web service and a data model such that feedback can be easily reported, retrieved and searched. The feedback records are also made available as Linked Data to promote integration with other sources on the Web. Vocabularies from Dublin Core and PROV-O are used to clarify the source and attribution of feedback. The application of the framework is illustrated with the CSIRO's Data Access Portal.

Heterogeneous compute in computer vision: OpenCL in OpenCV

NASA Astrophysics Data System (ADS)

Gasparakis, Harris

2014-02-01

We explore the relevance of Heterogeneous System Architecture (HSA) in Computer Vision, both as a long term vision, and as a near term emerging reality via the recently ratified OpenCL 2.0 Khronos standard. After a brief review of OpenCL 1.2 and 2.0, including HSA features such as Shared Virtual Memory (SVM) and platform atomics, we identify what genres of Computer Vision workloads stand to benefit by leveraging those features, and we suggest a new mental framework that replaces GPU compute with hybrid HSA APU compute. As a case in point, we discuss, in some detail, popular object recognition algorithms (part-based models), emphasizing the interplay and concurrent collaboration between the GPU and CPU. We conclude by describing how OpenCL has been incorporated in OpenCV, a popular open source computer vision library, emphasizing recent work on the Transparent API, to appear in OpenCV 3.0, which unifies the native CPU and OpenCL execution paths under a single API, allowing the same code to execute either on CPU or on a OpenCL enabled device, without even recompiling.

Federated querying architecture with clinical & translational health IT application.

PubMed

Livne, Oren E; Schultz, N Dustin; Narus, Scott P

2011-10-01

We present a software architecture that federates data from multiple heterogeneous health informatics data sources owned by multiple organizations. The architecture builds upon state-of-the-art open-source Java and XML frameworks in innovative ways. It consists of (a) federated query engine, which manages federated queries and result set aggregation via a patient identification service; and (b) data source facades, which translate the physical data models into a common model on-the-fly and handle large result set streaming. System modules are connected via reusable Apache Camel integration routes and deployed to an OSGi enterprise service bus. We present an application of our architecture that allows users to construct queries via the i2b2 web front-end, and federates patient data from the University of Utah Enterprise Data Warehouse and the Utah Population database. Our system can be easily adopted, extended and integrated with existing SOA Healthcare and HL7 frameworks such as i2b2 and caGrid.

An open framework for automated chemical hazard assessment based on GreenScreen for Safer Chemicals: A proof of concept.

PubMed

Wehage, Kristopher; Chenhansa, Panan; Schoenung, Julie M

2017-01-01

GreenScreen® for Safer Chemicals is a framework for comparative chemical hazard assessment. It is the first transparent, open and publicly accessible framework of its kind, allowing manufacturers and governmental agencies to make informed decisions about the chemicals and substances used in consumer products and buildings. In the GreenScreen® benchmarking process, chemical hazards are assessed and classified based on 18 hazard endpoints from up to 30 different sources. The result is a simple numerical benchmark score and accompanying assessment report that allows users to flag chemicals of concern and identify safer alternatives. Although the screening process is straightforward, aggregating and sorting hazard data is tedious, time-consuming, and prone to human error. In light of these challenges, the present work demonstrates the usage of automation to cull chemical hazard data from publicly available internet resources, assign metadata, and perform a GreenScreen® hazard assessment using the GreenScreen® "List Translator." The automated technique, written as a module in the Python programming language, generates GreenScreen® List Translation data for over 3000 chemicals in approximately 30 s. Discussion of the potential benefits and limitations of automated techniques is provided. By embedding the library into a web-based graphical user interface, the extensibility of the library is demonstrated. The accompanying source code is made available to the hazard assessment community. Integr Environ Assess Manag 2017;13:167-176. © 2016 SETAC. © 2016 SETAC.

An open-source framework for analyzing N-electron dynamics. II. Hybrid density functional theory/configuration interaction methodology.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe

2017-10-30

In this contribution, we extend our framework for analyzing and visualizing correlated many-electron dynamics to non-variational, highly scalable electronic structure method. Specifically, an explicitly time-dependent electronic wave packet is written as a linear combination of N-electron wave functions at the configuration interaction singles (CIS) level, which are obtained from a reference time-dependent density functional theory (TDDFT) calculation. The procedure is implemented in the open-source Python program detCI@ORBKIT, which extends the capabilities of our recently published post-processing toolbox (Hermann et al., J. Comput. Chem. 2016, 37, 1511). From the output of standard quantum chemistry packages using atom-centered Gaussian-type basis functions, the framework exploits the multideterminental structure of the hybrid TDDFT/CIS wave packet to compute fundamental one-electron quantities such as difference electronic densities, transient electronic flux densities, and transition dipole moments. The hybrid scheme is benchmarked against wave function data for the laser-driven state selective excitation in LiH. It is shown that all features of the electron dynamics are in good quantitative agreement with the higher-level method provided a judicious choice of functional is made. Broadband excitation of a medium-sized organic chromophore further demonstrates the scalability of the method. In addition, the time-dependent flux densities unravel the mechanistic details of the simulated charge migration process at a glance. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Impacts and Viability of Open Source Software on Earth Science Metadata Clearing House and Service Registry Applications

NASA Astrophysics Data System (ADS)

Pilone, D.; Cechini, M. F.; Mitchell, A.

2011-12-01

Earth Science applications typically deal with large amounts of data and high throughput rates, if not also high transaction rates. While Open Source is frequently used for smaller scientific applications, large scale, highly available systems frequently fall back to "enterprise" class solutions like Oracle RAC or commercial grade JEE Application Servers. NASA's Earth Observing System Data and Information System (EOSDIS) provides end-to-end capabilities for managing NASA's Earth science data from multiple sources - satellites, aircraft, field measurements, and various other programs. A core capability of EOSDIS, the Earth Observing System (EOS) Clearinghouse (ECHO), is a highly available search and order clearinghouse of over 100 million pieces of science data that has evolved from its early R&D days to a fully operational system. Over the course of this maturity ECHO has largely transitioned from commercial frameworks, databases, and operating systems to Open Source solutions...and in some cases, back. In this talk we discuss the progression of our technological solutions and our lessons learned in the areas of: ? High performance, large scale searching solutions ? GeoSpatial search capabilities and dealing with multiple coordinate systems ? Search and storage of variable format source (science) data ? Highly available deployment solutions ? Scalable (elastic) solutions to visual searching and image handling Throughout the evolution of the ECHO system we have had to evaluate solutions with respect to performance, cost, developer productivity, reliability, and maintainability in the context of supporting global science users. Open Source solutions have played a significant role in our architecture and development but several critical commercial components remain (or have been reinserted) to meet our operational demands.

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

NASA Astrophysics Data System (ADS)

Carniel, Roberto; Di Cecca, Mauro; Jaquet, Olivier

2006-05-01

In the framework of the EU-funded project "Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard" (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

pyBadlands: A framework to simulate sediment transport, landscape dynamics and basin stratigraphic evolution through space and time

PubMed Central

2018-01-01

Understanding Earth surface responses in terms of sediment dynamics to climatic variability and tectonics forcing is hindered by limited ability of current models to simulate long-term evolution of sediment transfer and associated morphological changes. This paper presents pyBadlands, an open-source python-based framework which computes over geological time (1) sediment transport from landmasses to coasts, (2) reworking of marine sediments by longshore currents and (3) development of coral reef systems. pyBadlands is cross-platform, distributed under the GPLv3 license and available on GitHub (http://github.com/badlands-model). Here, we describe the underlying physical assumptions behind the simulated processes and the main options already available in the numerical framework. Along with the source code, a list of hands-on examples is provided that illustrates the model capabilities. In addition, pre and post-processing classes have been built and are accessible as a companion toolbox which comprises a series of workflows to efficiently build, quantify and explore simulation input and output files. While the framework has been primarily designed for research, its simplicity of use and portability makes it a great tool for teaching purposes. PMID:29649301

Enabling a systems biology knowledgebase with gaggle and firegoose

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

Baliga, Nitin S.

The overall goal of this project was to extend the existing Gaggle and Firegoose systems to develop an open-source technology that runs over the web and links desktop applications with many databases and software applications. This technology would enable researchers to incorporate workflows for data analysis that can be executed from this interface to other online applications. The four specific aims were to (1) provide one-click mapping of genes, proteins, and complexes across databases and species; (2) enable multiple simultaneous workflows; (3) expand sophisticated data analysis for online resources; and enhance open-source development of the Gaggle-Firegoose infrastructure. Gaggle is anmore » open-source Java software system that integrates existing bioinformatics programs and data sources into a user-friendly, extensible environment to allow interactive exploration, visualization, and analysis of systems biology data. Firegoose is an extension to the Mozilla Firefox web browser that enables data transfer between websites and desktop tools including Gaggle. In the last phase of this funding period, we have made substantial progress on development and application of the Gaggle integration framework. We implemented the workspace to the Network Portal. Users can capture data from Firegoose and save them to the workspace. Users can create workflows to start multiple software components programmatically and pass data between them. Results of analysis can be saved to the cloud so that they can be easily restored on any machine. We also developed the Gaggle Chrome Goose, a plugin for the Google Chrome browser in tandem with an opencpu server in the Amazon EC2 cloud. This allows users to interactively perform data analysis on a single web page using the R packages deployed on the opencpu server. The cloud-based framework facilitates collaboration between researchers from multiple organizations. We have made a number of enhancements to the cmonkey2 application to enable and improve the integration within different environments, and we have created a new tools pipeline for generating EGRIN2 models in a largely automated way.« less

Zephyr: Open-source Parallel Seismic Waveform Inversion in an Integrated Python-based Framework

NASA Astrophysics Data System (ADS)

Smithyman, B. R.; Pratt, R. G.; Hadden, S. M.

2015-12-01

Seismic Full-Waveform Inversion (FWI) is an advanced method to reconstruct wave properties of materials in the Earth from a series of seismic measurements. These methods have been developed by researchers since the late 1980s, and now see significant interest from the seismic exploration industry. As researchers move towards implementing advanced numerical modelling (e.g., 3D, multi-component, anisotropic and visco-elastic physics), it is desirable to make use of a modular approach, minimizing the effort developing a new set of tools for each new numerical problem. SimPEG (http://simpeg.xyz) is an open source project aimed at constructing a general framework to enable geophysical inversion in various domains. In this abstract we describe Zephyr (https://github.com/bsmithyman/zephyr), which is a coupled research project focused on parallel FWI in the seismic context. The software is built on top of Python, Numpy and IPython, which enables very flexible testing and implementation of new features. Zephyr is an open source project, and is released freely to enable reproducible research. We currently implement a parallel, distributed seismic forward modelling approach that solves the 2.5D (two-and-one-half dimensional) viscoacoustic Helmholtz equation at a range modelling frequencies, generating forward solutions for a given source behaviour, and gradient solutions for a given set of observed data. Solutions are computed in a distributed manner on a set of heterogeneous workers. The researcher's frontend computer may be separated from the worker cluster by a network link to enable full support for computation on remote clusters from individual workstations or laptops. The present codebase introduces a numerical discretization equivalent to that used by FULLWV, a well-known seismic FWI research codebase. This makes it straightforward to compare results from Zephyr directly with FULLWV. The flexibility introduced by the use of a Python programming environment makes extension of the codebase with new methods much more straightforward. This enables comparison and integration of new efforts with existing results.

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

NASA Astrophysics Data System (ADS)

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

2015-05-01

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

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

Vision Based Autonomous Robotic Control for Advanced Inspection and Repair

NASA Technical Reports Server (NTRS)

Wehner, Walter S.

2014-01-01

The advanced inspection system is an autonomous control and analysis system that improves the inspection and remediation operations for ground and surface systems. It uses optical imaging technology with intelligent computer vision algorithms to analyze physical features of the real-world environment to make decisions and learn from experience. The advanced inspection system plans to control a robotic manipulator arm, an unmanned ground vehicle and cameras remotely, automatically and autonomously. There are many computer vision, image processing and machine learning techniques available as open source for using vision as a sensory feedback in decision-making and autonomous robotic movement. My responsibilities for the advanced inspection system are to create a software architecture that integrates and provides a framework for all the different subsystem components; identify open-source algorithms and techniques; and integrate robot hardware.

Harvest: a web-based biomedical data discovery and reporting application development platform.

PubMed

Italia, Michael J; Pennington, Jeffrey W; Ruth, Byron; Wrazien, Stacey; Loutrel, Jennifer G; Crenshaw, E Bryan; Miller, Jeffrey; White, Peter S

2013-01-01

Biomedical researchers share a common challenge of making complex data understandable and accessible. This need is increasingly acute as investigators seek opportunities for discovery amidst an exponential growth in the volume and complexity of laboratory and clinical data. To address this need, we developed Harvest, an open source framework that provides a set of modular components to aid the rapid development and deployment of custom data discovery software applications. Harvest incorporates visual representations of multidimensional data types in an intuitive, web-based interface that promotes a real-time, iterative approach to exploring complex clinical and experimental data. The Harvest architecture capitalizes on standards-based, open source technologies to address multiple functional needs critical to a research and development environment, including domain-specific data modeling, abstraction of complex data models, and a customizable web client.

An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics

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

Taylor, Ronald C.

Bioinformatics researchers are increasingly confronted with analysis of ultra large-scale data sets, a problem that will only increase at an alarming rate in coming years. Recent developments in open source software, that is, the Hadoop project and associated software, provide a foundation for scaling to petabyte scale data warehouses on Linux clusters, providing fault-tolerant parallelized analysis on such data using a programming style named MapReduce. An overview is given of the current usage within the bioinformatics community of Hadoop, a top-level Apache Software Foundation project, and of associated open source software projects. The concepts behind Hadoop and the associated HBasemore » project are defined, and current bioinformatics software that employ Hadoop is described. The focus is on next-generation sequencing, as the leading application area to date.« less

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

2016-11-02

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

Students' Use of the Energy Model to Account for Changes in Physical Systems

ERIC Educational Resources Information Center

Papadouris, Nico; Constantinou, Constantinos P.; Kyratsi, Theodora

2008-01-01

The aim of this study is to explore the ways in which students, aged 11-14 years, account for certain changes in physical systems and the extent to which they draw on an energy model as a common framework for explaining changes observed in diverse systems. Data were combined from two sources: interviews with 20 individuals and an open-ended…

A Model for an Open and Flexible E-Training Platform To Encourage Companies' Learning Culture and Meet Employees' Learning Needs.

ERIC Educational Resources Information Center

Bagnasco, Andrea; Chirico, Marco; Parodi, Giancarlo; Scapolla, A. Marina

2003-01-01

Distance education is an answer to the demand for flexibility in training. The aim is to build a virtual learning community on the basis of a knowledge model that meets different learning needs. This article analyzes possible innovations in corporate training, and proposes a framework that integrates all information sources and offers practice…

Design, implementation and validation of a novel open framework for agile development of mobile health applications.

PubMed

Banos, Oresti; Villalonga, Claudia; Garcia, Rafael; Saez, Alejandro; Damas, Miguel; Holgado-Terriza, Juan A; Lee, Sungyong; Pomares, Hector; Rojas, Ignacio

2015-01-01

The delivery of healthcare services has experienced tremendous changes during the last years. Mobile health or mHealth is a key engine of advance in the forefront of this revolution. Although there exists a growing development of mobile health applications, there is a lack of tools specifically devised for their implementation. This work presents mHealthDroid, an open source Android implementation of a mHealth Framework designed to facilitate the rapid and easy development of mHealth and biomedical apps. The framework is particularly planned to leverage the potential of mobile devices such as smartphones or tablets, wearable sensors and portable biomedical systems. These devices are increasingly used for the monitoring and delivery of personal health care and wellbeing. The framework implements several functionalities to support resource and communication abstraction, biomedical data acquisition, health knowledge extraction, persistent data storage, adaptive visualization, system management and value-added services such as intelligent alerts, recommendations and guidelines. An exemplary application is also presented along this work to demonstrate the potential of mHealthDroid. This app is used to investigate on the analysis of human behavior, which is considered to be one of the most prominent areas in mHealth. An accurate activity recognition model is developed and successfully validated in both offline and online conditions.

Framework GRASP: routine library for optimize processing of aerosol remote sensing observation

NASA Astrophysics Data System (ADS)

Fuertes, David; Torres, Benjamin; Dubovik, Oleg; Litvinov, Pavel; Lapyonok, Tatyana; Ducos, Fabrice; Aspetsberger, Michael; Federspiel, Christian

The present the development of a Framework for the Generalized Retrieval of Aerosol and Surface Properties (GRASP) developed by Dubovik et al., (2011). The framework is a source code project that attempts to strengthen the value of the GRASP inversion algorithm by transforming it into a library that will be used later for a group of customized application modules. The functions of the independent modules include the managing of the configuration of the code execution, as well as preparation of the input and output. The framework provides a number of advantages in utilization of the code. First, it implements loading data to the core of the scientific code directly from memory without passing through intermediary files on disk. Second, the framework allows consecutive use of the inversion code without the re-initiation of the core routine when new input is received. These features are essential for optimizing performance of the data production in processing of large observation sets, such as satellite images by the GRASP. Furthermore, the framework is a very convenient tool for further development, because this open-source platform is easily extended for implementing new features. For example, it could accommodate loading of raw data directly onto the inversion code from a specific instrument not included in default settings of the software. Finally, it will be demonstrated that from the user point of view, the framework provides a flexible, powerful and informative configuration system.

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.

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.

The Wildland Fire Emissions Information System: Providing information for carbon cycle studies with open source geospatial tools

NASA Astrophysics Data System (ADS)

French, N. H.; Erickson, T.; McKenzie, D.

2008-12-01

A major goal of the North American Carbon Program is to resolve uncertainties in understanding and managing the carbon cycle of North America. As carbon modeling tools become more comprehensive and spatially oriented, accurate datasets to spatially quantify carbon emissions from fire are needed, and these data resources need to be accessible to users for decision-making. Under a new NASA Carbon Cycle Science project, Drs. Nancy French and Tyler Erickson, of the Michigan Technological University, Michigan Tech Research Institute (MTRI), are teaming with specialists with the USDA Forest Service Fire and Environmental Research Applications (FERA) team to provide information for mapping fire-derived carbon emissions to users. The project focus includes development of a web-based system to provide spatially resolved fire emissions estimates for North America in a user-friendly environment. The web-based Decision Support System will be based on a variety of open source technologies. The Fuel Characteristic Classification System (FCCS) raster map of fuels and MODIS-derived burned area vector maps will be processed using the Geographic Data Abstraction Library (GDAL) and OGR Simple Features Library. Tabular and spatial project data will be stored in a PostgreSQL/PostGIS, a spatially enabled relational database server. The browser-based user interface will be created using the Django web page framework to allow user input for the decision support system. The OpenLayers mapping framework will be used to provide users with interactive maps within the browser. In addition, the data products will be made available in standard open data formats such as KML, to allow for easy integration into other spatial models and data systems.

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

PubMed

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

2013-07-01

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

GDAL Enhancements for Interoperability with EOS Data (GEE)

NASA Astrophysics Data System (ADS)

Tisdale, B.

2015-12-01

Historically, Earth Observing Satellite (EOS) data products have been difficult to consume by GIS tools, weather commercial or open-source. This has resulted in a reduced acceptance of these data products by GIS and general user communities. Common problems and challenges experienced by these data users include difficulty when: Consuming data products from NASA Distributed Active Archive Centers (DAACs) that pre-date modern application software with commercial and open-source geospatial tools; Identifying[MI1] an initial approach for developing a framework and plug-ins that interpret non-compliant data; Defining a methodology that is extensible across NASA Earth Observing System Data and Information System (EOSDIS), scientific communities, and GIS communities by enabling other data centers to construct their own plug-ins and adjust specific data products; and Promoting greater use of NASA Data and new analysis utilizing GIS tools. To address these challenges and make EOS data products more accessible and interpretable by GIS applications, a collaborative approach has been taken that includes the NASA Langley Atmospheric Science Data Center (ASDC), Esri, George Mason University (GMU), and the Hierarchical Data Format (HDF) Group to create a framework and plugins to be applied to Geospatial Data Abstraction Library (GDAL). This framework and its plugins offer advantages of extensibility within NASA EOSDIS, permitting other data centers to construct their own plugins necessary to adjust their data products. In this session findings related to the framework and the development of GDAL plugins will be reviewed. Specifically, this session will offer a workshop to review documentation and training materials that have been generated for the purpose of guiding other NASA DAACs through the process of constructing plug-ins consistent with the framework as well as a review of the certification process by which the plugins can be independently verified as properly converting the data to the format and content required for use in GIS software.

GDAL Enhancements for Interoperability with EOS Data

NASA Astrophysics Data System (ADS)

Tisdale, M.; Mathews, T. J.; Tisdale, B.; Sun, M.; Yang, C. P.; Lee, H.; Habermann, T.

2015-12-01

Historically, Earth Observing Satellite (EOS) data products have been difficult to consume by GIS tools, weather commercial or open-source. This has resulted in a reduced acceptance of these data products by GIS and general user communities. Common problems and challenges experienced by these data users include difficulty when: Consuming data products from NASA Distributed Active Archive Centers (DAACs) that pre-date modern application software with commercial and open-source geospatial tools; Identifying an initial approach for developing a framework and plug-ins that interpret non-compliant data; Defining a methodology that is extensible across NASA Earth Observing System Data and Information System (EOSDIS), scientific communities, and GIS communities by enabling other data centers to construct their own plug-ins and adjust specific data products; and Promoting greater use of NASA Data and new analysis utilizing GIS tools. To address these challenges and to make EOS data products more accessible and interpretable by GIS applications, a collaborative approach has been taken that includes the NASA Langley Atmospheric Science Data Center (ASDC), Esri, George Mason University (GMU), and the Hierarchical Data Format (HDF) Group to create a framework and plugins to be applied to Geospatial Data Abstraction Library (GDAL). This framework and its plugins offer advantages of extensibility within NASA EOSDIS, permitting other data centers to construct their own plugins necessary to adjust their data products. In this session findings related to the framework and the development of GDAL plugins will be reviewed. Specifically, this session will offer a workshop to review documentation and training materials that have been generated for the purpose of guiding other NASA DAACs through the process of constructing plug-ins consistent with the framework as well as a review of the certification process by which the plugins can be independently verified as properly converting the data to the format and content required for use in GIS software.

Advanced Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Technical Exchange Meeting

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

Smith, Curtis

2013-09-01

During FY13, the INL developed an advanced SMR PRA framework which has been described in the report Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Detailed Technical Framework Specification, INL/EXT-13-28974 (April 2013). In this framework, the various areas are considered: Probabilistic models to provide information specific to advanced SMRs Representation of specific SMR design issues such as having co-located modules and passive safety features Use of modern open-source and readily available analysis methods Internal and external events resulting in impacts to safety All-hazards considerations Methods to support the identification of design vulnerabilities Mechanistic and probabilistic data needs to support modelingmore » and tools In order to describe this framework more fully and obtain feedback on the proposed approaches, the INL hosted a technical exchange meeting during August 2013. This report describes the outcomes of that meeting.« less

Patient-controlled sharing of medical imaging data across unaffiliated healthcare organizations

PubMed Central

Ahn, David K; Unde, Bhagyashree; Gage, H Donald; Carr, J Jeffrey

2013-01-01

Background Current image sharing is carried out by manual transportation of CDs by patients or organization-coordinated sharing networks. The former places a significant burden on patients and providers. The latter faces challenges to patient privacy. Objective To allow healthcare providers efficient access to medical imaging data acquired at other unaffiliated healthcare facilities while ensuring strong protection of patient privacy and minimizing burden on patients, providers, and the information technology infrastructure. Methods An image sharing framework is described that involves patients as an integral part of, and with full control of, the image sharing process. Central to this framework is the Patient Controlled Access-key REgistry (PCARE) which manages the access keys issued by image source facilities. When digitally signed by patients, the access keys are used by any requesting facility to retrieve the associated imaging data from the source facility. A centralized patient portal, called a PCARE patient control portal, allows patients to manage all the access keys in PCARE. Results A prototype of the PCARE framework has been developed by extending open-source technology. The results for feasibility, performance, and user assessments are encouraging and demonstrate the benefits of patient-controlled image sharing. Discussion The PCARE framework is effective in many important clinical cases of image sharing and can be used to integrate organization-coordinated sharing networks. The same framework can also be used to realize a longitudinal virtual electronic health record. Conclusion The PCARE framework allows prior imaging data to be shared among unaffiliated healthcare facilities while protecting patient privacy with minimal burden on patients, providers, and infrastructure. A prototype has been implemented to demonstrate the feasibility and benefits of this approach. PMID:22886546

Fluid-structure coupling for wind turbine blade analysis using OpenFOAM

NASA Astrophysics Data System (ADS)

Dose, Bastian; Herraez, Ivan; Peinke, Joachim

2015-11-01

Modern wind turbine rotor blades are designed increasingly large and flexible. This structural flexibility represents a problem for the field of Computational Fluid Dynamics (CFD), which is used for accurate load calculations and detailed investigations of rotor aerodynamics. As the blade geometries within CFD simulations are considered stiff, the effect of blade deformation caused by aerodynamic loads cannot be captured by the common CFD approach. Coupling the flow solver with a structural solver can overcome this restriction and enables the investigation of flexible wind turbine blades. For this purpose, a new Finite Element (FE) solver was implemented into the open source CFD code OpenFOAM. Using a beam element formulation based on the Geometrically Exact Beam Theory (GEBT), the structural model can capture geometric non-linearities such as large deformations. Coupled with CFD solvers of the OpenFOAM package, the new framework represents a powerful tool for aerodynamic investigations. In this work, we investigated the aerodynamic performance of a state of the art wind turbine. For different wind speeds, aerodynamic key parameters are evaluated and compared for both, rigid and flexible blade geometries. The present work is funded within the framework of the joint project Smart Blades (0325601D) by the German Federal Ministry for Economic Affairs and Energy (BMWi) under decision of the German Federal Parliament.

A framework for integration of scientific applications into the OpenTopography workflow

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

ProjectQ Software Framework

NASA Astrophysics Data System (ADS)

Steiger, Damian S.; Haener, Thomas; Troyer, Matthias

Quantum computers promise to transform our notions of computation by offering a completely new paradigm. A high level quantum programming language and optimizing compilers are essential components to achieve scalable quantum computation. In order to address this, we introduce the ProjectQ software framework - an open source effort to support both theorists and experimentalists by providing intuitive tools to implement and run quantum algorithms. Here, we present our ProjectQ quantum compiler, which compiles a quantum algorithm from our high-level Python-embedded language down to low-level quantum gates available on the target system. We demonstrate how this compiler can be used to control actual hardware and to run high-performance simulations.

ProjectQ: Compiling quantum programs for various backends

NASA Astrophysics Data System (ADS)

Haener, Thomas; Steiger, Damian S.; Troyer, Matthias

In order to control quantum computers beyond the current generation, a high level quantum programming language and optimizing compilers will be essential. Therefore, we have developed ProjectQ - an open source software framework to facilitate implementing and running quantum algorithms both in software and on actual quantum hardware. Here, we introduce the backends available in ProjectQ. This includes a high-performance simulator and emulator to test and debug quantum algorithms, tools for resource estimation, and interfaces to several small-scale quantum devices. We demonstrate the workings of the framework and show how easily it can be further extended to control upcoming quantum hardware.

Computer Simulation of the VASIMR Engine

NASA Technical Reports Server (NTRS)

Garrison, David

2005-01-01

The goal of this project is to develop a magneto-hydrodynamic (MHD) computer code for simulation of the VASIMR engine. This code is designed be easy to modify and use. We achieve this using the Cactus framework, a system originally developed for research in numerical relativity. Since its release, Cactus has become an extremely powerful and flexible open source framework. The development of the code will be done in stages, starting with a basic fluid dynamic simulation and working towards a more complex MHD code. Once developed, this code can be used by students and researchers in order to further test and improve the VASIMR engine.

A Computational Framework for Automation of Point Defect Calculations

NASA Astrophysics Data System (ADS)

Goyal, Anuj; Gorai, Prashun; Peng, Haowei; Lany, Stephan; Stevanovic, Vladan; National Renewable Energy Laboratory, Golden, Colorado 80401 Collaboration

A complete and rigorously validated open-source Python framework to automate point defect calculations using density functional theory has been developed. The framework provides an effective and efficient method for defect structure generation, and creation of simple yet customizable workflows to analyze defect calculations. The package provides the capability to compute widely accepted correction schemes to overcome finite-size effects, including (1) potential alignment, (2) image-charge correction, and (3) band filling correction to shallow defects. Using Si, ZnO and In2O3as test examples, we demonstrate the package capabilities and validate the methodology. We believe that a robust automated tool like this will enable the materials by design community to assess the impact of point defects on materials performance. National Renewable Energy Laboratory, Golden, Colorado 80401.

SysSon - A Framework for Systematic Sonification Design

NASA Astrophysics Data System (ADS)

Vogt, Katharina; Goudarzi, Visda; Holger Rutz, Hanns

2015-04-01

SysSon is a research approach on introducing sonification systematically to a scientific community where it is not yet commonly used - e.g., in climate science. Thereby, both technical and socio-cultural barriers have to be met. The approach was further developed with climate scientists, who participated in contextual inquiries, usability tests and a workshop of collaborative design. Following from these extensive user tests resulted our final software framework. As frontend, a graphical user interface allows climate scientists to parametrize standard sonifications with their own data sets. Additionally, an interactive shell allows to code new sonifications for users competent in sound design. The framework is a standalone desktop application, available as open source (for details see http://sysson.kug.ac.at/) and works with data in NetCDF format.

Developing a low-cost open-source CTD for research and outreach

NASA Astrophysics Data System (ADS)

Thaler, A. D.; Sturdivant, K.

2013-12-01

Developing a low-cost open-source CTD for research and outreach Andrew David Thaler and Kersey Sturdivant Conductivity, temperature, and depth (CTD). With these three measurements, marine scientists can unlock ocean patterns hidden beneath the waves. The ocean is not uniform, it its filled with swirling eddies, temperature boundaries, layers of high and low salinity, changing densities, and many other physical characteristics. To reveal these patterns, oceanographers use a tool called the CTD. A CTD is found on almost every major research vessel. Rare is the scientific expedition-whether it be coastal work in shallow estuaries or journeys to the deepest ocean trenches-that doesn't begin with the humble CTD cast. The CTD is not cheap. Commercial CTD's start at more the 5,000 and can climb as high as 25,000 or more. We believe that the prohibitive cost of a CTD is an unacceptable barrier to open science. The price tag excludes individuals and groups who lack research grants or significant private funds from conducting oceanographic research. We want to make this tool-the workhorse of oceanographic research-available to anyone with an interest in the oceans. The OpenCTD is a low-cost, open-source CTD suitable for both educators and scientists. The platform is built using readily available parts and is powered by an Arduino-based microcontroller. Our goal is to create a device that is accurate enough to be used for scientific research and can be constructed for less than $200. Source codes, circuit diagrams, and building plans will be freely available. The final instrument will be effective to 200 meters depth. Why 200 meters? For many coastal regions, 200 meters of water depth covers the majority of the ocean that is accessible by small boat. The OpenCTD is targeted to people working in this niche, where entire research projects can be conducted for less than the cost of a commercial CTD. However, the Open CTD is scalable, and anyone with the inclination can adapt our plans to operate in deeper waters. Through a crowdfunding initiative and collaboration with numerous interested scientists, researchers, educators, and developers, we developed the framework for a low-cost, open-source, CTD that is appropriate for both scientific research and public outreach. We envision a network or researchers and educators using the OpenCTD to contribute to local and region scientific programs through open-source databases.

BioASF: a framework for automatically generating executable pathway models specified in BioPAX.

PubMed

Haydarlou, Reza; Jacobsen, Annika; Bonzanni, Nicola; Feenstra, K Anton; Abeln, Sanne; Heringa, Jaap

2016-06-15

Biological pathways play a key role in most cellular functions. To better understand these functions, diverse computational and cell biology researchers use biological pathway data for various analysis and modeling purposes. For specifying these biological pathways, a community of researchers has defined BioPAX and provided various tools for creating, validating and visualizing BioPAX models. However, a generic software framework for simulating BioPAX models is missing. Here, we attempt to fill this gap by introducing a generic simulation framework for BioPAX. The framework explicitly separates the execution model from the model structure as provided by BioPAX, with the advantage that the modelling process becomes more reproducible and intrinsically more modular; this ensures natural biological constraints are satisfied upon execution. The framework is based on the principles of discrete event systems and multi-agent systems, and is capable of automatically generating a hierarchical multi-agent system for a given BioPAX model. To demonstrate the applicability of the framework, we simulated two types of biological network models: a gene regulatory network modeling the haematopoietic stem cell regulators and a signal transduction network modeling the Wnt/β-catenin signaling pathway. We observed that the results of the simulations performed using our framework were entirely consistent with the simulation results reported by the researchers who developed the original models in a proprietary language. The framework, implemented in Java, is open source and its source code, documentation and tutorial are available at http://www.ibi.vu.nl/programs/BioASF CONTACT: j.heringa@vu.nl. © The Author 2016. Published by Oxford University Press.

Image Harvest: an open-source platform for high-throughput plant image processing and analysis

PubMed Central

Knecht, Avi C.; Campbell, Malachy T.; Caprez, Adam; Swanson, David R.; Walia, Harkamal

2016-01-01

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets. PMID:27141917

Plenario: An Open Data Discovery and Exploration Platform for Urban Science

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

Catlett, Charlie; Malik, Tanu; Goldstein, Brett J.

2014-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous po- tential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily dif- ficult, due to decentralized storage, heterogeneous formats, and poor documentation. Inmore » this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.« less

An open-source framework for stress-testing non-invasive foetal ECG extraction algorithms.

PubMed

Andreotti, Fernando; Behar, Joachim; Zaunseder, Sebastian; Oster, Julien; Clifford, Gari D

2016-05-01

Over the past decades, many studies have been published on the extraction of non-invasive foetal electrocardiogram (NI-FECG) from abdominal recordings. Most of these contributions claim to obtain excellent results in detecting foetal QRS (FQRS) complexes in terms of location. A small subset of authors have investigated the extraction of morphological features from the NI-FECG. However, due to the shortage of available public databases, the large variety of performance measures employed and the lack of open-source reference algorithms, most contributions cannot be meaningfully assessed. This article attempts to address these issues by presenting a standardised methodology for stress testing NI-FECG algorithms, including absolute data, as well as extraction and evaluation routines. To that end, a large database of realistic artificial signals was created, totaling 145.8 h of multichannel data and over one million FQRS complexes. An important characteristic of this dataset is the inclusion of several non-stationary events (e.g. foetal movements, uterine contractions and heart rate fluctuations) that are critical for evaluating extraction routines. To demonstrate our testing methodology, three classes of NI-FECG extraction algorithms were evaluated: blind source separation (BSS), template subtraction (TS) and adaptive methods (AM). Experiments were conducted to benchmark the performance of eight NI-FECG extraction algorithms on the artificial database focusing on: FQRS detection and morphological analysis (foetal QT and T/QRS ratio). The overall median FQRS detection accuracies (i.e. considering all non-stationary events) for the best performing methods in each group were 99.9% for BSS, 97.9% for AM and 96.0% for TS. Both FQRS detections and morphological parameters were shown to heavily depend on the extraction techniques and signal-to-noise ratio. Particularly, it is shown that their evaluation in the source domain, obtained after using a BSS technique, should be avoided. Data, extraction algorithms and evaluation routines were released as part of the fecgsyn toolbox on Physionet under an GNU GPL open-source license. This contribution provides a standard framework for benchmarking and regulatory testing of NI-FECG extraction algorithms.

WavePropaGator: interactive framework for X-ray free-electron laser optics design and simulations.

PubMed

Samoylova, Liubov; Buzmakov, Alexey; Chubar, Oleg; Sinn, Harald

2016-08-01

This article describes the WavePropaGator ( WPG ) package, a new interactive software framework for coherent and partially coherent X-ray wavefront propagation simulations. The package has been developed at European XFEL for users at the existing and emerging free-electron laser (FEL) facilities, as well as at the third-generation synchrotron sources and future diffraction-limited storage rings. The WPG addresses the needs of beamline scientists and user groups to facilitate the design, optimization and improvement of X-ray optics to meet their experimental requirements. The package uses the Synchrotron Radiation Workshop ( SRW ) C/C++ library and its Python binding for numerical wavefront propagation simulations. The framework runs reliably under Linux, Microsoft Windows 7 and Apple Mac OS X and is distributed under an open-source license. The available tools allow for varying source parameters and optics layouts and visualizing the results interactively. The wavefront history structure can be used for tracking changes in every particular wavefront during propagation. The batch propagation mode enables processing of multiple wavefronts in workflow mode. The paper presents a general description of the package and gives some recent application examples, including modeling of full X-ray FEL beamlines and start-to-end simulation of experiments.

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

Check-Cases for Verification of 6-Degree-of-Freedom Flight Vehicle Simulations. Volume 2; Appendices

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce; Shelton, Robert O.

2015-01-01

This NASA Engineering and Safety Center (NESC) assessment was established to develop a set of time histories for the flight behavior of increasingly complex example aerospacecraft that could be used to partially validate various simulation frameworks. The assessment was conducted by representatives from several NASA Centers and an open-source simulation project. This document contains details on models, implementation, and results.

CAGE IIIA Distributed Simulation Design Methodology

DTIC Science & Technology

2014-05-01

2 VHF Very High Frequency VLC Video LAN Codec – an Open-source cross-platform multimedia player and framework VM Virtual Machine VOIP Voice Over...Implementing Defence Experimentation (GUIDEx). The key challenges for this methodology are with understanding how to: • design it o define the...operation and to be available in the other nation’s simulations. The challenge for the CAGE campaign of experiments is to continue to build upon this

Survivability as a Tool for Evaluating Open Source Software

DTIC Science & Technology

2015-06-01

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

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

DTIC Science & Technology

2007-06-01

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

CSNS computing environment Based on OpenStack

NASA Astrophysics Data System (ADS)

Li, Yakang; Qi, Fazhi; Chen, Gang; Wang, Yanming; Hong, Jianshu

2017-10-01

Cloud computing can allow for more flexible configuration of IT resources and optimized hardware utilization, it also can provide computing service according to the real need. We are applying this computing mode to the China Spallation Neutron Source(CSNS) computing environment. So, firstly, CSNS experiment and its computing scenarios and requirements are introduced in this paper. Secondly, the design and practice of cloud computing platform based on OpenStack are mainly demonstrated from the aspects of cloud computing system framework, network, storage and so on. Thirdly, some improvments to openstack we made are discussed further. Finally, current status of CSNS cloud computing environment are summarized in the ending of this paper.

!CHAOS: A cloud of controls

NASA Astrophysics Data System (ADS)

Angius, S.; Bisegni, C.; Ciuffetti, P.; Di Pirro, G.; Foggetta, L. G.; Galletti, F.; Gargana, R.; Gioscio, E.; Maselli, D.; Mazzitelli, G.; Michelotti, A.; Orrù, R.; Pistoni, M.; Spagnoli, F.; Spigone, D.; Stecchi, A.; Tonto, T.; Tota, M. A.; Catani, L.; Di Giulio, C.; Salina, G.; Buzzi, P.; Checcucci, B.; Lubrano, P.; Piccini, M.; Fattibene, E.; Michelotto, M.; Cavallaro, S. R.; Diana, B. F.; Enrico, F.; Pulvirenti, S.

2016-01-01

The paper is aimed to present the !CHAOS open source project aimed to develop a prototype of a national private Cloud Computing infrastructure, devoted to accelerator control systems and large experiments of High Energy Physics (HEP). The !CHAOS project has been financed by MIUR (Italian Ministry of Research and Education) and aims to develop a new concept of control system and data acquisition framework by providing, with a high level of aaabstraction, all the services needed for controlling and managing a large scientific, or non-scientific, infrastructure. A beta version of the !CHAOS infrastructure will be released at the end of December 2015 and will run on private Cloud infrastructures based on OpenStack.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience.

PubMed

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases.

Informatics in radiology: web-based preliminary reporting system for radiology residents with PACS integration.

PubMed

O'Connell, Timothy; Chang, Debra

2012-01-01

While on call, radiology residents review imaging studies and issue preliminary reports to referring clinicians. In the absence of an integrated reporting system at the training sites of the authors' institution, residents were typing and faxing preliminary reports. To partially automate the on-call resident workflow, a Web-based system for resident reporting was developed by using the free open-source xAMP Web application framework and an open-source DICOM (Digital Imaging and Communications in Medicine) software toolkit, with the goals of reducing errors and lowering barriers to education. This reporting system integrates with the picture archiving and communication system to display a worklist of studies. Patient data are automatically entered in the preliminary report to prevent identification errors and simplify the report creation process. When the final report for a resident's on-call study is available, the reporting system queries the report broker for the final report, and then displays the preliminary report side by side with the final report, thus simplifying the review process and encouraging review of all of the resident's reports. The xAMP Web application framework should be considered for development of radiology department informatics projects owing to its zero cost, minimal hardware requirements, ease of programming, and large support community.

A new chapter in environmental sensing: The Open-Source Published Environmental Sensing (OPENS) laboratory

NASA Astrophysics Data System (ADS)

Selker, J. S.; Roques, C.; Higgins, C. W.; Good, S. P.; Hut, R.; Selker, A.

2015-12-01

The confluence of 3-Dimensional printing, low-cost solid-state-sensors, low-cost, low-power digital controllers (e.g., Arduinos); and open-source publishing (e.g., Github) is poised to transform environmental sensing. The Open-Source Published Environmental Sensing (OPENS) laboratory has launched and is available for all to use. OPENS combines cutting edge technologies and makes them available to the global environmental sensing community. OPENS includes a Maker lab space where people may collaborate in person or virtually via on-line forum for the publication and discussion of environmental sensing technology (Corvallis, Oregon, USA, please feel free to request a free reservation for space and equipment use). The physical lab houses a test-bed for sensors, as well as a complete classical machine shop, 3-D printers, electronics development benches, and workstations for code development. OPENS will provide a web-based formal publishing framework wherein global students and scientists can peer-review publish (with DOI) novel and evolutionary advancements in environmental sensor systems. This curated and peer-reviewed digital collection will include complete sets of "printable" parts and operating computer code for sensing systems. The physical lab will include all of the machines required to produce these sensing systems. These tools can be addressed in person or virtually, creating a truly global venue for advancement in monitoring earth's environment and agricultural systems. In this talk we will present an example of the process of design and publication the design and data from the OPENS-Permeameter. The publication includes 3-D printing code, Arduino (or other control/logging platform) operational code; sample data sets, and a full discussion of the design set in the scientific context of previous related devices. Editors for the peer-review process are currently sought - contact John.Selker@Oregonstate.edu or Clement.Roques@Oregonstate.edu.

Comparing, optimizing, and benchmarking quantum-control algorithms in a unifying programming framework

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

Machnes, S.; Institute for Theoretical Physics, University of Ulm, D-89069 Ulm; Sander, U.

2011-08-15

For paving the way to novel applications in quantum simulation, computation, and technology, increasingly large quantum systems have to be steered with high precision. It is a typical task amenable to numerical optimal control to turn the time course of pulses, i.e., piecewise constant control amplitudes, iteratively into an optimized shape. Here, we present a comparative study of optimal-control algorithms for a wide range of finite-dimensional applications. We focus on the most commonly used algorithms: GRAPE methods which update all controls concurrently, and Krotov-type methods which do so sequentially. Guidelines for their use are given and open research questions aremore » pointed out. Moreover, we introduce a unifying algorithmic framework, DYNAMO (dynamic optimization platform), designed to provide the quantum-technology community with a convenient matlab-based tool set for optimal control. In addition, it gives researchers in optimal-control techniques a framework for benchmarking and comparing newly proposed algorithms with the state of the art. It allows a mix-and-match approach with various types of gradients, update and step-size methods as well as subspace choices. Open-source code including examples is made available at http://qlib.info.« less

PlasmaPy: beginning a community developed Python package for plasma physics

NASA Astrophysics Data System (ADS)

Murphy, Nicholas A.; Huang, Yi-Min; PlasmaPy Collaboration

2016-10-01

In recent years, researchers in several disciplines have collaborated on community-developed open source Python packages such as Astropy, SunPy, and SpacePy. These packages provide core functionality, common frameworks for data analysis and visualization, and educational tools. We propose that our community begins the development of PlasmaPy: a new open source core Python package for plasma physics. PlasmaPy could include commonly used functions in plasma physics, easy-to-use plasma simulation codes, Grad-Shafranov solvers, eigenmode solvers, and tools to analyze both simulations and experiments. The development will include modern programming practices such as version control, embedding documentation in the code, unit tests, and avoiding premature optimization. We will describe early code development on PlasmaPy, and discuss plans moving forward. The success of PlasmaPy depends on active community involvement and a welcoming and inclusive environment, so anyone interested in joining this collaboration should contact the authors.

Instrument Control (iC) – An Open-Source Software to Automate Test Equipment

PubMed Central

Pernstich, K. P.

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming. PMID:26900522

PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

PubMed

Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

2017-06-05

We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Instrument Control (iC) - An Open-Source Software to Automate Test Equipment.

PubMed

Pernstich, K P

2012-01-01

It has become common practice to automate data acquisition from programmable instrumentation, and a range of different software solutions fulfill this task. Many routine measurements require sequential processing of certain tasks, for instance to adjust the temperature of a sample stage, take a measurement, and repeat that cycle for other temperatures. This paper introduces an open-source Java program that processes a series of text-based commands that define the measurement sequence. These commands are in an intuitive format which provides great flexibility and allows quick and easy adaptation to various measurement needs. For each of these commands, the iC-framework calls a corresponding Java method that addresses the specified instrument to perform the desired task. The functionality of iC can be extended with minimal programming effort in Java or Python, and new measurement equipment can be addressed by defining new commands in a text file without any programming.

GéoSAS: A modular and interoperable Open Source Spatial Data Infrastructure for research

NASA Astrophysics Data System (ADS)

Bera, R.; Squividant, H.; Le Henaff, G.; Pichelin, P.; Ruiz, L.; Launay, J.; Vanhouteghem, J.; Aurousseau, P.; Cudennec, C.

2015-05-01

To-date, the commonest way to deal with geographical information and processes still appears to consume local resources, i.e. locally stored data processed on a local desktop or server. The maturity and subsequent growing use of OGC standards to exchange data on the World Wide Web, enhanced in Europe by the INSPIRE Directive, is bound to change the way people (and among them research scientists, especially in environmental sciences) make use of, and manage, spatial data. A clever use of OGC standards can help scientists to better store, share and use data, in particular for modelling. We propose a framework for online processing by making an intensive use of OGC standards. We illustrate it using the Spatial Data Infrastructure (SDI) GéoSAS which is the SDI set up for researchers' needs in our department. It is based on the existing open source, modular and interoperable Spatial Data Architecture geOrchestra.

Low Data Drug Discovery with One-Shot Learning.

PubMed

Altae-Tran, Han; Ramsundar, Bharath; Pappu, Aneesh S; Pande, Vijay

2017-04-26

Recent advances in machine learning have made significant contributions to drug discovery. Deep neural networks in particular have been demonstrated to provide significant boosts in predictive power when inferring the properties and activities of small-molecule compounds (Ma, J. et al. J. Chem. Inf. 2015, 55, 263-274). However, the applicability of these techniques has been limited by the requirement for large amounts of training data. In this work, we demonstrate how one-shot learning can be used to significantly lower the amounts of data required to make meaningful predictions in drug discovery applications. We introduce a new architecture, the iterative refinement long short-term memory, that, when combined with graph convolutional neural networks, significantly improves learning of meaningful distance metrics over small-molecules. We open source all models introduced in this work as part of DeepChem, an open-source framework for deep-learning in drug discovery (Ramsundar, B. deepchem.io. https://github.com/deepchem/deepchem, 2016).

Long-term Science Data Curation Using a Digital Object Model and Open-Source Frameworks

NASA Astrophysics Data System (ADS)

Pan, J.; Lenhardt, W.; Wilson, B. E.; Palanisamy, G.; Cook, R. B.

2010-12-01

Scientific digital content, including Earth Science observations and model output, has become more heterogeneous in format and more distributed across the Internet. In addition, data and metadata are becoming necessarily linked internally and externally on the Web. As a result, such content has become more difficult for providers to manage and preserve and for users to locate, understand, and consume. Specifically, it is increasingly harder to deliver relevant metadata and data processing lineage information along with the actual content consistently. Readme files, data quality information, production provenance, and other descriptive metadata are often separated in the storage level as well as in the data search and retrieval interfaces available to a user. Critical archival metadata, such as auditing trails and integrity checks, are often even more difficult for users to access, if they exist at all. We investigate the use of several open-source software frameworks to address these challenges. We use Fedora Commons Framework and its digital object abstraction as the repository, Drupal CMS as the user-interface, and the Islandora module as the connector from Drupal to Fedora Repository. With the digital object model, metadata of data description and data provenance can be associated with data content in a formal manner, so are external references and other arbitrary auxiliary information. Changes are formally audited on an object, and digital contents are versioned and have checksums automatically computed. Further, relationships among objects are formally expressed with RDF triples. Data replication, recovery, metadata export are supported with standard protocols, such as OAI-PMH. We provide a tentative comparative analysis of the chosen software stack with the Open Archival Information System (OAIS) reference model, along with our initial results with the existing terrestrial ecology data collections at NASA’s ORNL Distributed Active Archive Center for Biogeochemical Dynamics (ORNL DAAC).

A software framework for real-time multi-modal detection of microsleeps.

PubMed

Knopp, Simon J; Bones, Philip J; Weddell, Stephen J; Jones, Richard D

2017-09-01

A software framework is described which was designed to process EEG, video of one eye, and head movement in real time, towards achieving early detection of microsleeps for prevention of fatal accidents, particularly in transport sectors. The framework is based around a pipeline structure with user-replaceable signal processing modules. This structure can encapsulate a wide variety of feature extraction and classification techniques and can be applied to detecting a variety of aspects of cognitive state. Users of the framework can implement signal processing plugins in C++ or Python. The framework also provides a graphical user interface and the ability to save and load data to and from arbitrary file formats. Two small studies are reported which demonstrate the capabilities of the framework in typical applications: monitoring eye closure and detecting simulated microsleeps. While specifically designed for microsleep detection/prediction, the software framework can be just as appropriately applied to (i) other measures of cognitive state and (ii) development of biomedical instruments for multi-modal real-time physiological monitoring and event detection in intensive care, anaesthesiology, cardiology, neurosurgery, etc. The software framework has been made freely available for researchers to use and modify under an open source licence.

A federated semantic metadata registry framework for enabling interoperability across clinical research and care domains.

PubMed

Sinaci, A Anil; Laleci Erturkmen, Gokce B

2013-10-01

In order to enable secondary use of Electronic Health Records (EHRs) by bridging the interoperability gap between clinical care and research domains, in this paper, a unified methodology and the supporting framework is introduced which brings together the power of metadata registries (MDR) and semantic web technologies. We introduce a federated semantic metadata registry framework by extending the ISO/IEC 11179 standard, and enable integration of data element registries through Linked Open Data (LOD) principles where each Common Data Element (CDE) can be uniquely referenced, queried and processed to enable the syntactic and semantic interoperability. Each CDE and their components are maintained as LOD resources enabling semantic links with other CDEs, terminology systems and with implementation dependent content models; hence facilitating semantic search, much effective reuse and semantic interoperability across different application domains. There are several important efforts addressing the semantic interoperability in healthcare domain such as IHE DEX profile proposal, CDISC SHARE and CDISC2RDF. Our architecture complements these by providing a framework to interlink existing data element registries and repositories for multiplying their potential for semantic interoperability to a greater extent. Open source implementation of the federated semantic MDR framework presented in this paper is the core of the semantic interoperability layer of the SALUS project which enables the execution of the post marketing safety analysis studies on top of existing EHR systems. Copyright © 2013 Elsevier Inc. All rights reserved.

A generic framework for individual-based modelling and physical-biological interaction

PubMed Central

2018-01-01

The increased availability of high-resolution ocean data globally has enabled more detailed analyses of physical-biological interactions and their consequences to the ecosystem. We present IBMlib, which is a versatile, portable and computationally effective framework for conducting Lagrangian simulations in the marine environment. The purpose of the framework is to handle complex individual-level biological models of organisms, combined with realistic 3D oceanographic model of physics and biogeochemistry describing the environment of the organisms without assumptions about spatial or temporal scales. The open-source framework features a minimal robust interface to facilitate the coupling between individual-level biological models and oceanographic models, and we provide application examples including forward/backward simulations, habitat connectivity calculations, assessing ocean conditions, comparison of physical circulation models, model ensemble runs and recently posterior Eulerian simulations using the IBMlib framework. We present the code design ideas behind the longevity of the code, our implementation experiences, as well as code performance benchmarking. The framework may contribute substantially to progresses in representing, understanding, predicting and eventually managing marine ecosystems. PMID:29351280

Brokered virtual hubs for facilitating access and use of geospatial Open Data

NASA Astrophysics Data System (ADS)

Mazzetti, Paolo; Latre, Miguel; Kamali, Nargess; Brumana, Raffaella; Braumann, Stefan; Nativi, Stefano

2016-04-01

Open Data is a major trend in current information technology scenario and it is often publicised as one of the pillars of the information society in the near future. In particular, geospatial Open Data have a huge potential also for Earth Sciences, through the enablement of innovative applications and services integrating heterogeneous information. However, open does not mean usable. As it was recognized at the very beginning of the Web revolution, many different degrees of openness exist: from simple sharing in a proprietary format to advanced sharing in standard formats and including semantic information. Therefore, to fully unleash the potential of geospatial Open Data, advanced infrastructures are needed to increase the data openness degree, enhancing their usability. In October 2014, the ENERGIC OD (European NEtwork for Redistributing Geospatial Information to user Communities - Open Data) project, funded by the European Union under the Competitiveness and Innovation framework Programme (CIP), has started. In response to the EU call, the general objective of the project is to "facilitate the use of open (freely available) geographic data from different sources for the creation of innovative applications and services through the creation of Virtual Hubs". The ENERGIC OD Virtual Hubs aim to facilitate the use of geospatial Open Data by lowering and possibly removing the main barriers which hampers geo-information (GI) usage by end-users and application developers. Data and services heterogeneity is recognized as one of the major barriers to Open Data (re-)use. It imposes end-users and developers to spend a lot of effort in accessing different infrastructures and harmonizing datasets. Such heterogeneity cannot be completely removed through the adoption of standard specifications for service interfaces, metadata and data models, since different infrastructures adopt different standards to answer to specific challenges and to address specific use-cases. Thus, beyond a certain extent, heterogeneity is irreducible especially in interdisciplinary contexts. ENERGIC OD Virtual Hubs address heterogeneity adopting a mediation and brokering approach: specific components (brokers) are dedicated to harmonize service interfaces, metadata and data models, enabling seamless discovery and access to heterogeneous infrastructures and datasets. As an innovation project, ENERGIC OD integrates several existing technologies to implement Virtual Hubs as single points of access to geospatial datasets provided by new or existing platforms and infrastructures, including INSPIRE-compliant systems and Copernicus services. A first version of the ENERGIC OD brokers has been implemented based on the GI-Suite Brokering Framework developed by CNR-IIA, and complemented with other tools under integration and development. It already enables mediated discovery and harmonized access to different geospatial Open Data sources. It is accessible by users as Software-as-a-Service through a browser. Moreover, open APIs and a Javascript library are available for application developers. Six ENERGIC OD Virtual Hubs have been currently deployed: one at regional level (Berlin metropolitan area) and five at national-level (in France, Germany, Italy, Poland and Spain). Each Virtual Hub manager decided the deployment strategy (local infrastructure or commercial Infrastructure-as-a-Service cloud), and the list of connected Open Data sources. The ENERGIC OD Virtual Hubs are under test and validation through the development of ten different mobile and Web applications.

Quality Analysis of Open Street Map Data

NASA Astrophysics Data System (ADS)

Wang, M.; Li, Q.; Hu, Q.; Zhou, M.

2013-05-01

Crowd sourcing geographic data is an opensource geographic data which is contributed by lots of non-professionals and provided to the public. The typical crowd sourcing geographic data contains GPS track data like OpenStreetMap, collaborative map data like Wikimapia, social websites like Twitter and Facebook, POI signed by Jiepang user and so on. These data will provide canonical geographic information for pubic after treatment. As compared with conventional geographic data collection and update method, the crowd sourcing geographic data from the non-professional has characteristics or advantages of large data volume, high currency, abundance information and low cost and becomes a research hotspot of international geographic information science in the recent years. Large volume crowd sourcing geographic data with high currency provides a new solution for geospatial database updating while it need to solve the quality problem of crowd sourcing geographic data obtained from the non-professionals. In this paper, a quality analysis model for OpenStreetMap crowd sourcing geographic data is proposed. Firstly, a quality analysis framework is designed based on data characteristic analysis of OSM data. Secondly, a quality assessment model for OSM data by three different quality elements: completeness, thematic accuracy and positional accuracy is presented. Finally, take the OSM data of Wuhan for instance, the paper analyses and assesses the quality of OSM data with 2011 version of navigation map for reference. The result shows that the high-level roads and urban traffic network of OSM data has a high positional accuracy and completeness so that these OSM data can be used for updating of urban road network database.

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage.

PubMed

Noor, Elad; Bar-Even, Arren; Flamholz, Avi; Lubling, Yaniv; Davidi, Dan; Milo, Ron

2012-08-01

The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions. Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG(○) of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K' and pK(a) data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM-3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions. Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux. ron.milo@weizmann.ac.il Supplementary data are available at Bioinformatics online.

An integrated open framework for thermodynamics of reactions that combines accuracy and coverage

PubMed Central

Noor, Elad; Bar-Even, Arren; Flamholz, Avi; Lubling, Yaniv; Davidi, Dan; Milo, Ron

2012-01-01

Motivation: The laws of thermodynamics describe a direct, quantitative relationship between metabolite concentrations and reaction directionality. Despite great efforts, thermodynamic data suffer from limited coverage, scattered accessibility and non-standard annotations. We present a framework for unifying thermodynamic data from multiple sources and demonstrate two new techniques for extrapolating the Gibbs energies of unmeasured reactions and conditions. Results: Both methods account for changes in cellular conditions (pH, ionic strength, etc.) by using linear regression over the ΔG○ of pseudoisomers and reactions. The Pseudoisomeric Reactant Contribution method systematically infers compound formation energies using measured K′ and pKa data. The Pseudoisomeric Group Contribution method extends the group contribution method and achieves a high coverage of unmeasured reactions. We define a continuous index that predicts the reversibility of a reaction under a given physiological concentration range. In the characteristic physiological range 3μM–3mM, we find that roughly half of the reactions in Escherichia coli's metabolism are reversible. These new tools can increase the accuracy of thermodynamic-based models, especially in non-standard pH and ionic strengths. The reversibility index can help modelers decide which reactions are reversible in physiological conditions. Availability: Freely available on the web at: http://equilibrator.weizmann.ac.il. Website implemented in Python, MySQL, Apache and Django, with all major browsers supported. The framework is open-source (code.google.com/p/milo-lab), implemented in pure Python and tested mainly on Linux. Contact: ron.milo@weizmann.ac.il Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:22645166

Owgis 2.0: Open Source Java Application that Builds Web GIS Interfaces for Desktop Andmobile Devices

NASA Astrophysics Data System (ADS)

Zavala Romero, O.; Chassignet, E.; Zavala-Hidalgo, J.; Pandav, H.; Velissariou, P.; Meyer-Baese, A.

2016-12-01

OWGIS is an open source Java and JavaScript application that builds easily configurable Web GIS sites for desktop and mobile devices. The current version of OWGIS generates mobile interfaces based on HTML5 technology and can be used to create mobile applications. The style of the generated websites can be modified using COMPASS, a well known CSS Authoring Framework. In addition, OWGIS uses several Open Geospatial Consortium standards to request datafrom the most common map servers, such as GeoServer. It is also able to request data from ncWMS servers, allowing the websites to display 4D data from NetCDF files. This application is configured by XML files that define which layers, geographic datasets, are displayed on the Web GIS sites. Among other features, OWGIS allows for animations; streamlines from vector data; virtual globe display; vertical profiles and vertical transects; different color palettes; the ability to download data; and display text in multiple languages. OWGIS users are mainly scientists in the oceanography, meteorology and climate fields.

Enabling Interoperable and Selective Data Sharing among Social Networking Sites

NASA Astrophysics Data System (ADS)

Shin, Dongwan; Lopes, Rodrigo

With the widespread use of social networking (SN) sites and even introduction of a social component in non-social oriented services, there is a growing concern over user privacy in general, how to handle and share user profiles across SN sites in particular. Although there have been several proprietary or open source-based approaches to unifying the creation of third party applications, the availability and retrieval of user profile information are still limited to the site where the third party application is run, mostly devoid of the support for data interoperability. In this paper we propose an approach to enabling interopearable and selective data sharing among SN sites. To support selective data sharing, we discuss an authenticated dictionary (ADT)-based credential which enables a user to share only a subset of her information certified by external SN sites with applications running on an SN site. For interoperable data sharing, we propose an extension to the OpenSocial API so that it can provide an open source-based framework for allowing the ADT-based credential to be used seamlessly among different SN sites.

Technical note: The Linked Paleo Data framework - a common tongue for paleoclimatology

NASA Astrophysics Data System (ADS)

McKay, Nicholas P.; Emile-Geay, Julien

2016-04-01

Paleoclimatology is a highly collaborative scientific endeavor, increasingly reliant on online databases for data sharing. Yet there is currently no universal way to describe, store and share paleoclimate data: in other words, no standard. Data standards are often regarded by scientists as mere technicalities, though they underlie much scientific and technological innovation, as well as facilitating collaborations between research groups. In this article, we propose a preliminary data standard for paleoclimate data, general enough to accommodate all the archive and measurement types encountered in a large international collaboration (PAGES 2k). We also introduce a vehicle for such structured data (Linked Paleo Data, or LiPD), leveraging recent advances in knowledge representation (Linked Open Data).The LiPD framework enables quick querying and extraction, and we expect that it will facilitate the writing of open-source community codes to access, analyze, model and visualize paleoclimate observations. We welcome community feedback on this standard, and encourage paleoclimatologists to experiment with the format for their own purposes.

The Open Global Glacier Model

NASA Astrophysics Data System (ADS)

Marzeion, B.; Maussion, F.

2017-12-01

Mountain glaciers are one of the few remaining sub-systems of the global climate system for which no globally applicable, open source, community-driven model exists. Notable examples from the ice sheet community include the Parallel Ice Sheet Model or Elmer/Ice. While the atmospheric modeling community has a long tradition of sharing models (e.g. the Weather Research and Forecasting model) or comparing them (e.g. the Coupled Model Intercomparison Project or CMIP), recent initiatives originating from the glaciological community show a new willingness to better coordinate global research efforts following the CMIP example (e.g. the Glacier Model Intercomparison Project or the Glacier Ice Thickness Estimation Working Group). In the recent past, great advances have been made in the global availability of data and methods relevant for glacier modeling, spanning glacier outlines, automatized glacier centerline identification, bed rock inversion methods, and global topographic data sets. Taken together, these advances now allow the ice dynamics of glaciers to be modeled on a global scale, provided that adequate modeling platforms are available. Here, we present the Open Global Glacier Model (OGGM), developed to provide a global scale, modular, and open source numerical model framework for consistently simulating past and future global scale glacier change. Global not only in the sense of leading to meaningful results for all glaciers combined, but also for any small ensemble of glaciers, e.g. at the headwater catchment scale. Modular to allow combinations of different approaches to the representation of ice flow and surface mass balance, enabling a new kind of model intercomparison. Open source so that the code can be read and used by anyone and so that new modules can be added and discussed by the community, following the principles of open governance. Consistent in order to provide uncertainty measures at all realizable scales.

ASaiM: a Galaxy-based framework to analyze microbiota data.

PubMed

Batut, Bérénice; Gravouil, Kévin; Defois, Clémence; Hiltemann, Saskia; Brugère, Jean-François; Peyretaillade, Eric; Peyret, Pierre

2018-05-22

New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore and visualize microbiota information from raw metataxonomic, metagenomic or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets, but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible and shareable.

Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows

NASA Astrophysics Data System (ADS)

Freedman, V. L.; Agarwal, D.; Bensema, K.; Finsterle, S.; Gable, C. W.; Keating, E. H.; Krishnan, H.; Lansing, C.; Moeglein, W.; Pau, G. S. H.; Porter, E.; Scheibe, T. D.

2014-12-01

The U.S. Department of Energy (DOE) is investing in development of a numerical modeling toolset called ASCEM (Advanced Simulation Capability for Environmental Management) to support modeling analyses at legacy waste sites. ASCEM is an open source and modular computing framework that incorporates new advances and tools for predicting contaminant fate and transport in natural and engineered systems. The ASCEM toolset includes both a Platform with Integrated Toolsets (called Akuna) and a High-Performance Computing multi-process simulator (called Amanzi). The focus of this presentation is on Akuna, an open-source user environment that manages subsurface simulation workflows and associated data and metadata. In this presentation, key elements of Akuna are demonstrated, which includes toolsets for model setup, database management, sensitivity analysis, parameter estimation, uncertainty quantification, and visualization of both model setup and simulation results. A key component of the workflow is in the automated job launching and monitoring capabilities, which allow a user to submit and monitor simulation runs on high-performance, parallel computers. Visualization of large outputs can also be performed without moving data back to local resources. These capabilities make high-performance computing accessible to the users who might not be familiar with batch queue systems and usage protocols on different supercomputers and clusters.

CognitionMaster: an object-based image analysis framework

PubMed Central

2013-01-01

Background Automated image analysis methods are becoming more and more important to extract and quantify image features in microscopy-based biomedical studies and several commercial or open-source tools are available. However, most of the approaches rely on pixel-wise operations, a concept that has limitations when high-level object features and relationships between objects are studied and if user-interactivity on the object-level is desired. Results In this paper we present an open-source software that facilitates the analysis of content features and object relationships by using objects as basic processing unit instead of individual pixels. Our approach enables also users without programming knowledge to compose “analysis pipelines“ that exploit the object-level approach. We demonstrate the design and use of example pipelines for the immunohistochemistry-based cell proliferation quantification in breast cancer and two-photon fluorescence microscopy data about bone-osteoclast interaction, which underline the advantages of the object-based concept. Conclusions We introduce an open source software system that offers object-based image analysis. The object-based concept allows for a straight-forward development of object-related interactive or fully automated image analysis solutions. The presented software may therefore serve as a basis for various applications in the field of digital image analysis. PMID:23445542

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking

PubMed Central

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin

2017-01-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software (www.bikalims.org) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server–client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines. PMID:28375759

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking.

PubMed

Bendou, Hocine; Sizani, Lunga; Reid, Tim; Swanepoel, Carmen; Ademuyiwa, Toluwaleke; Merino-Martinez, Roxana; Meuller, Heimo; Abayomi, Akin; Christoffels, Alan

2017-04-01

A laboratory information management system (LIMS) is central to the informatics infrastructure that underlies biobanking activities. To date, a wide range of commercial and open-source LIMSs are available and the decision to opt for one LIMS over another is often influenced by the needs of the biobank clients and researchers, as well as available financial resources. The Baobab LIMS was developed by customizing the Bika LIMS software ( www.bikalims.org ) to meet the requirements of biobanking best practices. The need to implement biobank standard operation procedures as well as stimulate the use of standards for biobank data representation motivated the implementation of Baobab LIMS, an open-source LIMS for Biobanking. Baobab LIMS comprises modules for biospecimen kit assembly, shipping of biospecimen kits, storage management, analysis requests, reporting, and invoicing. The Baobab LIMS is based on the Plone web-content management framework. All the system requirements for Plone are applicable to Baobab LIMS, including the need for a server with at least 8 GB RAM and 120 GB hard disk space. Baobab LIMS is a server-client-based system, whereby the end user is able to access the system securely through the internet on a standard web browser, thereby eliminating the need for standalone installations on all machines.

Real-time Neuroimaging and Cognitive Monitoring Using Wearable Dry EEG

PubMed Central

Mullen, Tim R.; Kothe, Christian A.E.; Chi, Mike; Ojeda, Alejandro; Kerth, Trevor; Makeig, Scott; Jung, Tzyy-Ping; Cauwenberghs, Gert

2015-01-01

Goal We present and evaluate a wearable high-density dry electrode EEG system and an open-source software framework for online neuroimaging and state classification. Methods The system integrates a 64-channel dry EEG form-factor with wireless data streaming for online analysis. A real-time software framework is applied, including adaptive artifact rejection, cortical source localization, multivariate effective connectivity inference, data visualization, and cognitive state classification from connectivity features using a constrained logistic regression approach (ProxConn). We evaluate the system identification methods on simulated 64-channel EEG data. Then we evaluate system performance, using ProxConn and a benchmark ERP method, in classifying response errors in 9 subjects using the dry EEG system. Results Simulations yielded high accuracy (AUC=0.97±0.021) for real-time cortical connectivity estimation. Response error classification using cortical effective connectivity (sdDTF) was significantly above chance with similar performance (AUC) for cLORETA (0.74±0.09) and LCMV (0.72±0.08) source localization. Cortical ERP-based classification was equivalent to ProxConn for cLORETA (0.74±0.16) but significantly better for LCMV (0.82±0.12). Conclusion We demonstrated the feasibility for real-time cortical connectivity analysis and cognitive state classification from high-density wearable dry EEG. Significance This paper is the first validated application of these methods to 64-channel dry EEG. The work addresses a need for robust real-time measurement and interpretation of complex brain activity in the dynamic environment of the wearable setting. Such advances can have broad impact in research, medicine, and brain-computer interfaces. The pipelines are made freely available in the open-source SIFT and BCILAB toolboxes. PMID:26415149

Issues on Building Kazakhstan Geospatial Portal to Implement E-Government

NASA Astrophysics Data System (ADS)

Sagadiyev, K.; Kang, H. K.; Li, K. J.

2016-06-01

A main issue in developing e-government is about how to integrate and organize many complicated processes and different stakeholders. Interestingly geospatial information provides an efficient framework to integrate and organized them. In particular, it is very useful to integrate the process of land management in e-government with geospatial information framework, since most of land management tasks are related with geospatial properties. In this paper, we present a use-case on the e-government project in Kazakhstan for land management. We develop a geoportal to connect many tasks and different users via geospatial information framework. This geoportal is based on open source geospatial software including GeoServer, PostGIS, and OpenLayers. With this geoportal, we expect three achievements as follows. First we establish a transparent governmental process, which is one of main goal of e-government. Every stakeholder monitors what is happening in land management process. Second, we can significantly reduce the time and efforts in the government process. For example, a grant procedure for a building construction has taken more than one year with more than 50 steps. It is expected that this procedure would be reduced to 2 weeks by the geoportal framework. Third we provide a collaborative environment between different governmental structures via the geoportal, while many conflicts and mismatches have been a critical issue of governmental administration processes.

Design, implementation and validation of a novel open framework for agile development of mobile health applications

PubMed Central

2015-01-01

The delivery of healthcare services has experienced tremendous changes during the last years. Mobile health or mHealth is a key engine of advance in the forefront of this revolution. Although there exists a growing development of mobile health applications, there is a lack of tools specifically devised for their implementation. This work presents mHealthDroid, an open source Android implementation of a mHealth Framework designed to facilitate the rapid and easy development of mHealth and biomedical apps. The framework is particularly planned to leverage the potential of mobile devices such as smartphones or tablets, wearable sensors and portable biomedical systems. These devices are increasingly used for the monitoring and delivery of personal health care and wellbeing. The framework implements several functionalities to support resource and communication abstraction, biomedical data acquisition, health knowledge extraction, persistent data storage, adaptive visualization, system management and value-added services such as intelligent alerts, recommendations and guidelines. An exemplary application is also presented along this work to demonstrate the potential of mHealthDroid. This app is used to investigate on the analysis of human behavior, which is considered to be one of the most prominent areas in mHealth. An accurate activity recognition model is developed and successfully validated in both offline and online conditions. PMID:26329639

BIOMedical Search Engine Framework: Lightweight and customized implementation of domain-specific biomedical search engines.

PubMed

Jácome, Alberto G; Fdez-Riverola, Florentino; Lourenço, Anália

2016-07-01

Text mining and semantic analysis approaches can be applied to the construction of biomedical domain-specific search engines and provide an attractive alternative to create personalized and enhanced search experiences. Therefore, this work introduces the new open-source BIOMedical Search Engine Framework for the fast and lightweight development of domain-specific search engines. The rationale behind this framework is to incorporate core features typically available in search engine frameworks with flexible and extensible technologies to retrieve biomedical documents, annotate meaningful domain concepts, and develop highly customized Web search interfaces. The BIOMedical Search Engine Framework integrates taggers for major biomedical concepts, such as diseases, drugs, genes, proteins, compounds and organisms, and enables the use of domain-specific controlled vocabulary. Technologies from the Typesafe Reactive Platform, the AngularJS JavaScript framework and the Bootstrap HTML/CSS framework support the customization of the domain-oriented search application. Moreover, the RESTful API of the BIOMedical Search Engine Framework allows the integration of the search engine into existing systems or a complete web interface personalization. The construction of the Smart Drug Search is described as proof-of-concept of the BIOMedical Search Engine Framework. This public search engine catalogs scientific literature about antimicrobial resistance, microbial virulence and topics alike. The keyword-based queries of the users are transformed into concepts and search results are presented and ranked accordingly. The semantic graph view portraits all the concepts found in the results, and the researcher may look into the relevance of different concepts, the strength of direct relations, and non-trivial, indirect relations. The number of occurrences of the concept shows its importance to the query, and the frequency of concept co-occurrence is indicative of biological relations meaningful to that particular scope of research. Conversely, indirect concept associations, i.e. concepts related by other intermediary concepts, can be useful to integrate information from different studies and look into non-trivial relations. The BIOMedical Search Engine Framework supports the development of domain-specific search engines. The key strengths of the framework are modularity and extensibilityin terms of software design, the use of open-source consolidated Web technologies, and the ability to integrate any number of biomedical text mining tools and information resources. Currently, the Smart Drug Search keeps over 1,186,000 documents, containing more than 11,854,000 annotations for 77,200 different concepts. The Smart Drug Search is publicly accessible at http://sing.ei.uvigo.es/sds/. The BIOMedical Search Engine Framework is freely available for non-commercial use at https://github.com/agjacome/biomsef. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

A Comparison of Monte Carlo Tree Search and Rolling Horizon Optimization for Large Scale Dynamic Resource Allocation Problems

DTIC Science & Technology

2015-05-01

decisions on the fly in an online retail environment. Tech. rep., Working Paper, Massachusetts Institute of Technology, Boston, MA. Arneson, Broderick , Ryan...Hayward, Philip Henderson. 2009. MoHex wins Hex tournament. International Computer Games Association Journal 32 114–116. Arneson, Broderick , Ryan B...Combina- torial Search. Enzenberger, Markus, Martin Muller, Broderick Arneson, Richard Segal. 2010. Fuego—an open-source framework for board games and

Mapping, Awareness, and Virtualization Network Administrator Training Tool (MAVNATT) Architecture and Framework

DTIC Science & Technology

2015-06-01

unit may setup and teardown the entire tactical infrastructure multiple times per day. This tactical network administrator training is a critical...language and runs on Linux and Unix based systems. All provisioning is based around the Nagios Core application, a powerful backend solution for network...start up a large number of virtual machines quickly. CORE supports the simulation of fixed and mobile networks. CORE is open-source, written in Python

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

Interoperable Open-Source Sensor-Net Frameworks with Sensor-Package Workbench Capabilities: Motivation, Survey of Resources, and Exploratory Results

DTIC Science & Technology

2010-06-01

Military Scenario Definition Language (MSDL) for Nontraditional Warfare Scenarios," Paper 09S- SIW -001, Proceedings of the Spring Simulation...Update to the M&S Community," Paper 09S- SIW -002, Proceedings of the Spring Simulation Interoperability Workshop, Simulation Interoperability...Multiple Simulations: An Application of the Military Scenario Definition Language (MSDL)," Paper 09S- SIW -003, Proc. of the Spring Simulation

The Heliophysics Data Environment: Open Source, Open Systems and Open Data.

NASA Astrophysics Data System (ADS)

King, Todd; Roberts, Aaron; Walker, Raymond; Thieman, James

2012-07-01

The Heliophysics Data Environment (HPDE) is a place for scientific discovery. Today the Heliophysics Data Environment is a framework of technologies, standards and services which enables the international community to collaborate more effectively in space physics research. Crafting a framework for a data environment begins with defining a model of the tasks to be performed, then defining the functional aspects and the work flow. The foundation of any data environment is an information model which defines the structure and content of the metadata necessary to perform the tasks. In the Heliophysics Data Environment the information model is the Space Physics Archive Search and Extract (SPASE) model and available resources are described by using this model. A described resource can reside anywhere on the internet which makes it possible for a national archive, mission, data center or individual researcher to be a provider. The generated metadata is shared, reviewed and harvested to enable services. Virtual Observatories use the metadata to provide community based portals. Through unique identifiers and registry services tools can quickly discover and access data available anywhere on the internet. This enables a researcher to quickly view and analyze data in a variety of settings and enhances the Heliophysics Data Environment. To illustrate the current Heliophysics Data Environment we present the design, architecture and operation of the Heliophysics framework. We then walk through a real example of using available tools to investigate the effects of the solar wind on Earth's magnetosphere.

The Ozone Widget Framework: towards modularity of C2 human interfaces

NASA Astrophysics Data System (ADS)

Hellar, David Benjamin; Vega, Laurian C.

2012-05-01

The Ozone Widget Framework (OWF) is a common webtop environment for distribution across the enterprise. A key mission driver for OWF is to enable rapid capability delivery by lowering time-to-market with lightweight components. OWF has been released as Government Open Source Software and has been deployed in a variety of C2 net-centric contexts ranging from real-time analytics, cyber-situational awareness, to strategic and operational planning. This paper discusses the current and future evolution of OWF including the availability of the OZONE Marketplace (OMP), useractivity driven metrics, and architecture enhancements for accessibility. Together, OWF is moving towards the rapid delivery of modular human interfaces supporting modern and future command and control contexts.

Science supervisors' conceptions of biology and the field of science: A qualitative study

NASA Astrophysics Data System (ADS)

Young, Jean Radcliff

1999-12-01

This study examined the nature, source and formation of science supervisors' cognitive frameworks for biology and for the field of science and the impact of these frameworks on their work in school divisions. The design for this qualitative study was an emergent case study using ethnographic methods. The purposeful sample consisted of five science supervisors selected from different school divisions in three geographic regions of a middle-Atlantic state. Each participant had a background in biology, classroom teaching and full-time supervisory experience. To collect data for this study, an open-ended questionnaire was used to gain an understanding of the nature of the supervisors' conceptions of biology and for the field of science. Two semi-structured interviews, each lasting 1--2 hours in length, were designed to explore the source and formation of the supervisors' conceptual frameworks, and the impact of these frameworks on their work in school divisions. Data were inductively analyzed using a constant comparative approach. The major findings of this study were: (1) All of the supervisors in this study were remarkably cognizant of possessing a framework for biology and for the field of science. (2) The supervisors' frameworks were well-formed, relatively highly complex and showed a variety of organizational patterns. (3) All of the supervisors' diagrams showed evidence of coherent, integrated themes with emphasis on the importance of connections and interrelationships. (4) The supervisors were able to readily articulate sound rationales for construction of their diagrams. (5) Instead of seeing biology as an isolated discipline, the supervisors view biology in the context of science. Overall, the supervisors no longer see their frameworks as biology-content related, but as science-related. (6) Major influences on the source and formation of the supervisors' conceptual frameworks were a result of selected work-related experiences. (7) The supervisors' conceptual frameworks, in the context of implementation of state Standards of Learning, have had a major impact on their work in their school divisions with teachers and indirectly with students, parents and the public. Results are discussed in comparison with prior studies of non-supervisors using a similar methodology. Implications for educational practice and further research are included.

Capitalizing on global demands for open data access and interoperability - the USGIN story

NASA Astrophysics Data System (ADS)

Richard, Stephen; Allison, Lee

2016-04-01

U.S. Geoscience Information Network (USGIN - http://usgin.org) data integration framework packages data so that it can be accessible through a broad array of open-source software and applications, including GeoServer, QGIS, GrassGIS, uDig, and gvSIG. USGIN data-sharing networks are designed to interact with other data exchange systems and have the ability to connect information on a granular level without jeopardizing data ownership. The system is compliant with international standards and protocols, scalable, extensible, and can be deployed throughout the world for a myriad of applications. Using GeoSciML as its data transfer standard and a collaborative approach to Content Model development and management, much of the architecture is publically available through GitHub. Initially developed by the USGS and Association of American State Geologists as a distributed, self-maintained platform for sharing geoscience information, USGIN meets all the requirements of the White House Open Data Access Initiative that applies to (almost) all federally-funded research and all federally-maintained data, opening up huge opportunities for further deployment. In December 2015, the USGIN Content Model schema was recommended for adoption by the White House-led US Group on Earth Observations (USGEO) "Draft Common Framework for Earth-Observation Data" for all US earth observation (i.e., satellite) data. The largest USGIN node is the U.S. National Geothermal Data System (NGDS - www.geothermaldata.org). NGDS provides free open access to ~ 10 million data records, maps, and reports, sharing relevant geoscience and land use data to propel geothermal development and production in the U.S. NGDS currently serves information from hundreds of the U.S. Department of Energy's sponsored projects and geologic data feeds from 60+ data providers in all 50 states, using free and open source software, in a federated system where data owners maintain control of their data. This interactive online system is opening new exploration opportunities and shortening project development by making data easily discoverable, accessible, and interoperable at no cost to users. USGIN Foundation, Inc. was established in 2014 as a not-for-profit company to deploy the USGIN data integration framework for other natural resource (energy, water, and minerals), natural hazards, and geoscience investigations applications, nationally and worldwide. The USGIN vision is that as each data node adds to its data repositories, the system-wide USGIN functions become increasingly valuable to it. The long term goal is that the data network reach a 'tipping point' at which it becomes like a data equivalent to the World Wide Web - where everyone will maintain the function because it is expected by its clientele and it fills critical needs.

FIA: An Open Forensic Integration Architecture for Composing Digital Evidence

NASA Astrophysics Data System (ADS)

Raghavan, Sriram; Clark, Andrew; Mohay, George

The analysis and value of digital evidence in an investigation has been the domain of discourse in the digital forensic community for several years. While many works have considered different approaches to model digital evidence, a comprehensive understanding of the process of merging different evidence items recovered during a forensic analysis is still a distant dream. With the advent of modern technologies, pro-active measures are integral to keeping abreast of all forms of cyber crimes and attacks. This paper motivates the need to formalize the process of analyzing digital evidence from multiple sources simultaneously. In this paper, we present the forensic integration architecture (FIA) which provides a framework for abstracting the evidence source and storage format information from digital evidence and explores the concept of integrating evidence information from multiple sources. The FIA architecture identifies evidence information from multiple sources that enables an investigator to build theories to reconstruct the past. FIA is hierarchically composed of multiple layers and adopts a technology independent approach. FIA is also open and extensible making it simple to adapt to technological changes. We present a case study using a hypothetical car theft case to demonstrate the concepts and illustrate the value it brings into the field.

Joint Seismic-Geodetic Algorithm for Finite-Fault Detection and Slip Inversion in the West Coast ShakeAlert System

NASA Astrophysics Data System (ADS)

Smith, D. E.; Felizardo, C.; Minson, S. E.; Boese, M.; Langbein, J. O.; Murray, J. R.

2016-12-01

Finite-fault source algorithms can greatly benefit earthquake early warning (EEW) systems. Estimates of finite-fault parameters provide spatial information, which can significantly improve real-time shaking calculations and help with disaster response. In this project, we have focused on integrating a finite-fault seismic-geodetic algorithm into the West Coast ShakeAlert framework. The seismic part is FinDer 2, a C++ version of the algorithm developed by Böse et al. (2012). It interpolates peak ground accelerations and calculates the best fault length and strike from template matching. The geodetic part is a C++ version of BEFORES, the algorithm developed by Minson et al. (2014) that uses a Bayesian methodology to search for the most probable slip distribution on a fault of unknown orientation. Ultimately, these two will be used together where FinDer generates a Bayesian prior for BEFORES via the methodology of Minson et al. (2015), and the joint solution will generate estimates of finite-fault extent, strike, dip, best slip distribution, and magnitude. We have created C++ versions of both FinDer and BEFORES using open source libraries and have developed a C++ Application Protocol Interface (API) for them both. Their APIs allow FinDer and BEFORES to contribute to the ShakeAlert system via an open source messaging system, ActiveMQ. FinDer has been receiving real-time data, detecting earthquakes, and reporting messages on the development system for several months. We are also testing FinDer extensively with Earthworm tankplayer files. BEFORES has been tested with ActiveMQ messaging in the ShakeAlert framework, and works off a FinDer trigger. We are finishing the FinDer-BEFORES connections in this framework, and testing this system via seismic-geodetic tankplayer files. This will include actual and simulated data.

Ensembl 2004.

PubMed

Birney, E; Andrews, D; Bevan, P; Caccamo, M; Cameron, G; Chen, Y; Clarke, L; Coates, G; Cox, T; Cuff, J; Curwen, V; Cutts, T; Down, T; Durbin, R; Eyras, E; Fernandez-Suarez, X M; Gane, P; Gibbins, B; Gilbert, J; Hammond, M; Hotz, H; Iyer, V; Kahari, A; Jekosch, K; Kasprzyk, A; Keefe, D; Keenan, S; Lehvaslaiho, H; McVicker, G; Melsopp, C; Meidl, P; Mongin, E; Pettett, R; Potter, S; Proctor, G; Rae, M; Searle, S; Slater, G; Smedley, D; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Storey, R; Ureta-Vidal, A; Woodwark, C; Clamp, M; Hubbard, T

2004-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organize biology around the sequences of large genomes. It is a comprehensive and integrated source of annotation of large genome sequences, available via interactive website, web services or flat files. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. The facilities of the system range from sequence analysis to data storage and visualization and installations exist around the world both in companies and at academic sites. With a total of nine genome sequences available from Ensembl and more genomes to follow, recent developments have focused mainly on closer integration between genomes and external data.

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/ .

Image Harvest: an open-source platform for high-throughput plant image processing and analysis.

PubMed

Knecht, Avi C; Campbell, Malachy T; Caprez, Adam; Swanson, David R; Walia, Harkamal

2016-05-01

High-throughput plant phenotyping is an effective approach to bridge the genotype-to-phenotype gap in crops. Phenomics experiments typically result in large-scale image datasets, which are not amenable for processing on desktop computers, thus creating a bottleneck in the image-analysis pipeline. Here, we present an open-source, flexible image-analysis framework, called Image Harvest (IH), for processing images originating from high-throughput plant phenotyping platforms. Image Harvest is developed to perform parallel processing on computing grids and provides an integrated feature for metadata extraction from large-scale file organization. Moreover, the integration of IH with the Open Science Grid provides academic researchers with the computational resources required for processing large image datasets at no cost. Image Harvest also offers functionalities to extract digital traits from images to interpret plant architecture-related characteristics. To demonstrate the applications of these digital traits, a rice (Oryza sativa) diversity panel was phenotyped and genome-wide association mapping was performed using digital traits that are used to describe different plant ideotypes. Three major quantitative trait loci were identified on rice chromosomes 4 and 6, which co-localize with quantitative trait loci known to regulate agronomically important traits in rice. Image Harvest is an open-source software for high-throughput image processing that requires a minimal learning curve for plant biologists to analyzephenomics datasets. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

ERP Reliability Analysis (ERA) Toolbox: An open-source toolbox for analyzing the reliability of event-related brain potentials.

PubMed

Clayson, Peter E; Miller, Gregory A

2017-01-01

Generalizability theory (G theory) provides a flexible, multifaceted approach to estimating score reliability. G theory's approach to estimating score reliability has important advantages over classical test theory that are relevant for research using event-related brain potentials (ERPs). For example, G theory does not require parallel forms (i.e., equal means, variances, and covariances), can handle unbalanced designs, and provides a single reliability estimate for designs with multiple sources of error. This monograph provides a detailed description of the conceptual framework of G theory using examples relevant to ERP researchers, presents the algorithms needed to estimate ERP score reliability, and provides a detailed walkthrough of newly-developed software, the ERP Reliability Analysis (ERA) Toolbox, that calculates score reliability using G theory. The ERA Toolbox is open-source, Matlab software that uses G theory to estimate the contribution of the number of trials retained for averaging, group, and/or event types on ERP score reliability. The toolbox facilitates the rigorous evaluation of psychometric properties of ERP scores recommended elsewhere in this special issue. Copyright © 2016 Elsevier B.V. All rights reserved.

The GenABEL Project for statistical genomics.

PubMed

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

2016-01-01

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

FREEWAT: an HORIZON 2020 project to build open source tools for water management.

NASA Astrophysics Data System (ADS)

Foglia, L.; Rossetto, R.; Borsi, I.; Mehl, S.; Velasco Mansilla, V.

2015-12-01

FREEWAT is an HORIZON 2020 EU project. FREEWAT main result will be an open source and public domain GIS integrated modelling environment for the simulation of water quantity and quality in surface water and groundwater with an integrated water management and planning module. FREEWAT aims at promoting water resource management by simplifying the application of the Water Framework Directive and related Directives. Specific objectives of the project are: to coordinate previous EU and national funded research to integrate existing software modules for water management in a single environment into the GIS based FREEWAT and to support the FREEWAT application in an innovative participatory approach gathering technical staff and relevant stakeholders (policy and decision makers) in designing scenarios for application of water policies. The open source characteristics of the platform allow to consider this an initiative "ad includendum", as further institutions or developers may contribute to the development. Core of the platform is the SID&GRID framework (GIS integrated physically-based distributed numerical hydrological model based on a modified version of MODFLOW 2005; Rossetto et al. 2013) in its version ported to QGIS desktop. Activities are carried out on two lines: (i) integration of modules to fulfill the end-users requirements, including tools for producing feasibility and management plans; (ii) a set of activities to fix bugs and to provide a well-integrated interface for the different tools implemented. Further capabilities to be integrated are: - module for water management and planning; - calibration, uncertainty and sensitivity analysis; - module for solute transport in unsaturated zone; - module for crop growth and water requirements in agriculture; - tools for groundwater quality issues and for the analysis, interpretation and visualization of hydrogeological data. Through creating a common environment among water research/professionals, policy makers and implementers, FREEWAT main impact will be on enhancing science- and participatory approach and evidence-based decision making in water resource management, hence producing relevant and appropriate outcomes for policy implementation. Large stakeholders involvement is thought to guarantee results dissemination and exploitation.

MASTODON: A geosciences simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture (extended finite-element method), and porous media, among others. The tensor mechanics and contact modules, in particular, are well suited for nonlinear geosciences problems. Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON; https://seismic-research.inl.gov/SitePages/Mastodon.aspx)--a MOOSE-based application--is capable of analyzing the response of 3D soil-structure systems to external hazards with current development focused on earthquakes. It is capable of simulating seismic events and can perform extensive "source-to-site" simulations including earthquake fault rupture, nonlinear wave propagation, and nonlinear soil-structure interaction analysis. MASTODON also includes a dynamic probabilistic risk assessment capability that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment. Although MASTODON has been developed for the nuclear industry, it can be used to assess the risk for any structure subjected to earthquakes.The geosciences community can learn from the nuclear industry and harness the enormous effort underway to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The geosciences community could benefit from existing tools by enabling collaboration between researchers and practitioners throughout the world and advance the state-of-the-art in line with other scientific research efforts.

Specifications and implementation of the RT MHD control system for the EC launcher of FTU

NASA Astrophysics Data System (ADS)

Galperti, C.; Alessi, E.; Boncagni, L.; Bruschi, A.; Granucci, G.; Grosso, A.; Iannone, F.; Marchetto, C.; Nowak, S.; Panella, M.; Sozzi, C.; Tilia, B.

2012-09-01

To perform real time plasma control experiments using EC heating waves by using the new fast launcher installed on FTU a dedicated data acquisition and elaboration system has been designed recently. A prototypical version of the acquisition/control system has been recently developed and will be tested on FTU machine in its next experimental campaign. The open-source framework MARTe (Multi-threaded Application Real-Time executor) on Linux/RTAI real-time operating system has been chosen as software platform to realize the control system. Standard open-architecture industrial PCs, based either on VME bus and CompactPCI bus equipped with standard input/output cards are the chosen hardware platform.

Effective communication during an influenza pandemic: the value of using a crisis and emergency risk communication framework.

PubMed

Reynolds, Barbara; Quinn Crouse, Sandra

2008-10-01

During a crisis, an open and empathetic style of communication that engenders the public's trust is the most effective when officials are attempting to galvanize the population to take a positive action or refrain from a harmful act. Although trust is imperative in a crisis, public suspicions of scientific experts and government are increasing for a variety of reasons, including access to more sources of conflicting information, a reduction in the use of scientific reasoning in decision making, and political infighting. Trust and credibility--which are demonstrated through empathy and caring, competence and expertise, honesty and openness, and dedication and commitment--are essential elements of persuasive communication.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

PubMed

David, Fabrice P A; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch.

HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis

PubMed Central

David, Fabrice P. A.; Delafontaine, Julien; Carat, Solenne; Ross, Frederick J.; Lefebvre, Gregory; Jarosz, Yohan; Sinclair, Lucas; Noordermeer, Daan; Rougemont, Jacques; Leleu, Marion

2014-01-01

The HTSstation analysis portal is a suite of simple web forms coupled to modular analysis pipelines for various applications of High-Throughput Sequencing including ChIP-seq, RNA-seq, 4C-seq and re-sequencing. HTSstation offers biologists the possibility to rapidly investigate their HTS data using an intuitive web application with heuristically pre-defined parameters. A number of open-source software components have been implemented and can be used to build, configure and run HTS analysis pipelines reactively. Besides, our programming framework empowers developers with the possibility to design their own workflows and integrate additional third-party software. The HTSstation web application is accessible at http://htsstation.epfl.ch. PMID:24475057

HEPData: a repository for high energy physics data

NASA Astrophysics Data System (ADS)

Maguire, Eamonn; Heinrich, Lukas; Watt, Graeme

2017-10-01

The Durham High Energy Physics Database (HEPData) has been built up over the past four decades as a unique open-access repository for scattering data from experimental particle physics papers. It comprises data points underlying several thousand publications. Over the last two years, the HEPData software has been completely rewritten using modern computing technologies as an overlay on the Invenio v3 digital library framework. The software is open source with the new site available at https://hepdata.net now replacing the previous site at http://hepdata.cedar.ac.uk. In this write-up, we describe the development of the new site and explain some of the advantages it offers over the previous platform.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry.

PubMed

Röst, Hannes L; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS.

Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry

PubMed Central

Röst, Hannes L.; Schmitt, Uwe; Aebersold, Ruedi; Malmström, Lars

2015-01-01

Motivation In mass spectrometry-based proteomics, XML formats such as mzML and mzXML provide an open and standardized way to store and exchange the raw data (spectra and chromatograms) of mass spectrometric experiments. These file formats are being used by a multitude of open-source and cross-platform tools which allow the proteomics community to access algorithms in a vendor-independent fashion and perform transparent and reproducible data analysis. Recent improvements in mass spectrometry instrumentation have increased the data size produced in a single LC-MS/MS measurement and put substantial strain on open-source tools, particularly those that are not equipped to deal with XML data files that reach dozens of gigabytes in size. Results Here we present a fast and versatile parsing library for mass spectrometric XML formats available in C++ and Python, based on the mature OpenMS software framework. Our library implements an API for obtaining spectra and chromatograms under memory constraints using random access or sequential access functions, allowing users to process datasets that are much larger than system memory. For fast access to the raw data structures, small XML files can also be completely loaded into memory. In addition, we have improved the parsing speed of the core mzML module by over 4-fold (compared to OpenMS 1.11), making our library suitable for a wide variety of algorithms that need fast access to dozens of gigabytes of raw mass spectrometric data. Availability Our C++ and Python implementations are available for the Linux, Mac, and Windows operating systems. All proposed modifications to the OpenMS code have been merged into the OpenMS mainline codebase and are available to the community at https://github.com/OpenMS/OpenMS. PMID:25927999

New virtual laboratories presenting advanced motion control concepts

NASA Astrophysics Data System (ADS)

Goubej, Martin; Krejčí, Alois; Reitinger, Jan

2015-11-01

The paper deals with development of software framework for rapid generation of remote virtual laboratories. Client-server architecture is chosen in order to employ real-time simulation core which is running on a dedicated server. Ordinary web browser is used as a final renderer to achieve hardware independent solution which can be run on different target platforms including laptops, tablets or mobile phones. The provided toolchain allows automatic generation of the virtual laboratory source code from the configuration file created in the open- source Inkscape graphic editor. Three virtual laboratories presenting advanced motion control algorithms have been developed showing the applicability of the proposed approach.

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/.

Integrated Multidisciplinary Optimization Objects

NASA Technical Reports Server (NTRS)

Alston, Katherine

2014-01-01

OpenMDAO is an open-source MDAO framework. It is used to develop an integrated analysis and design environment for engineering challenges. This Phase II project integrated additional modules and design tools into OpenMDAO to perform discipline-specific analysis across multiple flight regimes at varying levels of fidelity. It also showcased a refined system architecture that allows the system to be less customized to a specific configuration (i.e., system and configuration separation). By delivering a capable and validated MDAO system along with a set of example applications to be used as a template for future users, this work greatly expands NASA's high-fidelity, physics-based MDAO capabilities and enables the design of revolutionary vehicles in a cost-effective manner. This proposed work complements M4 Engineering's expertise in developing modeling and simulation toolsets that solve relevant subsonic, supersonic, and hypersonic demonstration applications.

Flight Software Development for the CHEOPS Instrument with the CORDET Framework

NASA Astrophysics Data System (ADS)

Cechticky, V.; Ottensamer, R.; Pasetti, A.

2015-09-01

CHEOPS is an ESA S-class mission dedicated to the precise measurement of radii of already known exoplanets using ultra-high precision photometry. The instrument flight software controlling the instrument and handling the science data is developed by the University of Vienna using the CORDET Framework offered by P&P Software GmbH. The CORDET Framework provides a generic software infrastructure for PUS-based applications. This paper describes how the framework is used for the CHEOPS application software to provide a consistent solution for to the communication and control services, event handling and FDIR procedures. This approach is innovative in four respects: (a) it is a true third-party reuse; (b) re-use is done at specification, validation and code level; (c) the re-usable assets and their qualification data package are entirely open-source; (d) re-use is based on call-back with the application developer providing functions which are called by the reusable architecture. File names missing from here on out (I tried to mimic the files names from before.)

Parametric estimation for reinforced concrete relief shelter for Aceh cases

NASA Astrophysics Data System (ADS)

Atthaillah; Saputra, Eri; Iqbal, Muhammad

2018-05-01

This paper was a work in progress (WIP) to discover a rapid parametric framework for post-disaster permanent shelter’s materials estimation. The intended shelters were reinforced concrete construction with bricks as its wall. Inevitably, in post-disaster cases, design variations were needed to help suited victims condition. It seemed impossible to satisfy a beneficiary with a satisfactory design utilizing the conventional method. This study offered a parametric framework to overcome slow construction-materials estimation issue against design variations. Further, this work integrated parametric tool, which was Grasshopper to establish algorithms that simultaneously model, visualize, calculate and write the calculated data to a spreadsheet in a real-time. Some customized Grasshopper components were created using GHPython scripting for a more optimized algorithm. The result from this study was a partial framework that successfully performed modeling, visualization, calculation and writing the calculated data simultaneously. It meant design alterations did not escalate time needed for modeling, visualization, and material estimation. Further, the future development of the parametric framework will be made open source.

The RISE Framework: Using Learning Analytics to Automatically Identify Open Educational Resources for Continuous Improvement

ERIC Educational Resources Information Center

Bodily, Robert; Nyland, Rob; Wiley, David

2017-01-01

The RISE (Resource Inspection, Selection, and Enhancement) Framework is a framework supporting the continuous improvement of open educational resources (OER). The framework is an automated process that identifies learning resources that should be evaluated and either eliminated or improved. This is particularly useful in OER contexts where the…

SensorWeb Hub infrastructure for open access to scientific research data

NASA Astrophysics Data System (ADS)

de Filippis, Tiziana; Rocchi, Leandro; Rapisardi, Elena

2015-04-01

The sharing of research data is a new challenge for the scientific community that may benefit from a large amount of information to solve environmental issues and sustainability in agriculture and urban contexts. Prerequisites for this challenge is the development of an infrastructure that ensure access, management and preservation of data, technical support for a coordinated and harmonious management of data that, in the framework of Open Data Policies, should encourages the reuse and the collaboration. The neogeography and the citizen as sensors approach, highlight that new data sources need a new set of tools and practices so to collect, validate, categorize, and use / access these "crowdsourced" data, that integrate the data sets produced in the scientific field, thus "feeding" the overall available data for analysis and research. When the scientific community embraces the dimension of collaboration and sharing, access and re-use, in order to accept the open innovation approach, it should redesign and reshape the processes of data management: the challenges of technological and cultural innovation, enabled by web 2.0 technologies, bring to the scenario where the sharing of structured and interoperable data will constitute the unavoidable building block to set up a new paradigm of scientific research. In this perspective the Institute of Biometeorology, CNR, whose aim is contributing to sharing and development of research data, has developed the "SensorWebHub" (SWH) infrastructure to support the scientific activities carried out in several research projects at national and international level. It is designed to manage both mobile and fixed open source meteorological and environmental sensors, in order to integrate the existing agro-meteorological and urban monitoring networks. The proposed architecture uses open source tools to ensure sustainability in the development and deployment of web applications with geographic features and custom analysis, as requested by the different research projects. The SWH components are organized in typical client-server architecture and interact from the sensing process to the representation of the results to the end-users. The Web Application enables to view and analyse the data stored in the GeoDB. The interface is designed following Internet browsers specifications allowing the visualization of collected data in different formats (tabular, chart and geographic map). The services for the dissemination of geo-referenced information, adopt the OGC specifications. SWH is a bottom-up collaborative initiative to share real time research data and pave the way for a open innovation approach in the scientific research. Until now this framework has been used for several WebGIS applications and WebApp for environmental monitoring at different temporal and spatial scales.

Hierarchical Testing with Automated Document Generation for Amanzi, ASCEM's Subsurface Flow and Reactive Transport Simulator

NASA Astrophysics Data System (ADS)

Moulton, J. D.; Steefel, C. I.; Yabusaki, S.; Castleton, K.; Scheibe, T. D.; Keating, E. H.; Freedman, V. L.

2013-12-01

The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments use a graded and iterative approach, beginning with simplified highly abstracted models, and adding geometric and geologic complexity as understanding is gained. To build confidence in this assessment capability, extensive testing of the underlying tools is needed. Since the tools themselves, such as the subsurface flow and reactive-transport simulator, Amanzi, are under active development, testing must be both hierarchical and highly automated. In this presentation we show how we have met these requirements, by leveraging the python-based open-source documentation system called Sphinx with several other open-source tools. Sphinx builds on the reStructured text tool docutils, with important extensions that include high-quality formatting of equations, and integrated plotting through matplotlib. This allows the documentation, as well as the input files for tests, benchmark and tutorial problems, to be maintained with the source code under a version control system. In addition, it enables developers to build documentation in several different formats (e.g., html and pdf) from a single source. We will highlight these features, and discuss important benefits of this approach for Amanzi. In addition, we'll show that some of ASCEM's other tools, such as the sampling provided by the Uncertainty Quantification toolset, are naturally leveraged to enable more comprehensive testing. Finally, we will highlight the integration of this hiearchical testing and documentation framework with our build system and tools (CMake, CTest, and CDash).

Mayday - integrative analytics for expression data

PubMed Central

2010-01-01

Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension possibilities using compiled plugins and ad-hoc scripting allow for the rapid adaption of Mayday also to very specialized data exploration. Mayday is available at http://microarray-analysis.org. PMID:20214778

Building a world-wide open source community around a software framework: progress, dos, and don'ts

NASA Astrophysics Data System (ADS)

Ibsen, Jorge; Antognini, Jonathan; Avarias, Jorge; Caproni, Alessandro; Fuessling, Matthias; Gimenez, Guillermo; Verma, Khushbu; Mora, Matias; Schwarz, Joseph; Staig, Tomás.

2016-08-01

As we all know too well, building up a collaborative community around a software infrastructure is not easy. Besides recruiting enthusiasts to work as part of it, mostly for free, to succeed you also need to overcome a number of technical, sociological, and, to our surprise, some political hurdles. The ALMA Common Software (ACS) was developed at ESO and partner institutions over the course of more than 10 years. While it was mainly intended for the ALMA Observatory, it was early on thought as a generic distributed control framework. ACS has been periodically released to the public through an LGPL license, which encouraged around a dozen non-ALMA institutions to make use of ACS for both industrial and educational applications. In recent years, the Cherenkov Telescope Array and the LLAMA Observatory have also decided to adopt the framework for their own control systems. The aim of the "ACS Community" is to support independent initiatives in making use of the ACS framework and to further contribute to its development. The Community provides access to a growing network of volunteers eager to develop ACS in areas that are not necessarily in ALMA's interests, and/or were not within the original system scope. Current examples are: support for additional OS platforms, extension of supported hardware interfaces, a public code repository and a build farm. The ACS Community makes use of existing collaborations with Chilean and Brazilian universities, reaching out to promising engineers in the making. At the same time, projects actively using ACS have committed valuable resources to assist the Community's work. Well established training programs like the ACS Workshops are also being continued through the Community's work. This paper aims to give a detailed account of the ongoing (second) journey towards establishing a world-wide open source collaboration around ACS. The ACS Community is growing into a horizontal partnership across a decentralized and diversified group of actors, and we are excited about its technical and human potential.

Impact of the social networking applications for health information management for patients and physicians.

PubMed

Sahama, Tony; Liang, Jian; Iannella, Renato

2012-01-01

Most social network users hold more than one social network account and utilize them in different ways depending on the digital context. For example, friendly chat on Facebook, professional discussion on LinkedIn, and health information exchange on PatientsLikeMe. Thus many web users need to manage many disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time consuming, inefficient, and leads to lost opportunity. In this paper we propose a framework for multiple profile management of online social networks and showcase a demonstrator utilising an open source platform. The result of the research enables a user to create and manage an integrated profile and share/synchronise their profiles with their social networks. A number of use cases were created to capture the functional requirements and describe the interactions between users and the online services. An innovative application of this project is in public health informatics. We utilize the prototype to examine how the framework can benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians.

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework

PubMed Central

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts. PMID:28360851

Neuroimaging, Genetics, and Clinical Data Sharing in Python Using the CubicWeb Framework.

PubMed

Grigis, Antoine; Goyard, David; Cherbonnier, Robin; Gareau, Thomas; Papadopoulos Orfanos, Dimitri; Chauvat, Nicolas; Di Mascio, Adrien; Schumann, Gunter; Spooren, Will; Murphy, Declan; Frouin, Vincent

2017-01-01

In neurosciences or psychiatry, the emergence of large multi-center population imaging studies raises numerous technological challenges. From distributed data collection, across different institutions and countries, to final data publication service, one must handle the massive, heterogeneous, and complex data from genetics, imaging, demographics, or clinical scores. These data must be both efficiently obtained and downloadable. We present a Python solution, based on the CubicWeb open-source semantic framework, aimed at building population imaging study repositories. In addition, we focus on the tools developed around this framework to overcome the challenges associated with data sharing and collaborative requirements. We describe a set of three highly adaptive web services that transform the CubicWeb framework into a (1) multi-center upload platform, (2) collaborative quality assessment platform, and (3) publication platform endowed with massive-download capabilities. Two major European projects, IMAGEN and EU-AIMS, are currently supported by the described framework. We also present a Python package that enables end users to remotely query neuroimaging, genetics, and clinical data from scripts.

Multivariate cross-frequency coupling via generalized eigendecomposition

PubMed Central

Cohen, Michael X

2017-01-01

This paper presents a new framework for analyzing cross-frequency coupling in multichannel electrophysiological recordings. The generalized eigendecomposition-based cross-frequency coupling framework (gedCFC) is inspired by source-separation algorithms combined with dynamics of mesoscopic neurophysiological processes. It is unaffected by factors that confound traditional CFC methods—such as non-stationarities, non-sinusoidality, and non-uniform phase angle distributions—attractive properties considering that brain activity is neither stationary nor perfectly sinusoidal. The gedCFC framework opens new opportunities for conceptualizing CFC as network interactions with diverse spatial/topographical distributions. Five specific methods within the gedCFC framework are detailed, these are validated in simulated data and applied in several empirical datasets. gedCFC accurately recovers physiologically plausible CFC patterns embedded in noise that causes traditional CFC methods to perform poorly. The paper also demonstrates that spike-field coherence in multichannel local field potential data can be analyzed using the gedCFC framework, which provides significant advantages over traditional spike-field coherence analyses. Null-hypothesis testing is also discussed. DOI: http://dx.doi.org/10.7554/eLife.21792.001 PMID:28117662

Amanzi: An Open-Source Multi-process Simulator for Environmental Applications

NASA Astrophysics Data System (ADS)

Moulton, J. D.; Molins, S.; Johnson, J. N.; Coon, E.; Lipnikov, K.; Day, M.; Barker, E.

2014-12-01

The Advanced Simulation Capabililty for Environmental Management (ASCEM) program is developing an approach and open-source tool suite for standardized risk and performance assessments at legacy nuclear waste sites. These assessments begin with simplified models, and add geometric and geologic complexity as understanding is gained. The Platform toolsets (Akuna) generates these conceptual models and Amanzi provides the computational engine to perform the simulations, returning the results for analysis and visualization. In this presentation we highlight key elements of the design, algorithms and implementations used in Amanzi. In particular, the hierarchical and modular design is aligned with the coupled processes being sumulated, and naturally supports a wide range of model complexity. This design leverages a dynamic data manager and the synergy of two graphs (one from the high-level perspective of the models the other from the dependencies of the variables in the model) to enable this flexible model configuration at run time. Moreover, to model sites with complex hydrostratigraphy, as well as engineered systems, we are developing a dual unstructured/structured capability. Recently, these capabilities have been collected in a framework named Arcos, and efforts have begun to improve interoperability between the unstructured and structured AMR approaches in Amanzi. To leverage a range of biogeochemistry capability from the community (e.g., CrunchFlow, PFLOTRAN, etc.), a biogeochemistry interface library was developed called Alquimia. To ensure that Amanzi is truly an open-source community code we require a completely open-source tool chain for our development. We will comment on elements of this tool chain, including the testing and documentation development tools such as docutils, and Sphinx. Finally, we will show simulation results from our phased demonstrations, including the geochemically complex Savannah River F-Area seepage basins.

Plenario: A Spatio-Temporal Platform for Discovery and Exploration of Urban Science Data

NASA Astrophysics Data System (ADS)

Engler, W. H.; Malik, T.; Catlett, C.; Foster, I.; Goldstein, B.

2015-12-01

The past decade has seen the widespread release of open data concerning city services, conditions, and activities by government bodies and public institutions of all sizes. Hundreds of open data portals now host thousands of datasets of many different types. These new data sources represent enormous potential for improved understanding of urban dynamics and processes—and, ultimately, for more livable, efficient, and prosperous communities. However, those who seek to realize this potential quickly discover that discovering and applying those data relevant to any particular question can be extraordinarily difficult, due to decentralized storage, heterogeneous formats, and poor documentation. In this context, we introduce Plenario, a platform designed to automating time-consuming tasks associated with the discovery, exploration, and application of open city data—and, in so doing, reduce barriers to data use for researchers, policymakers, service providers, journalists, and members of the general public. Key innovations include a geospatial data warehouse that allows data from many sources to be registered into a common spatial and temporal frame; simple and intuitive interfaces that permit rapid discovery and exploration of data subsets pertaining to a particular area and time, regardless of type and source; easy export of such data subsets for further analysis; a user-configurable data ingest framework for automated importing and periodic updating of new datasets into the data warehouse; cloud hosting for elastic scaling and rapid creation of new Plenario instances; and an open source implementation to enable community contributions. We describe here the architecture and implementation of the Plenario platform, discuss lessons learned from its use by several communities, and outline plans for future work.

Metadata mapping and reuse in caBIG.

PubMed

Kunz, Isaac; Lin, Ming-Chin; Frey, Lewis

2009-02-05

This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG framework or other frameworks that use metadata repositories. The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG framework and potentially any framework that uses a metadata repository. This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG. This effort contributes to facilitating the development of interoperable systems within caBIG as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

Open Inclusion or Shameful Secret: A Comparison of Characters with Fetal Alcohol Spectrum Disorders (FASD) and Characters with Autism Spectrum Disorders (ASD) in a North American Sample of Books for Children and Young Adults

ERIC Educational Resources Information Center

Barker, Conor; Kulyk, Juli; Knorr, Lyndsay; Brenna, Beverley

2011-01-01

Using a framework of critical literacy, and acknowledging the characteristics of Radical Change, the authors explore 75 North American youth fiction novels which depict characters with disabilities. Books were identified from a variety of sources (i.e., awards lists, book reviews, other research, and word-of-mouth), to represent a random sample…

AliEn—ALICE environment on the GRID

NASA Astrophysics Data System (ADS)

Saiz, P.; Aphecetche, L.; Bunčić, P.; Piskač, R.; Revsbech, J.-E.; Šego, V.; Alice Collaboration

2003-04-01

AliEn ( http://alien.cern.ch) (ALICE Environment) is a Grid framework built on top of the latest Internet standards for information exchange and authentication (SOAP, PKI) and common Open Source components. AliEn provides a virtual file catalogue that allows transparent access to distributed datasets and a number of collaborating Web services which implement the authentication, job execution, file transport, performance monitor and event logging. In the paper we will present the architecture and components of the system.

CVcat: An interactive database on cataclysmic variables

NASA Astrophysics Data System (ADS)

Kube, J.; Gänsicke, B. T.; Euchner, F.; Hoffmann, B.

2003-06-01

CVcat is a database that contains published data on cataclysmic variables and related objects. Unlike in the existing online sources, the users are allowed to add data to the catalogue. The concept of an ``open catalogue'' approach is reviewed together with the experience from one year of public usage of CVcat. New concepts to be included in the upcoming AstroCat framework and the next CVcat implementation are presented. CVcat can be found at http://www.cvcat.org.

The Ensembl genome database project.

PubMed

Hubbard, T; Barker, D; Birney, E; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Huminiecki, L; Kasprzyk, A; Lehvaslaiho, H; Lijnzaad, P; Melsopp, C; Mongin, E; Pettett, R; Pocock, M; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Clamp, M

2002-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of the human genome sequence, with confirmed gene predictions that have been integrated with external data sources, and is available as either an interactive web site or as flat files. It is also an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements from sequence analysis to data storage and visualisation. The Ensembl site is one of the leading sources of human genome sequence annotation and provided much of the analysis for publication by the international human genome project of the draft genome. The Ensembl system is being installed around the world in both companies and academic sites on machines ranging from supercomputers to laptops.

GoFFish: A Sub-Graph Centric Framework for Large-Scale Graph Analytics1

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

Simmhan, Yogesh; Kumbhare, Alok; Wickramaarachchi, Charith

2014-08-25

Large scale graph processing is a major research area for Big Data exploration. Vertex centric programming models like Pregel are gaining traction due to their simple abstraction that allows for scalable execution on distributed systems naturally. However, there are limitations to this approach which cause vertex centric algorithms to under-perform due to poor compute to communication overhead ratio and slow convergence of iterative superstep. In this paper we introduce GoFFish a scalable sub-graph centric framework co-designed with a distributed persistent graph storage for large scale graph analytics on commodity clusters. We introduce a sub-graph centric programming abstraction that combines themore » scalability of a vertex centric approach with the flexibility of shared memory sub-graph computation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation. We map Connected Components, SSSP and PageRank algorithms to this model to illustrate its flexibility. Further, we empirically analyze GoFFish using several real world graphs and demonstrate its significant performance improvement, orders of magnitude in some cases, compared to Apache Giraph, the leading open source vertex centric implementation.« less

ROSE::FTTransform - A Source-to-Source Translation Framework for Exascale Fault-Tolerance Research

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

Lidman, J; Quinlan, D; Liao, C

2012-03-26

Exascale computing systems will require sufficient resilience to tolerate numerous types of hardware faults while still assuring correct program execution. Such extreme-scale machines are expected to be dominated by processors driven at lower voltages (near the minimum 0.5 volts for current transistors). At these voltage levels, the rate of transient errors increases dramatically due to the sensitivity to transient and geographically localized voltage drops on parts of the processor chip. To achieve power efficiency, these processors are likely to be streamlined and minimal, and thus they cannot be expected to handle transient errors entirely in hardware. Here we present anmore » open, compiler-based framework to automate the armoring of High Performance Computing (HPC) software to protect it from these types of transient processor errors. We develop an open infrastructure to support research work in this area, and we define tools that, in the future, may provide more complete automated and/or semi-automated solutions to support software resiliency on future exascale architectures. Results demonstrate that our approach is feasible, pragmatic in how it can be separated from the software development process, and reasonably efficient (0% to 30% overhead for the Jacobi iteration on common hardware; and 20%, 40%, 26%, and 2% overhead for a randomly selected subset of benchmarks from the Livermore Loops [1]).« less

An Open Source Simulation Model for Soil and Sediment Bioturbation

PubMed Central

Schiffers, Katja; Teal, Lorna Rachel; Travis, Justin Mark John; Solan, Martin

2011-01-01

Bioturbation is one of the most widespread forms of ecological engineering and has significant implications for the structure and functioning of ecosystems, yet our understanding of the processes involved in biotic mixing remains incomplete. One reason is that, despite their value and utility, most mathematical models currently applied to bioturbation data tend to neglect aspects of the natural complexity of bioturbation in favour of mathematical simplicity. At the same time, the abstract nature of these approaches limits the application of such models to a limited range of users. Here, we contend that a movement towards process-based modelling can improve both the representation of the mechanistic basis of bioturbation and the intuitiveness of modelling approaches. In support of this initiative, we present an open source modelling framework that explicitly simulates particle displacement and a worked example to facilitate application and further development. The framework combines the advantages of rule-based lattice models with the application of parameterisable probability density functions to generate mixing on the lattice. Model parameters can be fitted by experimental data and describe particle displacement at the spatial and temporal scales at which bioturbation data is routinely collected. By using the same model structure across species, but generating species-specific parameters, a generic understanding of species-specific bioturbation behaviour can be achieved. An application to a case study and comparison with a commonly used model attest the predictive power of the approach. PMID:22162997

An open source simulation model for soil and sediment bioturbation.

PubMed

Schiffers, Katja; Teal, Lorna Rachel; Travis, Justin Mark John; Solan, Martin

2011-01-01

Bioturbation is one of the most widespread forms of ecological engineering and has significant implications for the structure and functioning of ecosystems, yet our understanding of the processes involved in biotic mixing remains incomplete. One reason is that, despite their value and utility, most mathematical models currently applied to bioturbation data tend to neglect aspects of the natural complexity of bioturbation in favour of mathematical simplicity. At the same time, the abstract nature of these approaches limits the application of such models to a limited range of users. Here, we contend that a movement towards process-based modelling can improve both the representation of the mechanistic basis of bioturbation and the intuitiveness of modelling approaches. In support of this initiative, we present an open source modelling framework that explicitly simulates particle displacement and a worked example to facilitate application and further development. The framework combines the advantages of rule-based lattice models with the application of parameterisable probability density functions to generate mixing on the lattice. Model parameters can be fitted by experimental data and describe particle displacement at the spatial and temporal scales at which bioturbation data is routinely collected. By using the same model structure across species, but generating species-specific parameters, a generic understanding of species-specific bioturbation behaviour can be achieved. An application to a case study and comparison with a commonly used model attest the predictive power of the approach.

BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience

PubMed Central

Van Geit, Werner; Gevaert, Michael; Chindemi, Giuseppe; Rössert, Christian; Courcol, Jean-Denis; Muller, Eilif B.; Schürmann, Felix; Segev, Idan; Markram, Henry

2016-01-01

At many scales in neuroscience, appropriate mathematical models take the form of complex dynamical systems. Parameterizing such models to conform to the multitude of available experimental constraints is a global non-linear optimisation problem with a complex fitness landscape, requiring numerical techniques to find suitable approximate solutions. Stochastic optimisation approaches, such as evolutionary algorithms, have been shown to be effective, but often the setting up of such optimisations and the choice of a specific search algorithm and its parameters is non-trivial, requiring domain-specific expertise. Here we describe BluePyOpt, a Python package targeted at the broad neuroscience community to simplify this task. BluePyOpt is an extensible framework for data-driven model parameter optimisation that wraps and standardizes several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures. The versatility of the BluePyOpt framework is demonstrated by working through three representative neuroscience specific use cases. PMID:27375471

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems.

PubMed

Baumgartner, William A; Cohen, K Bretonnel; Hunter, Lawrence

2008-01-29

Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain. Our evaluation framework was assembled using the Unstructured Information Management Architecture. It was used to analyze a set of gene mention identification systems involving 225 combinations of system, evaluation corpus, and correctness measure. Interactions between all three were found to affect the relative rankings of the systems. A second experiment evaluated gene normalization system performance using as input 4,097 combinations of gene mention systems and gene mention system-combining strategies. Gene mention system recall is shown to affect gene normalization system performance much more than does gene mention system precision, and high gene normalization performance is shown to be achievable with remarkably low levels of gene mention system precision. The software presented in this paper demonstrates the potential for novel discovery resulting from the structured evaluation of biomedical language processing systems, as well as the usefulness of such an evaluation framework for promoting collaboration between developers of biomedical language processing technologies. The code base is available as part of the BioNLP UIMA Component Repository on SourceForge.net.

An open-source framework for large-scale, flexible evaluation of biomedical text mining systems

PubMed Central

Baumgartner, William A; Cohen, K Bretonnel; Hunter, Lawrence

2008-01-01

Background Improved evaluation methodologies have been identified as a necessary prerequisite to the improvement of text mining theory and practice. This paper presents a publicly available framework that facilitates thorough, structured, and large-scale evaluations of text mining technologies. The extensibility of this framework and its ability to uncover system-wide characteristics by analyzing component parts as well as its usefulness for facilitating third-party application integration are demonstrated through examples in the biomedical domain. Results Our evaluation framework was assembled using the Unstructured Information Management Architecture. It was used to analyze a set of gene mention identification systems involving 225 combinations of system, evaluation corpus, and correctness measure. Interactions between all three were found to affect the relative rankings of the systems. A second experiment evaluated gene normalization system performance using as input 4,097 combinations of gene mention systems and gene mention system-combining strategies. Gene mention system recall is shown to affect gene normalization system performance much more than does gene mention system precision, and high gene normalization performance is shown to be achievable with remarkably low levels of gene mention system precision. Conclusion The software presented in this paper demonstrates the potential for novel discovery resulting from the structured evaluation of biomedical language processing systems, as well as the usefulness of such an evaluation framework for promoting collaboration between developers of biomedical language processing technologies. The code base is available as part of the BioNLP UIMA Component Repository on SourceForge.net. PMID:18230184

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

NASA Astrophysics Data System (ADS)

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

2017-10-01

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks. Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.

Materials Knowledge Systems in Python - A Data Science Framework for Accelerated Development of Hierarchical Materials.

PubMed

Brough, David B; Wheeler, Daniel; Kalidindi, Surya R

2017-03-01

There is a critical need for customized analytics that take into account the stochastic nature of the internal structure of materials at multiple length scales in order to extract relevant and transferable knowledge. Data driven Process-Structure-Property (PSP) linkages provide systemic, modular and hierarchical framework for community driven curation of materials knowledge, and its transference to design and manufacturing experts. The Materials Knowledge Systems in Python project (PyMKS) is the first open source materials data science framework that can be used to create high value PSP linkages for hierarchical materials that can be leveraged by experts in materials science and engineering, manufacturing, machine learning and data science communities. This paper describes the main functions available from this repository, along with illustrations of how these can be accessed, utilized, and potentially further refined by the broader community of researchers.

Automated Analysis of Stateflow Models

NASA Technical Reports Server (NTRS)

Bourbouh, Hamza; Garoche, Pierre-Loic; Garion, Christophe; Gurfinkel, Arie; Kahsaia, Temesghen; Thirioux, Xavier

2017-01-01

Stateflow is a widely used modeling framework for embedded and cyber physical systems where control software interacts with physical processes. In this work, we present a framework a fully automated safety verification technique for Stateflow models. Our approach is two-folded: (i) we faithfully compile Stateflow models into hierarchical state machines, and (ii) we use automated logic-based verification engine to decide the validity of safety properties. The starting point of our approach is a denotational semantics of State flow. We propose a compilation process using continuation-passing style (CPS) denotational semantics. Our compilation technique preserves the structural and modal behavior of the system. The overall approach is implemented as an open source toolbox that can be integrated into the existing Mathworks Simulink Stateflow modeling framework. We present preliminary experimental evaluations that illustrate the effectiveness of our approach in code generation and safety verification of industrial scale Stateflow models.

Materials Knowledge Systems in Python - A Data Science Framework for Accelerated Development of Hierarchical Materials

PubMed Central

Brough, David B; Wheeler, Daniel; Kalidindi, Surya R.

2017-01-01

There is a critical need for customized analytics that take into account the stochastic nature of the internal structure of materials at multiple length scales in order to extract relevant and transferable knowledge. Data driven Process-Structure-Property (PSP) linkages provide systemic, modular and hierarchical framework for community driven curation of materials knowledge, and its transference to design and manufacturing experts. The Materials Knowledge Systems in Python project (PyMKS) is the first open source materials data science framework that can be used to create high value PSP linkages for hierarchical materials that can be leveraged by experts in materials science and engineering, manufacturing, machine learning and data science communities. This paper describes the main functions available from this repository, along with illustrations of how these can be accessed, utilized, and potentially further refined by the broader community of researchers. PMID:28690971

Efficient LIDAR Point Cloud Data Managing and Processing in a Hadoop-Based Distributed Framework

NASA Astrophysics Data System (ADS)

Wang, C.; Hu, F.; Sha, D.; Han, X.

2017-10-01

Light Detection and Ranging (LiDAR) is one of the most promising technologies in surveying and mapping city management, forestry, object recognition, computer vision engineer and others. However, it is challenging to efficiently storage, query and analyze the high-resolution 3D LiDAR data due to its volume and complexity. In order to improve the productivity of Lidar data processing, this study proposes a Hadoop-based framework to efficiently manage and process LiDAR data in a distributed and parallel manner, which takes advantage of Hadoop's storage and computing ability. At the same time, the Point Cloud Library (PCL), an open-source project for 2D/3D image and point cloud processing, is integrated with HDFS and MapReduce to conduct the Lidar data analysis algorithms provided by PCL in a parallel fashion. The experiment results show that the proposed framework can efficiently manage and process big LiDAR data.

Modeling Geomagnetic Variations using a Machine Learning Framework

NASA Astrophysics Data System (ADS)

Cheung, C. M. M.; Handmer, C.; Kosar, B.; Gerules, G.; Poduval, B.; Mackintosh, G.; Munoz-Jaramillo, A.; Bobra, M.; Hernandez, T.; McGranaghan, R. M.

2017-12-01

We present a framework for data-driven modeling of Heliophysics time series data. The Solar Terrestrial Interaction Neural net Generator (STING) is an open source python module built on top of state-of-the-art statistical learning frameworks (traditional machine learning methods as well as deep learning). To showcase the capability of STING, we deploy it for the problem of predicting the temporal variation of geomagnetic fields. The data used includes solar wind measurements from the OMNI database and geomagnetic field data taken by magnetometers at US Geological Survey observatories. We examine the predictive capability of different machine learning techniques (recurrent neural networks, support vector machines) for a range of forecasting times (minutes to 12 hours). STING is designed to be extensible to other types of data. We show how STING can be used on large sets of data from different sensors/observatories and adapted to tackle other problems in Heliophysics.

CIM-EARTH: Community Integrated Model of Economic and Resource Trajectories for Humankind

NASA Astrophysics Data System (ADS)

Foster, I.; Elliott, J.; Munson, T.; Judd, K.; Moyer, E. J.; Sanstad, A. H.

2010-12-01

We report here on the development of an open source software framework termed CIM-EARTH that is intended to aid decision-making in climate and energy policy. Numerical modeling in support of evaluating policies to address climate change is difficult not only because of inherent uncertainties but because of the differences in scale and modeling approach required for various subcomponents of the system. Economic and climate models are structured quite differently, and while climate forcing can be assumed to be roughly global, climate impacts and the human response to them occur on small spatial scales. Mitigation policies likewise can be applied on scales ranging from the better part of a continent (e.g. a carbon cap-and-trade program for the entire U.S.) to a few hundred km (e.g. statewide renewable portfolio standards and local gasoline taxes). Both spatial and time resolution requirements can be challenging for global economic models. CIM-EARTH is a modular framework based around dynamic general equilibrium models. It is designed as a community tool that will enable study of the environmental benefits, transition costs, capitalization effects, and other consequences of both mitigation policies and unchecked climate change. Modularity enables both integration of highly resolved component sub-models for energy and other key systems and also user-directed choice of tradeoffs between e.g. spatial, sectoral, and time resolution. This poster describes the framework architecture, the current realized version, and plans for future releases. As with other open-source models familiar to the climate community (e.g. CCSM), deliverables will be made publicly available on a regular schedule, and community input is solicited for development of new features and modules.

An integrated development framework for rapid development of platform-independent and reusable satellite on-board software

NASA Astrophysics Data System (ADS)

Ziemke, Claas; Kuwahara, Toshinori; Kossev, Ivan

2011-09-01

Even in the field of small satellites, the on-board data handling subsystem has become complex and powerful. With the introduction of powerful CPUs and the availability of considerable amounts of memory on-board a small satellite it has become possible to utilize the flexibility and power of contemporary platform-independent real-time operating systems. Especially the non-commercial sector such like university institutes and community projects such as AMSAT or SSETI are characterized by the inherent lack of financial as well as manpower resources. The opportunity to utilize such real-time operating systems will contribute significantly to achieve a successful mission. Nevertheless the on-board software of a satellite is much more than just an operating system. It has to fulfill a multitude of functional requirements such as: Telecommand interpretation and execution, execution of control loops, generation of telemetry data and frames, failure detection isolation and recovery, the communication with peripherals and so on. Most of the aforementioned tasks are of generic nature and have to be conducted on any satellite with only minor modifications. A general set of functional requirements as well as a protocol for communication is defined in the SA ECSS-E-70-41A standard "Telemetry and telecommand packet utilization". This standard not only defines the communication protocol of the satellite-ground link but also defines a set of so called services which have to be available on-board of every compliant satellite and which are of generic nature. In this paper, a platform-independent and reusable framework is described which is implementing not only the ECSS-E-70-41A standard but also functionalities for interprocess communication, scheduling and a multitude of tasks commonly performed on-board of a satellite. By making use of the capabilities of the high-level programming language C/C++, the powerful open source library BOOST, the real-time operating system RTEMS and finally by providing generic functionalities compliant to the ECSS-E-70-41A standard the proposed framework can provide a great boost in productivity. Together with open source tools such like the GNU tool-chain, Eclipse SDK, the simulation framework OpenSimKit, the emulator QEMU, the proposed on-board software framework forms an integrated development framework. It is possible to design, code and build the on-board software together with the operating system and then run it on a simulated satellite for performance analysis and debugging purposes. This makes it possible to rapidly develop and deploy a full-fledged satellite on-board software with minimal cost and in a limited time frame.

Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation

PubMed Central

De Vos, Dirk; Dzhurakhalov, Abdiravuf; Stijven, Sean; Klosiewicz, Przemyslaw; Beemster, Gerrit T. S.; Broeckhove, Jan

2017-01-01

Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io. PMID:28523006

A flexible, interpretable framework for assessing sensitivity to unmeasured confounding.

PubMed

Dorie, Vincent; Harada, Masataka; Carnegie, Nicole Bohme; Hill, Jennifer

2016-09-10

When estimating causal effects, unmeasured confounding and model misspecification are both potential sources of bias. We propose a method to simultaneously address both issues in the form of a semi-parametric sensitivity analysis. In particular, our approach incorporates Bayesian Additive Regression Trees into a two-parameter sensitivity analysis strategy that assesses sensitivity of posterior distributions of treatment effects to choices of sensitivity parameters. This results in an easily interpretable framework for testing for the impact of an unmeasured confounder that also limits the number of modeling assumptions. We evaluate our approach in a large-scale simulation setting and with high blood pressure data taken from the Third National Health and Nutrition Examination Survey. The model is implemented as open-source software, integrated into the treatSens package for the R statistical programming language. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd. © 2016 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-08-30

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Tunable electrical conductivity in metal-organic framework thin film devices

DOEpatents

Talin, Albert Alec; Allendorf, Mark D.; Stavila, Vitalie; Leonard, Francois

2016-05-24

A composition including a porous metal organic framework (MOF) including an open metal site and a guest species capable of charge transfer that can coordinate with the open metal site, wherein the composition is electrically conductive. A method including infiltrating a porous metal organic framework (MOF) including an open metal site with a guest species that is capable of charge transfer; and coordinating the guest species to the open metal site to form a composition including an electrical conductivity greater than an electrical conductivity of the MOF.

Towards open collaborative health informatics - The Role of free/libre open source principles. Contribution of the IMIA Open Source Health Informatics Working Group.

PubMed

Karopka, T; Schmuhl, H; Marcelo, A; Molin, J Dal; Wright, G

2011-01-01

: To analyze the contribution of Free/Libre Open Source Software in health care (FLOSS-HC) and to give perspectives for future developments. The paper summarizes FLOSS-related trends in health care as anticipated by members of the IMIA Open Source Working Group. Data were obtained through literature review and personal experience and observations of the authors in the last two decades. A status quo is given by a frequency analysis of the database of Medfloss.org, one of the world's largest platforms dedicated to FLOSS-HC. The authors discuss current problems in the field of health care and finally give a prospective roadmap, a projection of the potential influences of FLOSS in health care. FLOSS-HC already exists for more than 2 decades. Several projects have shown that FLOSS may produce highly competitive alternatives to proprietary solutions that are at least equivalent in usability and have a better total cost of ownership ratio. The Medfloss.org database currently lists 221 projects of diverse application types. FLOSS principles hold a great potential for addressing several of the most critical problems in health care IT. The authors argue that an ecosystem perspective is relevant and that FLOSS principles are best suited to create health IT systems that are able to evolve over time as medical knowledge, technologies, insights, workflows etc. continuously change. All these factors that inherently influence the development of health IT systems are changing at an ever growing pace. Traditional models of software engineering are not able to follow these changes and provide up-to-date systems for an acceptable cost/value ratio. To allow FLOSS to positively influence Health IT in the future a "FLOSS-friendly" environment has to be provided. Policy makers should resolve uncertainties in the legal framework that disfavor FLOSS. Certification procedures should be specified in a way that they do not raise additional barriers for FLOSS.

Bonsai: an event-based framework for processing and controlling data streams

PubMed Central

Lopes, Gonçalo; Bonacchi, Niccolò; Frazão, João; Neto, Joana P.; Atallah, Bassam V.; Soares, Sofia; Moreira, Luís; Matias, Sara; Itskov, Pavel M.; Correia, Patrícia A.; Medina, Roberto E.; Calcaterra, Lorenza; Dreosti, Elena; Paton, Joseph J.; Kampff, Adam R.

2015-01-01

The design of modern scientific experiments requires the control and monitoring of many different data streams. However, the serial execution of programming instructions in a computer makes it a challenge to develop software that can deal with the asynchronous, parallel nature of scientific data. Here we present Bonsai, a modular, high-performance, open-source visual programming framework for the acquisition and online processing of data streams. We describe Bonsai's core principles and architecture and demonstrate how it allows for the rapid and flexible prototyping of integrated experimental designs in neuroscience. We specifically highlight some applications that require the combination of many different hardware and software components, including video tracking of behavior, electrophysiology and closed-loop control of stimulation. PMID:25904861

Convex Accelerated Maximum Entropy Reconstruction

PubMed Central

Worley, Bradley

2016-01-01

Maximum entropy (MaxEnt) spectral reconstruction methods provide a powerful framework for spectral estimation of nonuniformly sampled datasets. Many methods exist within this framework, usually defined based on the magnitude of a Lagrange multiplier in the MaxEnt objective function. An algorithm is presented here that utilizes accelerated first-order convex optimization techniques to rapidly and reliably reconstruct nonuniformly sampled NMR datasets using the principle of maximum entropy. This algorithm – called CAMERA for Convex Accelerated Maximum Entropy Reconstruction Algorithm – is a new approach to spectral reconstruction that exhibits fast, tunable convergence in both constant-aim and constant-lambda modes. A high-performance, open source NMR data processing tool is described that implements CAMERA, and brief comparisons to existing reconstruction methods are made on several example spectra. PMID:26894476

The Role of Semantics in Open-World, Integrative, Collaborative Science Data Platforms

NASA Astrophysics Data System (ADS)

Fox, Peter; Chen, Yanning; Wang, Han; West, Patrick; Erickson, John; Ma, Marshall

2014-05-01

As collaborative science spreads into more and more Earth and space science fields, both participants and funders are expressing stronger needs for highly functional data and information capabilities. Characteristics include a) easy to use, b) highly integrated, c) leverage investments, d) accommodate rapid technical change, and e) do not incur undue expense or time to build or maintain - these are not a small set of requirements. Based on our accumulated experience over the last ~ decade and several key technical approaches, we adapt, extend, and integrate several open source applications and frameworks to handle major portions of functionality for these platforms. This includes: an object-type repository, collaboration tools, identity management, all within a portal managing diverse content and applications. In this contribution, we present our methods and results of information models, adaptation, integration and evolution of a networked data science architecture based on several open source technologies (Drupal, VIVO, the Comprehensive Knowledge Archive Network; CKAN, and the Global Handle System; GHS). In particular we present the Deep Carbon Observatory - a platform for international science collaboration. We present and discuss key functional and non-functional attributes, and discuss the general applicability of the platform.

Scalable Regression Tree Learning on Hadoop using OpenPlanet

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

Yin, Wei; Simmhan, Yogesh; Prasanna, Viktor

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

An open source multivariate framework for n-tissue segmentation with evaluation on public data.

PubMed

Avants, Brian B; Tustison, Nicholas J; Wu, Jue; Cook, Philip A; Gee, James C

2011-12-01

We introduce Atropos, an ITK-based multivariate n-class open source segmentation algorithm distributed with ANTs ( http://www.picsl.upenn.edu/ANTs). The Bayesian formulation of the segmentation problem is solved using the Expectation Maximization (EM) algorithm with the modeling of the class intensities based on either parametric or non-parametric finite mixtures. Atropos is capable of incorporating spatial prior probability maps (sparse), prior label maps and/or Markov Random Field (MRF) modeling. Atropos has also been efficiently implemented to handle large quantities of possible labelings (in the experimental section, we use up to 69 classes) with a minimal memory footprint. This work describes the technical and implementation aspects of Atropos and evaluates its performance on two different ground-truth datasets. First, we use the BrainWeb dataset from Montreal Neurological Institute to evaluate three-tissue segmentation performance via (1) K-means segmentation without use of template data; (2) MRF segmentation with initialization by prior probability maps derived from a group template; (3) Prior-based segmentation with use of spatial prior probability maps derived from a group template. We also evaluate Atropos performance by using spatial priors to drive a 69-class EM segmentation problem derived from the Hammers atlas from University College London. These evaluation studies, combined with illustrative examples that exercise Atropos options, demonstrate both performance and wide applicability of this new platform-independent open source segmentation tool.

An Open Source Multivariate Framework for n-Tissue Segmentation with Evaluation on Public Data

PubMed Central

Tustison, Nicholas J.; Wu, Jue; Cook, Philip A.; Gee, James C.

2012-01-01

We introduce Atropos, an ITK-based multivariate n-class open source segmentation algorithm distributed with ANTs (http://www.picsl.upenn.edu/ANTs). The Bayesian formulation of the segmentation problem is solved using the Expectation Maximization (EM) algorithm with the modeling of the class intensities based on either parametric or non-parametric finite mixtures. Atropos is capable of incorporating spatial prior probability maps (sparse), prior label maps and/or Markov Random Field (MRF) modeling. Atropos has also been efficiently implemented to handle large quantities of possible labelings (in the experimental section, we use up to 69 classes) with a minimal memory footprint. This work describes the technical and implementation aspects of Atropos and evaluates its performance on two different ground-truth datasets. First, we use the BrainWeb dataset from Montreal Neurological Institute to evaluate three-tissue segmentation performance via (1) K-means segmentation without use of template data; (2) MRF segmentation with initialization by prior probability maps derived from a group template; (3) Prior-based segmentation with use of spatial prior probability maps derived from a group template. We also evaluate Atropos performance by using spatial priors to drive a 69-class EM segmentation problem derived from the Hammers atlas from University College London. These evaluation studies, combined with illustrative examples that exercise Atropos options, demonstrate both performance and wide applicability of this new platform-independent open source segmentation tool. PMID:21373993

Fisher Matrix Preloaded — FISHER4CAST

NASA Astrophysics Data System (ADS)

Bassett, Bruce A.; Fantaye, Yabebal; Hlozek, Renée; Kotze, Jacques

The Fisher Matrix is the backbone of modern cosmological forecasting. We describe the Fisher4Cast software: A general-purpose, easy-to-use, Fisher Matrix framework. It is open source, rigorously designed and tested and includes a Graphical User Interface (GUI) with automated LATEX file creation capability and point-and-click Fisher ellipse generation. Fisher4Cast was designed for ease of extension and, although written in Matlab, is easily portable to open-source alternatives such as Octave and Scilab. Here we use Fisher4Cast to present new 3D and 4D visualizations of the forecasting landscape and to investigate the effects of growth and curvature on future cosmological surveys. Early releases have been available at since mid-2008. The current release of the code is Version 2.2 which is described here. For ease of reference a Quick Start guide and the code used to produce the figures in this paper are included, in the hope that it will be useful to the cosmology and wider scientific communities.

Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images.

PubMed

Spagnolo, Daniel M; Al-Kofahi, Yousef; Zhu, Peihong; Lezon, Timothy R; Gough, Albert; Stern, Andrew M; Lee, Adrian V; Ginty, Fiona; Sarachan, Brion; Taylor, D Lansing; Chennubhotla, S Chakra

2017-11-01

We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71-74. ©2017 AACR . ©2017 American Association for Cancer Research.

Low Data Drug Discovery with One-Shot Learning

PubMed Central

2017-01-01

Recent advances in machine learning have made significant contributions to drug discovery. Deep neural networks in particular have been demonstrated to provide significant boosts in predictive power when inferring the properties and activities of small-molecule compounds (Ma, J. et al. J. Chem. Inf. Model.2015, 55, 263–27425635324). However, the applicability of these techniques has been limited by the requirement for large amounts of training data. In this work, we demonstrate how one-shot learning can be used to significantly lower the amounts of data required to make meaningful predictions in drug discovery applications. We introduce a new architecture, the iterative refinement long short-term memory, that, when combined with graph convolutional neural networks, significantly improves learning of meaningful distance metrics over small-molecules. We open source all models introduced in this work as part of DeepChem, an open-source framework for deep-learning in drug discovery (Ramsundar, B. deepchem.io. https://github.com/deepchem/deepchem, 2016). PMID:28470045

Numerical simulation of two-dimensional flow over a heated carbon surface with coupled heterogeneous and homogeneous reactions

NASA Astrophysics Data System (ADS)

Johnson, Ryan Federick; Chelliah, Harsha Kumar

2017-01-01

For a range of flow and chemical timescales, numerical simulations of two-dimensional laminar flow over a reacting carbon surface were performed to understand further the complex coupling between heterogeneous and homogeneous reactions. An open-source computational package (OpenFOAM®) was used with previously developed lumped heterogeneous reaction models for carbon surfaces and a detailed homogeneous reaction model for CO oxidation. The influence of finite-rate chemical kinetics was explored by varying the surface temperatures from 1800 to 2600 K, while flow residence time effects were explored by varying the free-stream velocity up to 50 m/s. The reacting boundary layer structure dependence on the residence time was analysed by extracting the ratio of chemical source and species diffusion terms. The important contributions of radical species reactions on overall carbon removal rate, which is often neglected in multi-dimensional simulations, are highlighted. The results provide a framework for future development and validation of lumped heterogeneous reaction models based on multi-dimensional reacting flow configurations.

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

PubMed Central

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

2014-01-01

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

Probabilistic consensus scoring improves tandem mass spectrometry peptide identification.

PubMed

Nahnsen, Sven; Bertsch, Andreas; Rahnenführer, Jörg; Nordheim, Alfred; Kohlbacher, Oliver

2011-08-05

Database search is a standard technique for identifying peptides from their tandem mass spectra. To increase the number of correctly identified peptides, we suggest a probabilistic framework that allows the combination of scores from different search engines into a joint consensus score. Central to the approach is a novel method to estimate scores for peptides not found by an individual search engine. This approach allows the estimation of p-values for each candidate peptide and their combination across all search engines. The consensus approach works better than any single search engine across all different instrument types considered in this study. Improvements vary strongly from platform to platform and from search engine to search engine. Compared to the industry standard MASCOT, our approach can identify up to 60% more peptides. The software for consensus predictions is implemented in C++ as part of OpenMS, a software framework for mass spectrometry. The source code is available in the current development version of OpenMS and can easily be used as a command line application or via a graphical pipeline designer TOPPAS.

An open and extensible framework for spatially explicit land use change modelling: the lulcc R package

NASA Astrophysics Data System (ADS)

Moulds, S.; Buytaert, W.; Mijic, A.

2015-10-01

We present the lulcc software package, an object-oriented framework for land use change modelling written in the R programming language. The contribution of the work is to resolve the following limitations associated with the current land use change modelling paradigm: (1) the source code for model implementations is frequently unavailable, severely compromising the reproducibility of scientific results and making it impossible for members of the community to improve or adapt models for their own purposes; (2) ensemble experiments to capture model structural uncertainty are difficult because of fundamental differences between implementations of alternative models; and (3) additional software is required because existing applications frequently perform only the spatial allocation of change. The package includes a stochastic ordered allocation procedure as well as an implementation of the CLUE-S algorithm. We demonstrate its functionality by simulating land use change at the Plum Island Ecosystems site, using a data set included with the package. It is envisaged that lulcc will enable future model development and comparison within an open environment.

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data

PubMed Central

Vukićević, Milan

2014-01-01

Rapid growth and storage of biomedical data enabled many opportunities for predictive modeling and improvement of healthcare processes. On the other side analysis of such large amounts of data is a difficult and computationally intensive task for most existing data mining algorithms. This problem is addressed by proposing a cloud based system that integrates metalearning framework for ranking and selection of best predictive algorithms for data at hand and open source big data technologies for analysis of biomedical data. PMID:24892101

Importing MAGE-ML format microarray data into BioConductor.

PubMed

Durinck, Steffen; Allemeersch, Joke; Carey, Vincent J; Moreau, Yves; De Moor, Bart

2004-12-12

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. http://www.bioconductor.org. Open Source.

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.

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

Ali, Amjad Majid; Albert, Don; Andersson, Par

SLURM is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for large and small computer clusters. As a cluster resource manager, SLURM has three key functions. First, it allocates exclusive and/or non-exclusive access to resources (compute nodes) to users for some duration of time so they can perform work. Second, it provides a framework for starting, executing, and monitoring work 9normally a parallel job) on the set of allocated nodes. Finally, it arbitrates conflicting requests for resources by managing a queue of pending work.

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

Automatic Tool for Local Assembly Structures

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

Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

Deep learning for media analysis in defense scenariosan evaluation of an open source framework for object detection in intelligence related image sets

DTIC Science & Technology

2017-06-01

Training time statistics from Jones’ thesis. . . . . . . . . . . . . . 15 Table 2.2 Evaluation runtime statistics from Camp’s thesis for a single image. 17...Table 2.3 Training and evaluation runtime statistics from Sharpe’s thesis. . . 19 Table 2.4 Sharpe’s screenshot detector results for combinations of...training resources available and time required for each algorithm Jones [15] tested. Table 2.1. Training time statistics from Jones’ [15] thesis. Algorithm

A Technology Enhanced Learning Model for Quality Education

NASA Astrophysics Data System (ADS)

Sherly, Elizabeth; Uddin, Md. Meraj

Technology Enhanced Learning and Teaching (TELT) Model provides learning through collaborations and interactions with a framework for content development and collaborative knowledge sharing system as a supplementary for learning to improve the quality of education system. TELT deals with a unique pedagogy model for Technology Enhanced Learning System which includes course management system, digital library, multimedia enriched contents and video lectures, open content management system and collaboration and knowledge sharing systems. Open sources like Moodle and Wiki for content development, video on demand solution with a low cost mid range system, an exhaustive digital library are provided in a portal system. The paper depicts a case study of e-learning initiatives with TELT model at IIITM-K and how effectively implemented.

Open-Source as a strategy for operational software - the case of Enki

NASA Astrophysics Data System (ADS)

Kolberg, Sjur; Bruland, Oddbjørn

2014-05-01

Since 2002, SINTEF Energy has been developing what is now known as the Enki modelling system. This development has been financed by Norway's largest hydropower producer Statkraft, motivated by a desire for distributed hydrological models in operational use. As the owner of the source code, Statkraft has recently decided on Open Source as a strategy for further development, and for migration from an R&D context to operational use. A current cooperation project is currently carried out between SINTEF Energy, 7 large Norwegian hydropower producers including Statkraft, three universities and one software company. Of course, the most immediate task is that of software maturing. A more important challenge, however, is one of gaining experience within the operational hydropower industry. A transition from lumped to distributed models is likely to also require revision of measurement program, calibration strategy, use of GIS and modern data sources like weather radar and satellite imagery. On the other hand, map based visualisations enable a richer information exchange between hydrologic forecasters and power market traders. The operating context of a distributed hydrology model within hydropower planning is far from settled. Being both a modelling framework and a library of plugin-routines to build models from, Enki supports the flexibility needed in this situation. Recent development has separated the core from the user interface, paving the way for a scripting API, cross-platform compilation, and front-end programs serving different degrees of flexibility, robustness and security. The open source strategy invites anyone to use Enki and to develop and contribute new modules. Once tested, the same modules are available for the operational versions of the program. A core challenge is to offer rigid testing procedures and mechanisms to reject routines in an operational setting, without limiting the experimentation with new modules. The Open Source strategy also has implications for building and maintaining competence around the source code and the advanced hydrological and statistical routines in Enki. Originally developed by hydrologists, the Enki code is now approaching a state where maintenance requires a background in professional software development. Without the advantage of proprietary source code, both hydrologic improvements and software maintenance depend on donations or development support on a case-to-case basis, a situation well known within the open source community. It remains to see whether these mechanisms suffice to keep Enki at the maintenance level required by the hydropower sector. ENKI is available from www.opensource-enki.org.

TH-C-12A-12: Veritas: An Open Source Tool to Facilitate User Interaction with TrueBeam Developer Mode

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

Mishra, P; Varian Medical Systems, Palo Alto, CA; Lewis, J

2014-06-15

Purpose: To address the challenges of creating delivery trajectories and imaging sequences with TrueBeam Developer Mode, a new open-source graphical XML builder, Veritas, has been developed, tested and made freely available. Veritas eliminates most of the need to understand the underlying schema and write XML scripts, by providing a graphical menu for each control point specifying the state of 30 mechanical/dose axes. All capabilities of Developer Mode are accessible in Veritas. Methods: Veritas was designed using QT Designer, a ‘what-you-is-what-you-get’ (WYSIWIG) tool for building graphical user interfaces (GUI). Different components of the GUI are integrated using QT's signals and slotsmore » mechanism. Functionalities are added using PySide, an open source, cross platform Python binding for the QT framework. The XML code generated is immediately visible, making it an interactive learning tool. A user starts from an anonymized DICOM file or XML example and introduces delivery modifications, or begins their experiment from scratch, then uses the GUI to modify control points as desired. The software automatically generates XML plans following the appropriate schema. Results: Veritas was tested by generating and delivering two XML plans at Brigham and Women's Hospital. The first example was created to irradiate the letter ‘B’ with a narrow MV beam using dynamic couch movements. The second was created to acquire 4D CBCT projections for four minutes. The delivery of the letter ‘B’ was observed using a 2D array of ionization chambers. Both deliveries were generated quickly in Veritas by non-expert Developer Mode users. Conclusion: We introduced a new open source tool Veritas for generating XML plans (delivery trajectories and imaging sequences). Veritas makes Developer Mode more accessible by reducing the learning curve for quick translation of research ideas into XML plans. Veritas is an open source initiative, creating the possibility for future developments and collaboration with other researchers. I am an employee of Varian Medical Systems.« less

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 )

A Conceptual Framework for Achieving Good Governance at Open and Distance Learning Institutions

ERIC Educational Resources Information Center

Khanna, Pankaj

2017-01-01

This paper describes a good governance architecture framework that would bring significant improvements in the overall working of open and distance learning institutions in a well-structured and systematic way. The good governance framework is articulated with seven basic principles which are performance, transparency, accountability,…

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

The GenABEL Project for statistical genomics

PubMed Central

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

2016-01-01

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

Falcon: a highly flexible open-source software for closed-loop neuroscience.

PubMed

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Falcon: a highly flexible open-source software for closed-loop neuroscience

NASA Astrophysics Data System (ADS)

Ciliberti, Davide; Kloosterman, Fabian

2017-08-01

Objective. Closed-loop experiments provide unique insights into brain dynamics and function. To facilitate a wide range of closed-loop experiments, we created an open-source software platform that enables high-performance real-time processing of streaming experimental data. Approach. We wrote Falcon, a C++ multi-threaded software in which the user can load and execute an arbitrary processing graph. Each node of a Falcon graph is mapped to a single thread and nodes communicate with each other through thread-safe buffers. The framework allows for easy implementation of new processing nodes and data types. Falcon was tested both on a 32-core and a 4-core workstation. Streaming data was read from either a commercial acquisition system (Neuralynx) or the open-source Open Ephys hardware, while closed-loop TTL pulses were generated with a USB module for digital output. We characterized the round-trip latency of our Falcon-based closed-loop system, as well as the specific latency contribution of the software architecture, by testing processing graphs with up to 32 parallel pipelines and eight serial stages. We finally deployed Falcon in a task of real-time detection of population bursts recorded live from the hippocampus of a freely moving rat. Main results. On Neuralynx hardware, round-trip latency was well below 1 ms and stable for at least 1 h, while on Open Ephys hardware latencies were below 15 ms. The latency contribution of the software was below 0.5 ms. Round-trip and software latencies were similar on both 32- and 4-core workstations. Falcon was used successfully to detect population bursts online with ~40 ms average latency. Significance. Falcon is a novel open-source software for closed-loop neuroscience. It has sub-millisecond intrinsic latency and gives the experimenter direct control of CPU resources. We envisage Falcon to be a useful tool to the neuroscientific community for implementing a wide variety of closed-loop experiments, including those requiring use of complex data structures and real-time execution of computationally intensive algorithms, such as population neural decoding/encoding from large cell assemblies.

Ensembl 2002: accommodating comparative genomics.

PubMed

Clamp, M; Andrews, D; Barker, D; Bevan, P; Cameron, G; Chen, Y; Clark, L; Cox, T; Cuff, J; Curwen, V; Down, T; Durbin, R; Eyras, E; Gilbert, J; Hammond, M; Hubbard, T; Kasprzyk, A; Keefe, D; Lehvaslaiho, H; Iyer, V; Melsopp, C; Mongin, E; Pettett, R; Potter, S; Rust, A; Schmidt, E; Searle, S; Slater, G; Smith, J; Spooner, W; Stabenau, A; Stalker, J; Stupka, E; Ureta-Vidal, A; Vastrik, I; Birney, E

2003-01-01

The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic annotation of human, mouse and other genome sequences, available as either an interactive web site or as flat files. Ensembl also integrates manually annotated gene structures from external sources where available. As well as being one of the leading sources of genome annotation, Ensembl is an open source software engineering project to develop a portable system able to handle very large genomes and associated requirements. These range from sequence analysis to data storage and visualisation and installations exist around the world in both companies and at academic sites. With both human and mouse genome sequences available and more vertebrate sequences to follow, many of the recent developments in Ensembl have focusing on developing automatic comparative genome analysis and visualisation.

A Framework for Open, Flexible and Distributed Learning.

ERIC Educational Resources Information Center

Khan, Badrul H.

Designing open, flexible distance learning systems on the World Wide Web requires thoughtful analysis and investigation combined with an understanding of both the Web's attributes and resources and the ways instructional design principles can be applied to tap the Web's potential. A framework for open, flexible, and distributed learning has been…

Development and application of the RE-AIM QuEST mixed methods framework for program evaluation.

PubMed

Forman, Jane; Heisler, Michele; Damschroder, Laura J; Kaselitz, Elizabeth; Kerr, Eve A

2017-06-01

To increase the likelihood of successful implementation of interventions and promote dissemination across real-world settings, it is essential to evaluate outcomes related to dimensions other than Effectiveness alone. Glasgow and colleagues' RE-AIM framework specifies four additional types of outcomes that are important to decision-makers: Reach, Adoption, Implementation (including cost), and Maintenance. To further strengthen RE-AIM, we propose integrating qualitative assessments in an expanded framework: RE-AIM Qualitative Evaluation for Systematic Translation (RE-AIM QuEST), a mixed methods framework. RE-AIM QuEST guides formative evaluation to identify real-time implementation barriers and explain how implementation context may influence translation to additional settings. RE-AIM QuEST was used to evaluate a pharmacist-led hypertension management intervention at 3 VA facilities in 2008-2009. We systematically reviewed each of the five RE-AIM dimensions and created open-ended companion questions to quantitative measures and identified qualitative and quantitative data sources, measures, and analyses. To illustrate use of the RE-AIM QuEST framework, we provide examples of real-time, coordinated use of quantitative process measures and qualitative methods to identify site-specific issues, and retrospective use of these data sources and analyses to understand variation across sites and explain outcomes. For example, in the Reach dimension, we conducted real-time measurement of enrollment across sites and used qualitative data to better understand and address barriers at a low-enrollment site. The RE-AIM QuEST framework may be a useful tool for improving interventions in real-time, for understanding retrospectively why an intervention did or did not work, and for enhancing its sustainability and translation to other settings.

OpenMDAO Framework Status

NASA Technical Reports Server (NTRS)

Naiman, Cynthia Gutierrez

2010-01-01

Advancing and exploring the science of Multidisciplinary Analysis & Optimization (MDAO) capabilities are high-level goals in the Fundamental Aeronautics Program s Subsonic Fixed Wing (SFW) project. The OpenMDAO team has made significant progress toward completing the Alpha OpenMDAO deliverable due in September 2010. Included in the presentation are: details of progress on developing the OpenMDAO framework, example usage of OpenMDAO, technology transfer plans, near term plans, progress toward establishing partnerships with external parties, and discussion of additional potential collaborations.

OpenMS - A platform for reproducible analysis of mass spectrometry data.

PubMed

Pfeuffer, Julianus; Sachsenberg, Timo; Alka, Oliver; Walzer, Mathias; Fillbrunn, Alexander; Nilse, Lars; Schilling, Oliver; Reinert, Knut; Kohlbacher, Oliver

2017-11-10

In recent years, several mass spectrometry-based omics technologies emerged to investigate qualitative and quantitative changes within thousands of biologically active components such as proteins, lipids and metabolites. The research enabled through these methods potentially contributes to the diagnosis and pathophysiology of human diseases as well as to the clarification of structures and interactions between biomolecules. Simultaneously, technological advances in the field of mass spectrometry leading to an ever increasing amount of data, demand high standards in efficiency, accuracy and reproducibility of potential analysis software. This article presents the current state and ongoing developments in OpenMS, a versatile open-source framework aimed at enabling reproducible analyses of high-throughput mass spectrometry data. It provides implementations of frequently occurring processing operations on MS data through a clean application programming interface in C++ and Python. A collection of 185 tools and ready-made workflows for typical MS-based experiments enable convenient analyses for non-developers and facilitate reproducible research without losing flexibility. OpenMS will continue to increase its ease of use for developers as well as users with improved continuous integration/deployment strategies, regular trainings with updated training materials and multiple sources of support. The active developer community ensures the incorporation of new features to support state of the art research. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface.

PubMed

Jeliazkova, Nina; Jeliazkov, Vedrin

2011-05-16

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations.The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems.

AMBIT RESTful web services: an implementation of the OpenTox application programming interface

PubMed Central

2011-01-01

The AMBIT web services package is one of the several existing independent implementations of the OpenTox Application Programming Interface and is built according to the principles of the Representational State Transfer (REST) architecture. The Open Source Predictive Toxicology Framework, developed by the partners in the EC FP7 OpenTox project, aims at providing a unified access to toxicity data and predictive models, as well as validation procedures. This is achieved by i) an information model, based on a common OWL-DL ontology ii) links to related ontologies; iii) data and algorithms, available through a standardized REST web services interface, where every compound, data set or predictive method has a unique web address, used to retrieve its Resource Description Framework (RDF) representation, or initiate the associated calculations. The AMBIT web services package has been developed as an extension of AMBIT modules, adding the ability to create (Quantitative) Structure-Activity Relationship (QSAR) models and providing an OpenTox API compliant interface. The representation of data and processing resources in W3C Resource Description Framework facilitates integrating the resources as Linked Data. By uploading datasets with chemical structures and arbitrary set of properties, they become automatically available online in several formats. The services provide unified interfaces to several descriptor calculation, machine learning and similarity searching algorithms, as well as to applicability domain and toxicity prediction models. All Toxtree modules for predicting the toxicological hazard of chemical compounds are also integrated within this package. The complexity and diversity of the processing is reduced to the simple paradigm "read data from a web address, perform processing, write to a web address". The online service allows to easily run predictions, without installing any software, as well to share online datasets and models. The downloadable web application allows researchers to setup an arbitrary number of service instances for specific purposes and at suitable locations. These services could be used as a distributed framework for processing of resource-intensive tasks and data sharing or in a fully independent way, according to the specific needs. The advantage of exposing the functionality via the OpenTox API is seamless interoperability, not only within a single web application, but also in a network of distributed services. Last, but not least, the services provide a basis for building web mashups, end user applications with friendly GUIs, as well as embedding the functionalities in existing workflow systems. PMID:21575202

Automated population of an i2b2 clinical data warehouse from an openEHR-based data repository.

PubMed

Haarbrandt, Birger; Tute, Erik; Marschollek, Michael

2016-10-01

Detailed Clinical Model (DCM) approaches have recently seen wider adoption. More specifically, openEHR-based application systems are now used in production in several countries, serving diverse fields of application such as health information exchange, clinical registries and electronic medical record systems. However, approaches to efficiently provide openEHR data to researchers for secondary use have not yet been investigated or established. We developed an approach to automatically load openEHR data instances into the open source clinical data warehouse i2b2. We evaluated query capabilities and the performance of this approach in the context of the Hanover Medical School Translational Research Framework (HaMSTR), an openEHR-based data repository. Automated creation of i2b2 ontologies from archetypes and templates and the integration of openEHR data instances from 903 patients of a paediatric intensive care unit has been achieved. In total, it took an average of ∼2527s to create 2.311.624 facts from 141.917 XML documents. Using the imported data, we conducted sample queries to compare the performance with two openEHR systems and to investigate if this representation of data is feasible to support cohort identification and record level data extraction. We found the automated population of an i2b2 clinical data warehouse to be a feasible approach to make openEHR data instances available for secondary use. Such an approach can facilitate timely provision of clinical data to researchers. It complements analytics based on the Archetype Query Language by allowing querying on both, legacy clinical data sources and openEHR data instances at the same time and by providing an easy-to-use query interface. However, due to different levels of expressiveness in the data models, not all semantics could be preserved during the ETL process. Copyright © 2016 Elsevier Inc. All rights reserved.

Metadata mapping and reuse in caBIG™

PubMed Central

Kunz, Isaac; Lin, Ming-Chin; Frey, Lewis

2009-01-01

Background This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG™). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG™ framework or other frameworks that use metadata repositories. Results The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG™ framework and potentially any framework that uses a metadata repository. Conclusion This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG™. This effort contributes to facilitating the development of interoperable systems within caBIG™ as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies. PMID:19208192

MzJava: An open source library for mass spectrometry data processing.

PubMed

Horlacher, Oliver; Nikitin, Frederic; Alocci, Davide; Mariethoz, Julien; Müller, Markus; Lisacek, Frederique

2015-11-03

Mass spectrometry (MS) is a widely used and evolving technique for the high-throughput identification of molecules in biological samples. The need for sharing and reuse of code among bioinformaticians working with MS data prompted the design and implementation of MzJava, an open-source Java Application Programming Interface (API) for MS related data processing. MzJava provides data structures and algorithms for representing and processing mass spectra and their associated biological molecules, such as metabolites, glycans and peptides. MzJava includes functionality to perform mass calculation, peak processing (e.g. centroiding, filtering, transforming), spectrum alignment and clustering, protein digestion, fragmentation of peptides and glycans as well as scoring functions for spectrum-spectrum and peptide/glycan-spectrum matches. For data import and export MzJava implements readers and writers for commonly used data formats. For many classes support for the Hadoop MapReduce (hadoop.apache.org) and Apache Spark (spark.apache.org) frameworks for cluster computing was implemented. The library has been developed applying best practices of software engineering. To ensure that MzJava contains code that is correct and easy to use the library's API was carefully designed and thoroughly tested. MzJava is an open-source project distributed under the AGPL v3.0 licence. MzJava requires Java 1.7 or higher. Binaries, source code and documentation can be downloaded from http://mzjava.expasy.org and https://bitbucket.org/sib-pig/mzjava. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Exploring the "what if?" in geology through a RESTful open-source framework for cloud-based simulation and analysis

NASA Astrophysics Data System (ADS)

Klump, Jens; Robertson, Jess

2016-04-01

The spatial and temporal extent of geological phenomena makes experiments in geology difficult to conduct, if not entirely impossible and collection of data is laborious and expensive - so expensive that most of the time we cannot test a hypothesis. The aim, in many cases, is to gather enough data to build a predictive geological model. Even in a mine, where data are abundant, a model remains incomplete because the information at the level of a blasting block is two orders of magnitude larger than the sample from a drill core, and we have to take measurement errors into account. So, what confidence can we have in a model based on sparse data, uncertainties and measurement error? Our framework consist of two layers: (a) a ground-truth layer that contains geological models, which can be statistically based on historical operations data, and (b) a network of RESTful synthetic sensor microservices which can query the ground-truth for underlying properties and produce a simulated measurement to a control layer, which could be a database or LIMS, a machine learner or a companies' existing data infrastructure. Ground truth data are generated by an implicit geological model which serves as a host for nested models of geological processes as smaller scales. Our two layers are implemented using Flask and Gunicorn, which are open source Python web application framework and server, the PyData stack (numpy, scipy etc) and Rabbit MQ (an open-source queuing library). Sensor data is encoded using a JSON-LD version of the SensorML and Observations and Measurements standards. Containerisation of the synthetic sensors using Docker and CoreOS allows rapid and scalable deployment of large numbers of sensors, as well as sensor discovery to form a self-organized dynamic network of sensors. Real-time simulation of data sources can be used to investigate crucial questions such as the potential information gain from future sensing capabilities, or from new sampling strategies, or the combination of both, and it enables us to test many "what if?" questions, both in geology and in data engineering. What would we be able to see if we could obtain data at higher resolution? How would real-time data analysis change sampling strategies? Does our data infrastructure handle many new real-time data streams? What feature engineering can be deducted for machine learning approaches? By providing a 'data sandbox' able to scale to realistic geological scenarios we hope to start answering some of these questions. Faults happen in real world networks. Future work will investigate the effect of failure on dynamic sensor networks and the impact on the predictive capability of machine learning algorithms.

Modelling Biogeochemistry Across Domains with The Modular System for Shelves and Coasts (MOSSCO)

NASA Astrophysics Data System (ADS)

Burchard, H.; Lemmen, C.; Hofmeister, R.; Knut, K.; Nasermoaddeli, M. H.; Kerimoglu, O.; Koesters, F.; Wirtz, K.

2016-02-01

Coastal biogeochemical processes extend from the atmosphere through the water column and the epibenthos into the ocean floor, laterally they are determined by freshwater inflows and open water exchange, and in situ they are mediated by physical, chemical and biological interactions. We use the new Modular System for Shelves and Coasts (MOSSCO, http://www.mossco.de) to obtain an integrated view of coastal biogeochemistry. MOSSCO is a coupling framework that builds on existing coupling technologies like the Earth System Modeling Framework (ESMF, for domain-coupling) and the Framework for Aquatic Biogeochemistry (FABM, for process coupling). MOSSCO facilitates the communication about and the integration of existing and of new process models into a threedimensional regional coastal modelling context. In the MOSSCO concept, the integrating framework imposes very few restrictions on contributed data or models; in fact, there is no distinction made between data and models. The few requirements are: (1) principle coupleability, i.e. access to I/O and timing information in submodels, which has recently been referred to as the Basic Model Interface (BMI) (2) open source/open data access and licencing and (3) communication of metadata, such as spatiotemporal information, naming conventions, and physical units. These requirements suffice to integrate different models and data sets into the MOSSCO infrastructure and subsequently built a modular integrated modeling tool that can span a diversity of processes and domains. Here, we demonstrate a MOSSCO application for the southern North Sea, where atmospheric deposition, biochemical processing in the water column and the ocean floor, lateral nutrient replenishment, and wave- and current-dependent remobilization from sediments are accounted for by modular components. A multi-annual simulation yields realistic succession of the spatial gradients of dissolved nutrients, of chlorophyll variability and gross primary production rates and of benthic denitrification rates for this intriguing coastal system.

Student concepts of Natural Selection from a resource-based perspective

NASA Astrophysics Data System (ADS)

Benjamin, Scott Shawn

The past two decades have produced a substantial amount of research about the teaching and learning of evolution; however, recent research often lacks a theoretical foundation. Application of a new theoretical framework could help fill the void and improve research about student concepts of evolution. This study seeks to show that a resource-based framework (Hammer et al., 2005) can improve research into student concepts of natural selection. Concepts of natural selection from urban community college students were assessed via qualitative (interviews, written open-response questions, and write/think aloud procedures) and quantitative methods (coded open response analysis, Concept Inventory for Natural Selection (CINS)(Anderson, Fisher, & Norman, 2002). Results showed that students demonstrate four important aspects of resource-based framework: the multi-faceted construction of concepts, context sensitivity/ concept flexibility, at-the-moment activation of resources, and perceptual frames. In open response assessment, evolutionary-gain responses produced significantly different responses than evolutionary-loss questions with: 1) significantly more correct answers for the gain than loss question (Wilcoxon signed rank test, z = -3.68, p=0.0002); 2) more Lamarckian responses to loss than the gain question (Fisher exact, p=0.0039); and significantly different distributions in expanded need vs basic need answers (Fishers exact, p = 0.02). Results from CINS scores showed significant differences in post activity scores between students that held different naive concepts associated with origin of variation, origin of species, differential reproduction, and limited survival suggesting that some naive ideas facilitate learning. Outcomes also suggest that an everyday or self-experience typological perceptual frame is an underlying source of many incorrect ideas about evolution. Interview and write/think aloud assessments propose four process resources applied by students as they explain evolutionary change: list what I know, why story, compare past to present, mapping self-experience. The study concludes that a resource-based framework is a valuable tool to advance the study student concepts of natural selection.

A task scheduler framework for self-powered wireless sensors.

PubMed

Nordman, Mikael M

2003-10-01

The cost and inconvenience of cabling is a factor limiting widespread use of intelligent sensors. Recent developments in short-range, low-power radio seem to provide an opening to this problem, making development of wireless sensors feasible. However, for these sensors the energy availability is a main concern. The common solution is either to use a battery or to harvest ambient energy. The benefit of harvested ambient energy is that the energy feeder can be considered as lasting a lifetime, thus it saves the user from concerns related to energy management. The problem is, however, the unpredictability and unsteady behavior of ambient energy sources. This becomes a main concern for sensors that run multiple tasks at different priorities. This paper proposes a new scheduler framework that enables the reliable assignment of task priorities and scheduling in sensors powered by ambient energy. The framework being based on environment parameters, virtual queues, and a state machine with transition conditions, dynamically manages task execution according to priorities. The framework is assessed in a test system powered by a solar panel. The results show the functionality of the framework and how task execution reliably is handled without violating the priority scheme that has been assigned to it.

EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.

PubMed

Schott, Benjamin; Traub, Manuel; Schlagenhauf, Cornelia; Takamiya, Masanari; Antritter, Thomas; Bartschat, Andreas; Löffler, Katharina; Blessing, Denis; Otte, Jens C; Kobitski, Andrei Y; Nienhaus, G Ulrich; Strähle, Uwe; Mikut, Ralf; Stegmaier, Johannes

2018-04-01

State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user applications that can be performed using the new framework.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

PubMed Central

Audeh, Bissan; Beigbeder, Michel; Zimmermann, Antoine; Jaillon, Philippe; Bousquet, Cédric

2017-01-01

The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites. PMID:28122056

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

PubMed

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

2017-10-01

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

Reproducible Hydrogeophysical Inversions through the Open-Source Library pyGIMLi

NASA Astrophysics Data System (ADS)

Wagner, F. M.; Rücker, C.; Günther, T.

2017-12-01

Many tasks in applied geosciences cannot be solved by a single measurement method and require the integration of geophysical, geotechnical and hydrological methods. In the emerging field of hydrogeophysics, researchers strive to gain quantitative information on process-relevant subsurface parameters by means of multi-physical models, which simulate the dynamic process of interest as well as its geophysical response. However, such endeavors are associated with considerable technical challenges, since they require coupling of different numerical models. This represents an obstacle for many practitioners and students. Even technically versatile users tend to build individually tailored solutions by coupling different (and potentially proprietary) forward simulators at the cost of scientific reproducibility. We argue that the reproducibility of studies in computational hydrogeophysics, and therefore the advancement of the field itself, requires versatile open-source software. To this end, we present pyGIMLi - a flexible and computationally efficient framework for modeling and inversion in geophysics. The object-oriented library provides management for structured and unstructured meshes in 2D and 3D, finite-element and finite-volume solvers, various geophysical forward operators, as well as Gauss-Newton based frameworks for constrained, joint and fully-coupled inversions with flexible regularization. In a step-by-step demonstration, it is shown how the hydrogeophysical response of a saline tracer migration can be simulated. Tracer concentration data from boreholes and measured voltages at the surface are subsequently used to estimate the hydraulic conductivity distribution of the aquifer within a single reproducible Python script.

Sharing Human-Generated Observations by Integrating HMI and the Semantic Sensor Web

PubMed Central

Sigüenza, Álvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current “Internet of Things” concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound. PMID:22778643

Sharing human-generated observations by integrating HMI and the Semantic Sensor Web.

PubMed

Sigüenza, Alvaro; Díaz-Pardo, David; Bernat, Jesús; Vancea, Vasile; Blanco, José Luis; Conejero, David; Gómez, Luis Hernández

2012-01-01

Current "Internet of Things" concepts point to a future where connected objects gather meaningful information about their environment and share it with other objects and people. In particular, objects embedding Human Machine Interaction (HMI), such as mobile devices and, increasingly, connected vehicles, home appliances, urban interactive infrastructures, etc., may not only be conceived as sources of sensor information, but, through interaction with their users, they can also produce highly valuable context-aware human-generated observations. We believe that the great promise offered by combining and sharing all of the different sources of information available can be realized through the integration of HMI and Semantic Sensor Web technologies. This paper presents a technological framework that harmonizes two of the most influential HMI and Sensor Web initiatives: the W3C's Multimodal Architecture and Interfaces (MMI) and the Open Geospatial Consortium (OGC) Sensor Web Enablement (SWE) with its semantic extension, respectively. Although the proposed framework is general enough to be applied in a variety of connected objects integrating HMI, a particular development is presented for a connected car scenario where drivers' observations about the traffic or their environment are shared across the Semantic Sensor Web. For implementation and evaluation purposes an on-board OSGi (Open Services Gateway Initiative) architecture was built, integrating several available HMI, Sensor Web and Semantic Web technologies. A technical performance test and a conceptual validation of the scenario with potential users are reported, with results suggesting the approach is sound.

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

EHDViz: clinical dashboard development using open-source technologies

PubMed Central

Badgeley, Marcus A; Shameer, Khader; Glicksberg, Benjamin S; Tomlinson, Max S; Levin, Matthew A; McCormick, Patrick J; Kasarskis, Andrew; Reich, David L; Dudley, Joel T

2016-01-01

Objective To design, develop and prototype clinical dashboards to integrate high-frequency health and wellness data streams using interactive and real-time data visualisation and analytics modalities. Materials and methods We developed a clinical dashboard development framework called electronic healthcare data visualization (EHDViz) toolkit for generating web-based, real-time clinical dashboards for visualising heterogeneous biomedical, healthcare and wellness data. The EHDViz is an extensible toolkit that uses R packages for data management, normalisation and producing high-quality visualisations over the web using R/Shiny web server architecture. We have developed use cases to illustrate utility of EHDViz in different scenarios of clinical and wellness setting as a visualisation aid for improving healthcare delivery. Results Using EHDViz, we prototyped clinical dashboards to demonstrate the contextual versatility of EHDViz toolkit. An outpatient cohort was used to visualise population health management tasks (n=14 221), and an inpatient cohort was used to visualise real-time acuity risk in a clinical unit (n=445), and a quantified-self example using wellness data from a fitness activity monitor worn by a single individual was also discussed (n-of-1). The back-end system retrieves relevant data from data source, populates the main panel of the application and integrates user-defined data features in real-time and renders output using modern web browsers. The visualisation elements can be customised using health features, disease names, procedure names or medical codes to populate the visualisations. The source code of EHDViz and various prototypes developed using EHDViz are available in the public domain at http://ehdviz.dudleylab.org. Conclusions Collaborative data visualisations, wellness trend predictions, risk estimation, proactive acuity status monitoring and knowledge of complex disease indicators are essential components of implementing data-driven precision medicine. As an open-source visualisation framework capable of integrating health assessment, EHDViz aims to be a valuable toolkit for rapid design, development and implementation of scalable clinical data visualisation dashboards. PMID:27013597

Multiscale modeling and characterization for performance and safety of lithium-ion batteries

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

Pannala, Sreekanth; Turner, John A.; Allu, Srikanth

Lithium-ion batteries are highly complex electrochemical systems whose performance and safety are governed by coupled nonlinear electrochemical-electrical-thermal-mechanical processes over a range of spatiotemporal scales. In this paper we describe a new, open source computational framework for Lithium-ion battery simulations that is designed to support a variety of model types and formulations. This framework has been used to create three-dimensional cell and battery pack models that explicitly simulate all the battery components (current collectors, electrodes, and separator). The models are used to predict battery performance under normal operations and to study thermal and mechanical safety aspects under adverse conditions. The modelmore » development and validation are supported by experimental methods such as IR-imaging, X-ray tomography and micro-Raman mapping.« less

Multiscale modeling and characterization for performance and safety of lithium-ion batteries

DOE PAGES

Pannala, Sreekanth; Turner, John A.; Allu, Srikanth; ...

2015-08-19

Lithium-ion batteries are highly complex electrochemical systems whose performance and safety are governed by coupled nonlinear electrochemical-electrical-thermal-mechanical processes over a range of spatiotemporal scales. In this paper we describe a new, open source computational framework for Lithium-ion battery simulations that is designed to support a variety of model types and formulations. This framework has been used to create three-dimensional cell and battery pack models that explicitly simulate all the battery components (current collectors, electrodes, and separator). The models are used to predict battery performance under normal operations and to study thermal and mechanical safety aspects under adverse conditions. The modelmore » development and validation are supported by experimental methods such as IR-imaging, X-ray tomography and micro-Raman mapping.« less

Development of solute transport models in YMPYRÄ framework to simulate solute migration in military shooting and training areas

NASA Astrophysics Data System (ADS)

Warsta, L.; Karvonen, T.

2017-12-01

There are currently 25 shooting and training areas in Finland managed by The Finnish Defence Forces (FDF), where military activities can cause contamination of open waters and groundwater reservoirs. In the YMPYRÄ project, a computer software framework is being developed that combines existing open environmental data and proprietary information collected by FDF with computational models to investigate current and prevent future environmental problems. A data centric philosophy is followed in the development of the system, i.e. the models are updated and extended to handle available data from different areas. The results generated by the models are summarized as easily understandable flow and risk maps that can be opened in GIS programs and used in environmental assessments by experts. Substances investigated with the system include explosives and metals such as lead, and both surface and groundwater dominated areas can be simulated. The YMPYRÄ framework is composed of a three dimensional soil and groundwater flow model, several solute transport models and an uncertainty assessment system. Solute transport models in the framework include particle based, stream tube and finite volume based approaches. The models can be used to simulate solute dissolution from source area, transport in the unsaturated layers to groundwater and finally migration in groundwater to water extraction wells and springs. The models can be used to simulate advection, dispersion, equilibrium adsorption on soil particles, solubility and dissolution from solute phase and dendritic solute decay chains. Correct numerical solutions were confirmed by comparing results to analytical 1D and 2D solutions and by comparing the numerical solutions to each other. The particle based and stream tube type solute transport models were useful as they could complement the traditional finite volume based approach which in certain circumstances produced numerical dispersion due to piecewise solution of the governing equations in computational grids and included computationally intensive and in some cases unstable iterative solutions. The YMPYRÄ framework is being developed by WaterHope, Gain Oy, and SITO Oy consulting companies and funded by FDF.

Creating More Credible and Persuasive Recommender Systems: The Influence of Source Characteristics on Recommender System Evaluations

NASA Astrophysics Data System (ADS)

Yoo, Kyung-Hyan; Gretzel, Ulrike

Whether users are likely to accept the recommendations provided by a recommender system is of utmost importance to system designers and the marketers who implement them. By conceptualizing the advice seeking and giving relationship as a fundamentally social process, important avenues for understanding the persuasiveness of recommender systems open up. Specifically, research regarding the influence of source characteristics, which is abundant in the context of humanhuman relationships, can provide an important framework for identifying potential influence factors. This chapter reviews the existing literature on source characteristics in the context of human-human, human-computer, and human-recommender system interactions. It concludes that many social cues that have been identified as influential in other contexts have yet to be implemented and tested with respect to recommender systems. Implications for recommender system research and design are discussed.

eTOXlab, an open source modeling framework for implementing predictive models in production environments.

PubMed

Carrió, Pau; López, Oriol; Sanz, Ferran; Pastor, Manuel

2015-01-01

Computational models based in Quantitative-Structure Activity Relationship (QSAR) methodologies are widely used tools for predicting the biological properties of new compounds. In many instances, such models are used as a routine in the industry (e.g. food, cosmetic or pharmaceutical industry) for the early assessment of the biological properties of new compounds. However, most of the tools currently available for developing QSAR models are not well suited for supporting the whole QSAR model life cycle in production environments. We have developed eTOXlab; an open source modeling framework designed to be used at the core of a self-contained virtual machine that can be easily deployed in production environments, providing predictions as web services. eTOXlab consists on a collection of object-oriented Python modules with methods mapping common tasks of standard modeling workflows. This framework allows building and validating QSAR models as well as predicting the properties of new compounds using either a command line interface or a graphic user interface (GUI). Simple models can be easily generated by setting a few parameters, while more complex models can be implemented by overriding pieces of the original source code. eTOXlab benefits from the object-oriented capabilities of Python for providing high flexibility: any model implemented using eTOXlab inherits the features implemented in the parent model, like common tools and services or the automatic exposure of the models as prediction web services. The particular eTOXlab architecture as a self-contained, portable prediction engine allows building models with confidential information within corporate facilities, which can be safely exported and used for prediction without disclosing the structures of the training series. The software presented here provides full support to the specific needs of users that want to develop, use and maintain predictive models in corporate environments. The technologies used by eTOXlab (web services, VM, object-oriented programming) provide an elegant solution to common practical issues; the system can be installed easily in heterogeneous environments and integrates well with other software. Moreover, the system provides a simple and safe solution for building models with confidential structures that can be shared without disclosing sensitive information.

GIAnT - Generic InSAR Analysis Toolbox

NASA Astrophysics Data System (ADS)

Agram, P.; Jolivet, R.; Riel, B. V.; Simons, M.; Doin, M.; Lasserre, C.; Hetland, E. A.

2012-12-01

We present a computing framework for studying the spatio-temporal evolution of ground deformation from interferometric synthetic aperture radar (InSAR) data. Several open-source tools including Repeat Orbit Interferometry PACkage (ROI-PAC) and InSAR Scientific Computing Environment (ISCE) from NASA-JPL, and Delft Object-oriented Repeat Interferometric Software (DORIS), have enabled scientists to generate individual interferograms from raw radar data with relative ease. Numerous computational techniques and algorithms that reduce phase information from multiple interferograms to a deformation time-series have been developed and verified over the past decade. However, the sharing and direct comparison of products from multiple processing approaches has been hindered by - 1) absence of simple standards for sharing of estimated time-series products, 2) use of proprietary software tools with license restrictions and 3) the closed source nature of the exact implementation of many of these algorithms. We have developed this computing framework to address all of the above issues. We attempt to take the first steps towards creating a community software repository for InSAR time-series analysis. To date, we have implemented the short baseline subset algorithm (SBAS), NSBAS and multi-scale interferometric time-series (MInTS) in this framework and the associated source code is included in the GIAnT distribution. A number of the associated routines have been optimized for performance and scalability with large data sets. Some of the new features in our processing framework are - 1) the use of daily solutions from continuous GPS stations to correct for orbit errors, 2) the use of meteorological data sets to estimate the tropospheric delay screen and 3) a data-driven bootstrapping approach to estimate the uncertainties associated with estimated time-series products. We are currently working on incorporating tidal load corrections for individual interferograms and propagation of noise covariance models through the processing chain for robust estimation of uncertainties in the deformation estimates. We will demonstrate the ease of use of our framework with results ranging from regional scale analysis around Long Valley, CA and Parkfield, CA to continental scale analysis in Western South America. We will also present preliminary results from a new time-series approach that simultaneously estimates deformation over the complete spatial domain at all time epochs on a distributed computing platform. GIAnT has been developed entirely using open source tools and uses Python as the underlying platform. We build on the extensive numerical (NumPy) and scientific (SciPy) computing Python libraries to develop an object-oriented, flexible and modular framework for time-series InSAR applications. The toolbox is currently configured to work with outputs from ROI-PAC, ISCE and DORIS, but can easily be extended to support products from other SAR/InSAR processors. The toolbox libraries include support for hierarchical data format (HDF5) memory mapped files, parallel processing with Python's multi-processing module and support for many convex optimization solvers like CSDP, CVXOPT etc. An extensive set of routines to deal with ASCII and XML files has also been included for controlling the processing parameters.

Web-based GIS for spatial pattern detection: application to malaria incidence in Vietnam.

PubMed

Bui, Thanh Quang; Pham, Hai Minh

2016-01-01

There is a great concern on how to build up an interoperable health information system of public health and health information technology within the development of public information and health surveillance programme. Technically, some major issues remain regarding to health data visualization, spatial processing of health data, health information dissemination, data sharing and the access of local communities to health information. In combination with GIS, we propose a technical framework for web-based health data visualization and spatial analysis. Data was collected from open map-servers and geocoded by open data kit package and data geocoding tools. The Web-based system is designed based on Open-source frameworks and libraries. The system provides Web-based analyst tool for pattern detection through three spatial tests: Nearest neighbour, K function, and Spatial Autocorrelation. The result is a web-based GIS, through which end users can detect disease patterns via selecting area, spatial test parameters and contribute to managers and decision makers. The end users can be health practitioners, educators, local communities, health sector authorities and decision makers. This web-based system allows for the improvement of health related services to public sector users as well as citizens in a secure manner. The combination of spatial statistics and web-based GIS can be a solution that helps empower health practitioners in direct and specific intersectional actions, thus provide for better analysis, control and decision-making.

Implementation of density-based solver for all speeds in the framework of OpenFOAM

NASA Astrophysics Data System (ADS)

Shen, Chun; Sun, Fengxian; Xia, Xinlin

2014-10-01

In the framework of open source CFD code OpenFOAM, a density-based solver for all speeds flow field is developed. In this solver the preconditioned all speeds AUSM+(P) scheme is adopted and the dual time scheme is implemented to complete the unsteady process. Parallel computation could be implemented to accelerate the solving process. Different interface reconstruction algorithms are implemented, and their accuracy with respect to convection is compared. Three benchmark tests of lid-driven cavity flow, flow crossing over a bump, and flow over a forward-facing step are presented to show the accuracy of the AUSM+(P) solver for low-speed incompressible flow, transonic flow, and supersonic/hypersonic flow. Firstly, for the lid driven cavity flow, the computational results obtained by different interface reconstruction algorithms are compared. It is indicated that the one dimensional reconstruction scheme adopted in this solver possesses high accuracy and the solver developed in this paper can effectively catch the features of low incompressible flow. Then via the test cases regarding the flow crossing over bump and over forward step, the ability to capture characteristics of the transonic and supersonic/hypersonic flows are confirmed. The forward-facing step proves to be the most challenging for the preconditioned solvers with and without the dual time scheme. Nonetheless, the solvers described in this paper reproduce the main features of this flow, including the evolution of the initial transient.

SedInConnect: a stand-alone, free and open source tool for the assessment of sediment connectivity

NASA Astrophysics Data System (ADS)

Crema, Stefano; Cavalli, Marco

2018-02-01

There is a growing call, within the scientific community, for solid theoretic frameworks and usable indices/models to assess sediment connectivity. Connectivity plays a significant role in characterizing structural properties of the landscape and, when considered in combination with forcing processes (e.g., rainfall-runoff modelling), can represent a valuable analysis for an improved landscape management. In this work, the authors present the development and application of SedInConnect: a free, open source and stand-alone application for the computation of the Index of Connectivity (IC), as expressed in Cavalli et al. (2013) with the addition of specific innovative features. The tool is intended to have a wide variety of users, both from the scientific community and from the authorities involved in the environmental planning. Thanks to its open source nature, the tool can be adapted and/or integrated according to the users' requirements. Furthermore, presenting an easy-to-use interface and being a stand-alone application, the tool can help management experts in the quantitative assessment of sediment connectivity in the context of hazard and risk assessment. An application to a sample dataset and an overview on up-to-date applications of the approach and of the tool shows the development potential of such analyses. The modelled connectivity, in fact, appears suitable not only to characterize sediment dynamics at the catchment scale but also to integrate prediction models and as a tool for helping geomorphological interpretation.

Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

NASA Technical Reports Server (NTRS)

Jedlovec, Gary; Srikishen, Jayanthi; Edwards, Rita; Cross, David; Welch, Jon; Smith, Matt

2013-01-01

The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of "big data" available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Shortterm Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video-teleconferences, presentation slides, documents, spreadsheets or laptop screens. SAGE is cross-platform, community-driven, open-source visualization and collaboration middleware that utilizes shared national and international cyberinfrastructure for the advancement of scientific research and education.

Scalable Adaptive Graphics Environment (SAGE) Software for the Visualization of Large Data Sets on a Video Wall

NASA Astrophysics Data System (ADS)

Jedlovec, G.; Srikishen, J.; Edwards, R.; Cross, D.; Welch, J. D.; Smith, M. R.

2013-12-01

The use of collaborative scientific visualization systems for the analysis, visualization, and sharing of 'big data' available from new high resolution remote sensing satellite sensors or four-dimensional numerical model simulations is propelling the wider adoption of ultra-resolution tiled display walls interconnected by high speed networks. These systems require a globally connected and well-integrated operating environment that provides persistent visualization and collaboration services. This abstract and subsequent presentation describes a new collaborative visualization system installed for NASA's Short-term Prediction Research and Transition (SPoRT) program at Marshall Space Flight Center and its use for Earth science applications. The system consists of a 3 x 4 array of 1920 x 1080 pixel thin bezel video monitors mounted on a wall in a scientific collaboration lab. The monitors are physically and virtually integrated into a 14' x 7' for video display. The display of scientific data on the video wall is controlled by a single Alienware Aurora PC with a 2nd Generation Intel Core 4.1 GHz processor, 32 GB memory, and an AMD Fire Pro W600 video card with 6 mini display port connections. Six mini display-to-dual DVI cables are used to connect the 12 individual video monitors. The open source Scalable Adaptive Graphics Environment (SAGE) windowing and media control framework, running on top of the Ubuntu 12 Linux operating system, allows several users to simultaneously control the display and storage of high resolution still and moving graphics in a variety of formats, on tiled display walls of any size. The Ubuntu operating system supports the open source Scalable Adaptive Graphics Environment (SAGE) software which provides a common environment, or framework, enabling its users to access, display and share a variety of data-intensive information. This information can be digital-cinema animations, high-resolution images, high-definition video-teleconferences, presentation slides, documents, spreadsheets or laptop screens. SAGE is cross-platform, community-driven, open-source visualization and collaboration middleware that utilizes shared national and international cyberinfrastructure for the advancement of scientific research and education.

Open data models for smart health interconnected applications: the example of openEHR.

PubMed

Demski, Hans; Garde, Sebastian; Hildebrand, Claudia

2016-10-22

Smart Health is known as a concept that enhances networking, intelligent data processing and combining patient data with other parameters. Open data models can play an important role in creating a framework for providing interoperable data services that support the development of innovative Smart Health applications profiting from data fusion and sharing. This article describes a model-driven engineering approach based on standardized clinical information models and explores its application for the development of interoperable electronic health record systems. The following possible model-driven procedures were considered: provision of data schemes for data exchange, automated generation of artefacts for application development and native platforms that directly execute the models. The applicability of the approach in practice was examined using the openEHR framework as an example. A comprehensive infrastructure for model-driven engineering of electronic health records is presented using the example of the openEHR framework. It is shown that data schema definitions to be used in common practice software development processes can be derived from domain models. The capabilities for automatic creation of implementation artefacts (e.g., data entry forms) are demonstrated. Complementary programming libraries and frameworks that foster the use of open data models are introduced. Several compatible health data platforms are listed. They provide standard based interfaces for interconnecting with further applications. Open data models help build a framework for interoperable data services that support the development of innovative Smart Health applications. Related tools for model-driven application development foster semantic interoperability and interconnected innovative applications.

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.

A service-oriented distributed semantic mediator: integrating multiscale biomedical information.

PubMed

Mora, Oscar; Engelbrecht, Gerhard; Bisbal, Jesus

2012-11-01

Biomedical research continuously generates large amounts of heterogeneous and multimodal data spread over multiple data sources. These data, if appropriately shared and exploited, could dramatically improve the research practice itself, and ultimately the quality of health care delivered. This paper presents DISMED (DIstributed Semantic MEDiator), an open source semantic mediator that provides a unified view of a federated environment of multiscale biomedical data sources. DISMED is a Web-based software application to query and retrieve information distributed over a set of registered data sources, using semantic technologies. It also offers a userfriendly interface specifically designed to simplify the usage of these technologies by non-expert users. Although the architecture of the software mediator is generic and domain independent, in the context of this paper, DISMED has been evaluated for managing biomedical environments and facilitating research with respect to the handling of scientific data distributed in multiple heterogeneous data sources. As part of this contribution, a quantitative evaluation framework has been developed. It consist of a benchmarking scenario and the definition of five realistic use-cases. This framework, created entirely with public datasets, has been used to compare the performance of DISMED against other available mediators. It is also available to the scientific community in order to evaluate progress in the domain of semantic mediation, in a systematic and comparable manner. The results show an average improvement in the execution time by DISMED of 55% compared to the second best alternative in four out of the five use-cases of the experimental evaluation.

GeNN: a code generation framework for accelerated brain simulations

NASA Astrophysics Data System (ADS)

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

Chaos-Based Simultaneous Compression and Encryption for Hadoop.

PubMed

Usama, Muhammad; Zakaria, Nordin

2017-01-01

Data compression and encryption are key components of commonly deployed platforms such as Hadoop. Numerous data compression and encryption tools are presently available on such platforms and the tools are characteristically applied in sequence, i.e., compression followed by encryption or encryption followed by compression. This paper focuses on the open-source Hadoop framework and proposes a data storage method that efficiently couples data compression with encryption. A simultaneous compression and encryption scheme is introduced that addresses an important implementation issue of source coding based on Tent Map and Piece-wise Linear Chaotic Map (PWLM), which is the infinite precision of real numbers that result from their long products. The approach proposed here solves the implementation issue by removing fractional components that are generated by the long products of real numbers. Moreover, it incorporates a stealth key that performs a cyclic shift in PWLM without compromising compression capabilities. In addition, the proposed approach implements a masking pseudorandom keystream that enhances encryption quality. The proposed algorithm demonstrated a congruent fit within the Hadoop framework, providing robust encryption security and compression.

GeNN: a code generation framework for accelerated brain simulations.

PubMed

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-07

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/.

GeNN: a code generation framework for accelerated brain simulations

PubMed Central

Yavuz, Esin; Turner, James; Nowotny, Thomas

2016-01-01

Large-scale numerical simulations of detailed brain circuit models are important for identifying hypotheses on brain functions and testing their consistency and plausibility. An ongoing challenge for simulating realistic models is, however, computational speed. In this paper, we present the GeNN (GPU-enhanced Neuronal Networks) framework, which aims to facilitate the use of graphics accelerators for computational models of large-scale neuronal networks to address this challenge. GeNN is an open source library that generates code to accelerate the execution of network simulations on NVIDIA GPUs, through a flexible and extensible interface, which does not require in-depth technical knowledge from the users. We present performance benchmarks showing that 200-fold speedup compared to a single core of a CPU can be achieved for a network of one million conductance based Hodgkin-Huxley neurons but that for other models the speedup can differ. GeNN is available for Linux, Mac OS X and Windows platforms. The source code, user manual, tutorials, Wiki, in-depth example projects and all other related information can be found on the project website http://genn-team.github.io/genn/. PMID:26740369

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

PubMed

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

2009-08-25

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

Investigation of soft component in cosmic ray detection

NASA Astrophysics Data System (ADS)

Oláh, László; Varga, Dezső

2017-07-01

Cosmic ray detection is a research area which finds various applications in tomographic imaging of large size objects. In such applications, the background sources which contaminate cosmic muon signal require a good understanding of the creation processes, as well as reliable simulation frameworks with high predictive power are needed. One of the main background source is the ;soft component;, that is electrons and positrons. In this paper a simulation framework based on GEANT4 has been established to pin down the key features of the soft component. We have found that the electron and positron flux shows a remarkable invariance against various model parameters including the muon emission altitude or primary particle energy distribution. The correlation between simultaneously arriving particles have been quantitatively investigated, demonstrating that electrons and positrons tend to arrive within a close distance and with low relative angle. This feature, which is highly relevant for counting detectors, has been experimentally verified under open sky and at shallow depth underground. The simulation results have been compared to existing other measurements as well as other simulation programs.

Chaos-Based Simultaneous Compression and Encryption for Hadoop

PubMed Central

Zakaria, Nordin

2017-01-01

Data compression and encryption are key components of commonly deployed platforms such as Hadoop. Numerous data compression and encryption tools are presently available on such platforms and the tools are characteristically applied in sequence, i.e., compression followed by encryption or encryption followed by compression. This paper focuses on the open-source Hadoop framework and proposes a data storage method that efficiently couples data compression with encryption. A simultaneous compression and encryption scheme is introduced that addresses an important implementation issue of source coding based on Tent Map and Piece-wise Linear Chaotic Map (PWLM), which is the infinite precision of real numbers that result from their long products. The approach proposed here solves the implementation issue by removing fractional components that are generated by the long products of real numbers. Moreover, it incorporates a stealth key that performs a cyclic shift in PWLM without compromising compression capabilities. In addition, the proposed approach implements a masking pseudorandom keystream that enhances encryption quality. The proposed algorithm demonstrated a congruent fit within the Hadoop framework, providing robust encryption security and compression. PMID:28072850

Functional Additive Mixed Models

PubMed Central

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2014-01-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach. PMID:26347592

A software framework for assessing the resilience of drinking water systems to disasters with an example earthquake case study

DOE PAGES

Klise, Katherine A.; Bynum, Michael; Moriarty, Dylan; ...

2017-07-07

Water utilities are vulnerable to a wide variety of human-caused and natural disasters. The Water Network Tool for Resilience (WNTR) is a new open source PythonTM package designed to help water utilities investigate resilience of water distribution systems to hazards and evaluate resilience-enhancing actions. In this paper, the WNTR modeling framework is presented and a case study is described that uses WNTR to simulate the effects of an earthquake on a water distribution system. The case study illustrates that the severity of damage is not only a function of system integrity and earthquake magnitude, but also of the available resourcesmore » and repair strategies used to return the system to normal operating conditions. While earthquakes are particularly concerning since buried water distribution pipelines are highly susceptible to damage, the software framework can be applied to other types of hazards, including power outages and contamination incidents.« less

Shiny FHIR: An Integrated Framework Leveraging Shiny R and HL7 FHIR to Empower Standards-Based Clinical Data Applications.

PubMed

Hong, Na; Prodduturi, Naresh; Wang, Chen; Jiang, Guoqian

2017-01-01

In this study, we describe our efforts in building a clinical statistics and analysis application platform using an emerging clinical data standard, HL7 FHIR, and an open source web application framework, Shiny. We designed two primary workflows that integrate a series of R packages to enable both patient-centered and cohort-based interactive analyses. We leveraged Shiny with R to develop interactive interfaces on FHIR-based data and used ovarian cancer study datasets as a use case to implement a prototype. Specifically, we implemented patient index, patient-centered data report and analysis, and cohort analysis. The evaluation of our study was performed by testing the adaptability of the framework on two public FHIR servers. We identify common research requirements and current outstanding issues, and discuss future enhancement work of the current studies. Overall, our study demonstrated that it is feasible to use Shiny for implementing interactive analysis on FHIR-based standardized clinical data.

Functional Additive Mixed Models.

PubMed

Scheipl, Fabian; Staicu, Ana-Maria; Greven, Sonja

2015-04-01

We propose an extensive framework for additive regression models for correlated functional responses, allowing for multiple partially nested or crossed functional random effects with flexible correlation structures for, e.g., spatial, temporal, or longitudinal functional data. Additionally, our framework includes linear and nonlinear effects of functional and scalar covariates that may vary smoothly over the index of the functional response. It accommodates densely or sparsely observed functional responses and predictors which may be observed with additional error and includes both spline-based and functional principal component-based terms. Estimation and inference in this framework is based on standard additive mixed models, allowing us to take advantage of established methods and robust, flexible algorithms. We provide easy-to-use open source software in the pffr() function for the R-package refund. Simulations show that the proposed method recovers relevant effects reliably, handles small sample sizes well and also scales to larger data sets. Applications with spatially and longitudinally observed functional data demonstrate the flexibility in modeling and interpretability of results of our approach.

A software framework for assessing the resilience of drinking water systems to disasters with an example earthquake case study

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

Klise, Katherine A.; Bynum, Michael; Moriarty, Dylan

Water utilities are vulnerable to a wide variety of human-caused and natural disasters. The Water Network Tool for Resilience (WNTR) is a new open source PythonTM package designed to help water utilities investigate resilience of water distribution systems to hazards and evaluate resilience-enhancing actions. In this paper, the WNTR modeling framework is presented and a case study is described that uses WNTR to simulate the effects of an earthquake on a water distribution system. The case study illustrates that the severity of damage is not only a function of system integrity and earthquake magnitude, but also of the available resourcesmore » and repair strategies used to return the system to normal operating conditions. While earthquakes are particularly concerning since buried water distribution pipelines are highly susceptible to damage, the software framework can be applied to other types of hazards, including power outages and contamination incidents.« less

A python framework for environmental model uncertainty analysis

USGS Publications Warehouse

White, Jeremy; Fienen, Michael N.; Doherty, John E.

2016-01-01

We have developed pyEMU, a python framework for Environmental Modeling Uncertainty analyses, open-source tool that is non-intrusive, easy-to-use, computationally efficient, and scalable to highly-parameterized inverse problems. The framework implements several types of linear (first-order, second-moment (FOSM)) and non-linear uncertainty analyses. The FOSM-based analyses can also be completed prior to parameter estimation to help inform important modeling decisions, such as parameterization and objective function formulation. Complete workflows for several types of FOSM-based and non-linear analyses are documented in example notebooks implemented using Jupyter that are available in the online pyEMU repository. Example workflows include basic parameter and forecast analyses, data worth analyses, and error-variance analyses, as well as usage of parameter ensemble generation and management capabilities. These workflows document the necessary steps and provides insights into the results, with the goal of educating users not only in how to apply pyEMU, but also in the underlying theory of applied uncertainty quantification.

Differential impact of monsoon and large amplitude internal waves on coral reef development in the Andaman Sea.

PubMed

Wall, Marlene; Schmidt, Gertraud Maria; Janjang, Pornpan; Khokiattiwong, Somkiat; Richter, Claudio

2012-01-01

The Andaman Sea and other macrotidal semi-enclosed tropical seas feature large amplitude internal waves (LAIW). Although LAIW induce strong fluctuations i.e. of temperature, pH, and nutrients, their influence on reef development is so far unknown. A better-known source of disturbance is the monsoon affecting corals due to turbulent mixing and sedimentation. Because in the Andaman Sea both, LAIW and monsoon, act from the same westerly direction their relative contribution to reef development is difficult to discern. Here, we explore the framework development in a number of offshore island locations subjected to differential LAIW- and SW-monsoon impact to address this open question. Cumulative negative temperature anomalies - a proxy for LAIW impact - explained a higher percentage of the variability in coral reef framework height, than sedimentation rates which resulted mainly from the monsoon. Temperature anomalies and sediment grain size provided the best correlation with framework height suggesting that so far neglected subsurface processes (LAIW) play a significant role in shaping coral reefs.

Integrating Visualization Applications, such as ParaView, into HEP Software Frameworks for In-situ Event Displays

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

Lyon, A. L.; Kowalkowski, J. B.; Jones, C. D.

ParaView is a high performance visualization application not widely used in High Energy Physics (HEP). It is a long standing open source project led by Kitware and involves several Department of Energy (DOE) and Department of Defense (DOD) laboratories. Futhermore, it has been adopted by many DOE supercomputing centers and other sites. ParaView is unique in speed and efficiency by using state-of-the-art techniques developed by the academic visualization community that are often not found in applications written by the HEP community. In-situ visualization of events, where event details are visualized during processing/analysis, is a common task for experiment software frameworks.more » Kitware supplies Catalyst, a library that enables scientific software to serve visualization objects to client ParaView viewers yielding a real-time event display. Connecting ParaView to the Fermilab art framework will be described and the capabilities it brings discussed.« less