Next generation sequence assembly with AMOS.

PubMed

Treangen, Todd J; Sommer, Dan D; Angly, Florent E; Koren, Sergey; Pop, Mihai

2011-03-01

A Modular Open-Source Assembler (AMOS) was designed to offer a modular approach to genome assembly. AMOS includes a wide range of tools for assembly, including the lightweight de novo assemblers Minimus and Minimo, and Bambus 2, a robust scaffolder able to handle metagenomic and polymorphic data. This protocol describes how to configure and use AMOS for the assembly of Next Generation sequence data. Additionally, we provide three tutorial examples that include bacterial, viral, and metagenomic datasets with specific tips for improving assembly quality. © 2011 by John Wiley & Sons, Inc.

Localizer: fast, accurate, open-source, and modular software package for superresolution microscopy

PubMed Central

Duwé, Sam; Neely, Robert K.; Zhang, Jin

2012-01-01

Abstract. We present Localizer, a freely available and open source software package that implements the computational data processing inherent to several types of superresolution fluorescence imaging, such as localization (PALM/STORM/GSDIM) and fluctuation imaging (SOFI/pcSOFI). Localizer delivers high accuracy and performance and comes with a fully featured and easy-to-use graphical user interface but is also designed to be integrated in higher-level analysis environments. Due to its modular design, Localizer can be readily extended with new algorithms as they become available, while maintaining the same interface and performance. We provide front-ends for running Localizer from Igor Pro, Matlab, or as a stand-alone program. We show that Localizer performs favorably when compared with two existing superresolution packages, and to our knowledge is the only freely available implementation of SOFI/pcSOFI microscopy. By dramatically improving the analysis performance and ensuring the easy addition of current and future enhancements, Localizer strongly improves the usability of superresolution imaging in a variety of biomedical studies. PMID:23208219

STORMSeq: an open-source, user-friendly pipeline for processing personal genomics data in the cloud.

PubMed

Karczewski, Konrad J; Fernald, Guy Haskin; Martin, Alicia R; Snyder, Michael; Tatonetti, Nicholas P; Dudley, Joel T

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5-10 hours to process a full exome sequence and $30 and 3-8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2.

Stratway: A Modular Approach to Strategic Conflict Resolution

NASA Technical Reports Server (NTRS)

Hagen, George E.; Butler, Ricky W.; Maddalon, Jeffrey M.

2011-01-01

In this paper we introduce Stratway, a modular approach to finding long-term strategic resolutions to conflicts between aircraft. The modular approach provides both advantages and disadvantages. Our primary concern is to investigate the implications on the verification of safety-critical properties of a strategic resolution algorithm. By partitioning the problem into verifiable modules much stronger verification claims can be established. Since strategic resolution involves searching for solutions over an enormous state space, Stratway, like most similar algorithms, searches these spaces by applying heuristics, which present especially difficult verification challenges. An advantage of a modular approach is that it makes a clear distinction between the resolution function and the trajectory generation function. This allows the resolution computation to be independent of any particular vehicle. The Stratway algorithm was developed in both Java and C++ and is available through a open source license. Additionally there is a visualization application that is helpful when analyzing and quickly creating conflict scenarios.

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.

The Biopsychology-Toolbox: a free, open-source Matlab-toolbox for the control of behavioral experiments.

PubMed

Rose, Jonas; Otto, Tobias; Dittrich, Lars

2008-10-30

The Biopsychology-Toolbox is a free, open-source Matlab-toolbox for the control of behavioral experiments. The major aim of the project was to provide a set of basic tools that allow programming novices to control basic hardware used for behavioral experimentation without limiting the power and flexibility of the underlying programming language. The modular design of the toolbox allows portation of parts as well as entire paradigms between different types of hardware. In addition to the toolbox, this project offers a platform for the exchange of functions, hardware solutions and complete behavioral paradigms.

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.

STORMSeq: An Open-Source, User-Friendly Pipeline for Processing Personal Genomics Data in the Cloud

PubMed Central

Karczewski, Konrad J.; Fernald, Guy Haskin; Martin, Alicia R.; Snyder, Michael; Tatonetti, Nicholas P.; Dudley, Joel T.

2014-01-01

The increasing public availability of personal complete genome sequencing data has ushered in an era of democratized genomics. However, read mapping and variant calling software is constantly improving and individuals with personal genomic data may prefer to customize and update their variant calls. Here, we describe STORMSeq (Scalable Tools for Open-Source Read Mapping), a graphical interface cloud computing solution that does not require a parallel computing environment or extensive technical experience. This customizable and modular system performs read mapping, read cleaning, and variant calling and annotation. At present, STORMSeq costs approximately $2 and 5–10 hours to process a full exome sequence and $30 and 3–8 days to process a whole genome sequence. We provide this open-access and open-source resource as a user-friendly interface in Amazon EC2. PMID:24454756

A modular approach to addressing model design, scale, and parameter estimation issues in distributed hydrological modelling

USGS Publications Warehouse

Leavesley, G.H.; Markstrom, S.L.; Restrepo, Pedro J.; Viger, R.J.

2002-01-01

A modular approach to model design and construction provides a flexible framework in which to focus the multidisciplinary research and operational efforts needed to facilitate the development, selection, and application of the most robust distributed modelling methods. A variety of modular approaches have been developed, but with little consideration for compatibility among systems and concepts. Several systems are proprietary, limiting any user interaction. The US Geological Survey modular modelling system (MMS) is a modular modelling framework that uses an open source software approach to enable all members of the scientific community to address collaboratively the many complex issues associated with the design, development, and application of distributed hydrological and environmental models. Implementation of a common modular concept is not a trivial task. However, it brings the resources of a larger community to bear on the problems of distributed modelling, provides a framework in which to compare alternative modelling approaches objectively, and provides a means of sharing the latest modelling advances. The concepts and components of the MMS are described and an example application of the MMS, in a decision-support system context, is presented to demonstrate current system capabilities. Copyright ?? 2002 John Wiley and Sons, Ltd.

Modular Chemical Descriptor Language (MCDL): Stereochemical modules

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

Gakh, Andrei A; Burnett, Michael N; Trepalin, Sergei V.

2011-01-01

In our previous papers we introduced the Modular Chemical Descriptor Language (MCDL) for providing a linear representation of chemical information. A subsequent development was the MCDL Java Chemical Structure Editor which is capable of drawing chemical structures from linear representations and generating MCDL descriptors from structures. In this paper we present MCDL modules and accompanying software that incorporate unique representation of molecular stereochemistry based on Cahn-Ingold-Prelog and Fischer ideas in constructing stereoisomer descriptors. The paper also contains additional discussions regarding canonical representation of stereochemical isomers, and brief algorithm descriptions of the open source LINDES, Java applet, and Open Babel MCDLmore » processing module software packages. Testing of the upgraded MCDL Java Chemical Structure Editor on compounds taken from several large and diverse chemical databases demonstrated satisfactory performance for storage and processing of stereochemical information in MCDL format.« less

ATLAS (Automatic Tool for Local Assembly Structures) - A Comprehensive Infrastructure for Assembly, Annotation, and Genomic Binning of Metagenomic and Metaranscripomic Data

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

White, Richard A.; Brown, Joseph M.; Colby, Sean M.

ATLAS (Automatic Tool for Local Assembly Structures) is a comprehensive multiomics data analysis pipeline that is massively parallel and scalable. ATLAS contains a modular analysis pipeline for assembly, annotation, quantification and genome binning of metagenomics and metatranscriptomics data and a framework for reference metaproteomic database construction. ATLAS transforms raw sequence data into functional and taxonomic data at the microbial population level and provides genome-centric resolution through genome binning. ATLAS provides robust taxonomy based on majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS provides robust taxonomy based onmore » majority voting of protein coding open reading frames rolled-up at the contig level using modified lowest common ancestor (LCA) analysis. ATLAS is user-friendly, easy install through bioconda maintained as open-source on GitHub, and is implemented in Snakemake for modular customizable workflows.« less

77 FR 28861 - Secretary of Energy Advisory Board, Small Modular Reactor Subcommittee

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-16

... DEPARTMENT OF ENERGY Secretary of Energy Advisory Board, Small Modular Reactor Subcommittee AGENCY: Department of Energy. ACTION: Notice of Open Meeting. SUMMARY: This notice announces an open meeting of the Secretary of Energy Advisory Board (SEAB), Small Modular Reactor Subcommittee (SMR). The Federal Advisory...

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

OpenCOR: a modular and interoperable approach to computational biology

PubMed Central

Garny, Alan; Hunter, Peter J.

2015-01-01

Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks. PMID:25705192

Modular assembly for supporting, straining, and directing flow to a core in a nuclear reactor

DOEpatents

Pennell, William E.

1977-01-01

A reactor core support arrangement for supporting, straining, and providing fluid flow to the core and periphery of a nuclear reactor during normal operation. A plurality of removable inlet modular units are contained within permanent liners in the lower supporting plate of the reactor vessel lower internals. During normal operation (1) each inlet modular unit directs main coolant flow to a plurality of core assemblies, the latter being removably supported in receptacles in the upper portion of the modular unit and (2) each inlet modular unit may direct bypass flow to a low pressure annular region of the reactor vessel. Each inlet modular unit may include special fluid seals interposed between mating surfaces of the inlet modular units and the core assemblies and between the inlet modular units and the liners, to minimize leakage and achieve an hydraulic balance. Utilizing the hydraulic balance, the modular units are held in the liners and the assemblies are held in the modular unit receptacles by their own respective weight. Included as part of the permanent liners below the horizontal support plate are generally hexagonal axial debris barriers. The axial debris barriers collectively form a bottom boundary of a secondary high pressure plenum, the upper boundary of which is the bottom surface of the horizontal support plate. Peripheral liners include radial debris barriers which collectively form a barrier against debris entry radially. During normal operation primary coolant inlet openings in the liner, below the axial debris barriers, pass a large amount of coolant into the inlet modular units, and secondary coolant inlet openings in the portion of the liners within the secondary plenum pass a small amount of coolant into the inlet modular units. The secondary coolant inlet openings also provide alternative coolant inlet flow paths in the unlikely event of blockage of the primary inlet openings. The primary inlet openings have characteristics which limit the entry of debris and minimize the potential for debris entering the primary inlets blocking the secondary inlets from inside the modular unit.

Oculomatic: High speed, reliable, and accurate open-source eye tracking for humans and non-human primates.

PubMed

Zimmermann, Jan; Vazquez, Yuriria; Glimcher, Paul W; Pesaran, Bijan; Louie, Kenway

2016-09-01

Video-based noninvasive eye trackers are an extremely useful tool for many areas of research. Many open-source eye trackers are available but current open-source systems are not designed to track eye movements with the temporal resolution required to investigate the mechanisms of oculomotor behavior. Commercial systems are available but employ closed source hardware and software and are relatively expensive, limiting wide-spread use. Here we present Oculomatic, an open-source software and modular hardware solution to eye tracking for use in humans and non-human primates. Oculomatic features high temporal resolution (up to 600Hz), real-time eye tracking with high spatial accuracy (<0.5°), and low system latency (∼1.8ms, 0.32ms STD) at a relatively low-cost. Oculomatic compares favorably to our existing scleral search-coil system while being fully non invasive. We propose that Oculomatic can support a wide range of research into the properties and neural mechanisms of oculomotor behavior. Copyright © 2016 Elsevier B.V. All rights reserved.

FieldTrip: Open source software for advanced analysis of MEG, EEG, and invasive electrophysiological data.

PubMed

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages.

Progress toward Modular UAS for Geoscience Applications

NASA Astrophysics Data System (ADS)

Dahlgren, R. P.; Clark, M. A.; Comstock, R. J.; Fladeland, M.; Gascot, H., III; Haig, T. H.; Lam, S. J.; Mazhari, A. A.; Palomares, R. R.; Pinsker, E. A.; Prathipati, R. T.; Sagaga, J.; Thurling, J. S.; Travers, S. V.

2017-12-01

Small Unmanned Aerial Systems (UAS) have become accepted tools for geoscience, ecology, agriculture, disaster response, land management, and industry. A variety of consumer UAS options exist as science and engineering payload platforms, but their incompatibilities with one another contribute to high operational costs compared with those of piloted aircraft. This research explores the concept of modular UAS, demonstrating airframes that can be reconfigured in the field for experimental optimization, to enable multi-mission support, facilitate rapid repair, or respond to changing field conditions. Modular UAS is revolutionary in allowing aircraft to be optimized around the payload, reversing the conventional wisdom of designing the payload to accommodate an unmodifiable aircraft. UAS that are reconfigurable like Legos™ are ideal for airborne science service providers, system integrators, instrument designers and end users to fulfill a wide range of geoscience experiments. Modular UAS facilitate the adoption of open-source software and rapid prototyping technology where design reuse is important in the context of a highly regulated industry like aerospace. The industry is now at a stage where consolidation, acquisition, and attrition will reduce the number of small manufacturers, with a reduction of innovation and motivation to reduce costs. Modularity leads to interface specifications, which can evolve into de facto or formal standards which contain minimum (but sufficient) details such that multiple vendors can then design to those standards and demonstrate interoperability. At that stage, vendor coopetition leads to robust interface standards, interoperability standards and multi-source agreements which in turn drive costs down significantly.

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

FieldTrip: Open Source Software for Advanced Analysis of MEG, EEG, and Invasive Electrophysiological Data

PubMed Central

Oostenveld, Robert; Fries, Pascal; Maris, Eric; Schoffelen, Jan-Mathijs

2011-01-01

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete set of consistent and user-friendly high-level functions that allow experimental neuroscientists to analyze experimental data. It includes algorithms for simple and advanced analysis, such as time-frequency analysis using multitapers, source reconstruction using dipoles, distributed sources and beamformers, connectivity analysis, and nonparametric statistical permutation tests at the channel and source level. The implementation as toolbox allows the user to perform elaborate and structured analyses of large data sets using the MATLAB command line and batch scripting. Furthermore, users and developers can easily extend the functionality and implement new algorithms. The modular design facilitates the reuse in other software packages. PMID:21253357

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.

PubMed

Bonnal, Raoul J P; Aerts, Jan; Githinji, George; Goto, Naohisa; MacLean, Dan; Miller, Chase A; Mishima, Hiroyuki; Pagani, Massimiliano; Ramirez-Gonzalez, Ricardo; Smant, Geert; Strozzi, Francesco; Syme, Rob; Vos, Rutger; Wennblom, Trevor J; Woodcroft, Ben J; Katayama, Toshiaki; Prins, Pjotr

2012-04-01

Biogem provides a software development environment for the Ruby programming language, which encourages community-based software development for bioinformatics while lowering the barrier to entry and encouraging best practices. Biogem, with its targeted modular and decentralized approach, software generator, tools and tight web integration, is an improved general model for scaling up collaborative open source software development in bioinformatics. Biogem and modules are free and are OSS. Biogem runs on all systems that support recent versions of Ruby, including Linux, Mac OS X and Windows. Further information at http://www.biogems.info. A tutorial is available at http://www.biogems.info/howto.html bonnal@ingm.org.

Modular Aquatic Simulation System 1D

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

2017-04-19

MASS1 simulates open channel hydrodynamics and transport in branched channel networks, using cross-section averaged forms of the continuity, momentum, and convection diffusion equations. Thermal energy transport (temperature), including meteorological influences is supported. The thermodynamics of total dissolved gas (TDG) can be directly simulated. MASS1 has been developed over the last 20 years. It is currently being used on DOE projects that require MASS1 to beopen source. Hence, the authors would like to distribute MASS1 in source form.

A modular, open-source, slide-scanning microscope for diagnostic applications in resource-constrained settings

PubMed Central

Lu, Qiang; Liu, Guanghui; Xiao, Chuanli; Hu, Chuanzhen; Zhang, Shiwu; Xu, Ronald X.; Chu, Kaiqin; Xu, Qianming

2018-01-01

In this paper we report the development of a cost-effective, modular, open source, and fully automated slide-scanning microscope, composed entirely of easily available off-the-shelf parts, and capable of bright field and fluorescence modes. The automated X-Y stage is composed of two low-cost micrometer stages coupled to stepper motors operated in open-loop mode. The microscope is composed of a low-cost CMOS sensor and low-cost board lenses placed in a 4f configuration. The system has approximately 1 micron resolution, limited by the f/# of available board lenses. The microscope is compact, measuring just 25×25×30 cm, and has an absolute positioning accuracy of ±1 μm in the X and Y directions. A Z-stage enables autofocusing and imaging over large fields of view even on non-planar samples, and custom software enables automatic determination of sample boundaries and image mosaicking. We demonstrate the utility of our device through imaging of fluorescent- and transmission-dye stained blood and fecal smears containing human and animal parasites, as well as several prepared tissue samples. These results demonstrate image quality comparable to high-end commercial microscopes at a cost of less than US$400 for a bright-field system, with an extra US$100 needed for the fluorescence module. PMID:29543835

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.

A Graphics Processing Unit Accelerated Motion Correction Algorithm and Modular System for Real-time fMRI

PubMed Central

Scheinost, Dustin; Hampson, Michelle; Qiu, Maolin; Bhawnani, Jitendra; Constable, R. Todd; Papademetris, Xenophon

2013-01-01

Real-time functional magnetic resonance imaging (rt-fMRI) has recently gained interest as a possible means to facilitate the learning of certain behaviors. However, rt-fMRI is limited by processing speed and available software, and continued development is needed for rt-fMRI to progress further and become feasible for clinical use. In this work, we present an open-source rt-fMRI system for biofeedback powered by a novel Graphics Processing Unit (GPU) accelerated motion correction strategy as part of the BioImage Suite project (www.bioimagesuite.org). Our system contributes to the development of rt-fMRI by presenting a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design. Using empirical data from rt-fMRI scans, we assessed the quality of motion correction in this new system. The present algorithm performed comparably to standard (non real-time) offline methods and outperformed other real-time methods based on zero order interpolation of motion parameters. The modular approach to the rt-fMRI system allows the system to be flexible to the experiment and feedback design, a valuable feature for many applications. We illustrate the flexibility of the system by describing several of our ongoing studies. Our hope is that continuing development of open-source rt-fMRI algorithms and software will make this new technology more accessible and adaptable, and will thereby accelerate its application in the clinical and cognitive neurosciences. PMID:23319241

A graphics processing unit accelerated motion correction algorithm and modular system for real-time fMRI.

PubMed

Scheinost, Dustin; Hampson, Michelle; Qiu, Maolin; Bhawnani, Jitendra; Constable, R Todd; Papademetris, Xenophon

2013-07-01

Real-time functional magnetic resonance imaging (rt-fMRI) has recently gained interest as a possible means to facilitate the learning of certain behaviors. However, rt-fMRI is limited by processing speed and available software, and continued development is needed for rt-fMRI to progress further and become feasible for clinical use. In this work, we present an open-source rt-fMRI system for biofeedback powered by a novel Graphics Processing Unit (GPU) accelerated motion correction strategy as part of the BioImage Suite project ( www.bioimagesuite.org ). Our system contributes to the development of rt-fMRI by presenting a motion correction algorithm that provides an estimate of motion with essentially no processing delay as well as a modular rt-fMRI system design. Using empirical data from rt-fMRI scans, we assessed the quality of motion correction in this new system. The present algorithm performed comparably to standard (non real-time) offline methods and outperformed other real-time methods based on zero order interpolation of motion parameters. The modular approach to the rt-fMRI system allows the system to be flexible to the experiment and feedback design, a valuable feature for many applications. We illustrate the flexibility of the system by describing several of our ongoing studies. Our hope is that continuing development of open-source rt-fMRI algorithms and software will make this new technology more accessible and adaptable, and will thereby accelerate its application in the clinical and cognitive neurosciences.

The General Mission Analysis Tool (GMAT): Current Features And Adding Custom Functionality

NASA Technical Reports Server (NTRS)

Conway, Darrel J.; Hughes, Steven P.

2010-01-01

The General Mission Analysis Tool (GMAT) is a software system for trajectory optimization, mission analysis, trajectory estimation, and prediction developed by NASA, the Air Force Research Lab, and private industry. GMAT's design and implementation are based on four basic principles: open source visibility for both the source code and design documentation; platform independence; modular design; and user extensibility. The system, released under the NASA Open Source Agreement, runs on Windows, Mac and Linux. User extensions, loaded at run time, have been built for optimization, trajectory visualization, force model extension, and estimation, by parties outside of GMAT's development group. The system has been used to optimize maneuvers for the Lunar Crater Observation and Sensing Satellite (LCROSS) and ARTEMIS missions and is being used for formation design and analysis for the Magnetospheric Multiscale Mission (MMS).

MOSFiT: Modular Open Source Fitter for Transients

NASA Astrophysics Data System (ADS)

Guillochon, James; Nicholl, Matt; Villar, V. Ashley; Mockler, Brenna; Narayan, Gautham; Mandel, Kaisey S.; Berger, Edo; Williams, Peter K. G.

2018-05-01

Much of the progress made in time-domain astronomy is accomplished by relating observational multiwavelength time-series data to models derived from our understanding of physical laws. This goal is typically accomplished by dividing the task in two: collecting data (observing), and constructing models to represent that data (theorizing). Owing to the natural tendency for specialization, a disconnect can develop between the best available theories and the best available data, potentially delaying advances in our understanding new classes of transients. We introduce MOSFiT: the Modular Open Source Fitter for Transients, a Python-based package that downloads transient data sets from open online catalogs (e.g., the Open Supernova Catalog), generates Monte Carlo ensembles of semi-analytical light-curve fits to those data sets and their associated Bayesian parameter posteriors, and optionally delivers the fitting results back to those same catalogs to make them available to the rest of the community. MOSFiT is designed to help bridge the gap between observations and theory in time-domain astronomy; in addition to making the application of existing models and creation of new models as simple as possible, MOSFiT yields statistically robust predictions for transient characteristics, with a standard output format that includes all the setup information necessary to reproduce a given result. As large-scale surveys such as that conducted with the Large Synoptic Survey Telescope (LSST), discover entirely new classes of transients, tools such as MOSFiT will be critical for enabling rapid comparison of models against data in statistically consistent, reproducible, and scientifically beneficial ways.

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.

Embracing the Open-Source Movement for the Management of Spatial Data: A Case Study of African Trypanosomiasis in Kenya

PubMed Central

Langley, Shaun A.; Messina, Joseph P.

2011-01-01

The past decade has seen an explosion in the availability of spatial data not only for researchers, but the public alike. As the quantity of data increases, the ability to effectively navigate and understand the data becomes more challenging. Here we detail a conceptual model for a spatially explicit database management system that addresses the issues raised with the growing data management problem. We demonstrate utility with a case study in disease ecology: to develop a multi-scale predictive model of African Trypanosomiasis in Kenya. International collaborations and varying technical expertise necessitate a modular open-source software solution. Finally, we address three recurring problems with data management: scalability, reliability, and security. PMID:21686072

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.

Embracing the Open-Source Movement for the Management of Spatial Data: A Case Study of African Trypanosomiasis in Kenya.

PubMed

Langley, Shaun A; Messina, Joseph P

2011-01-01

The past decade has seen an explosion in the availability of spatial data not only for researchers, but the public alike. As the quantity of data increases, the ability to effectively navigate and understand the data becomes more challenging. Here we detail a conceptual model for a spatially explicit database management system that addresses the issues raised with the growing data management problem. We demonstrate utility with a case study in disease ecology: to develop a multi-scale predictive model of African Trypanosomiasis in Kenya. International collaborations and varying technical expertise necessitate a modular open-source software solution. Finally, we address three recurring problems with data management: scalability, reliability, and security.

Low-cost, portable open-source gas monitoring device based on chemosensory technology

NASA Astrophysics Data System (ADS)

Gotor, Raúl; Gaviña, Pablo; Costero, Ana M.

2015-08-01

We report herein the construction of an electronic device to perform the real-time digitalization of the color state of the optical chemosensors used in the detection of dangerous gases. To construct the device, we used open-source modular electronics, such as Arduino and Sparkfun components, as well as free and open-source software (FOSS). The basic principle of the operation of this device is the continuous color measurement of a chemosensor-doped sensing film, whose color changes in the presence of a specific gas. The chemosensor-sensing film can be prepared by using any of the widely available chemosensors for the desired gas. Color measurement is taken by two TCS230 color sensor ICs, reported to the microcontroller, and the results are displayed on an LCD display and pushed through a USB serial port. By using a cyanide optical chemosensor, we demonstrated the operation of the device as a HCN gas detector at low concentrations.

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

PubMed

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

2015-03-01

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

OpenNFT: An open-source Python/Matlab framework for real-time fMRI neurofeedback training based on activity, connectivity and multivariate pattern analysis.

PubMed

Koush, Yury; Ashburner, John; Prilepin, Evgeny; Sladky, Ronald; Zeidman, Peter; Bibikov, Sergei; Scharnowski, Frank; Nikonorov, Artem; De Ville, Dimitri Van

2017-08-01

Neurofeedback based on real-time functional magnetic resonance imaging (rt-fMRI) is a novel and rapidly developing research field. It allows for training of voluntary control over localized brain activity and connectivity and has demonstrated promising clinical applications. Because of the rapid technical developments of MRI techniques and the availability of high-performance computing, new methodological advances in rt-fMRI neurofeedback become possible. Here we outline the core components of a novel open-source neurofeedback framework, termed Open NeuroFeedback Training (OpenNFT), which efficiently integrates these new developments. This framework is implemented using Python and Matlab source code to allow for diverse functionality, high modularity, and rapid extendibility of the software depending on the user's needs. In addition, it provides an easy interface to the functionality of Statistical Parametric Mapping (SPM) that is also open-source and one of the most widely used fMRI data analysis software. We demonstrate the functionality of our new framework by describing case studies that include neurofeedback protocols based on brain activity levels, effective connectivity models, and pattern classification approaches. This open-source initiative provides a suitable framework to actively engage in the development of novel neurofeedback approaches, so that local methodological developments can be easily made accessible to a wider range of users. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

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.

The Current Status of Modular Coordination. A Research Correlation Conference of Building Research Institute, Division of Engineering and Industrial Research (Fall 1959).

ERIC Educational Resources Information Center

National Academy of Sciences - National Research Council, Washington, DC.

Publication of conference presentations include--(1) a brief review of current modular standard development, (2) the statistical status of modular practice, (3) availability of modular products, and (4) educational programs on modular coordination. Included are--(1) explanatory diagrams, (2) text of an open panel discussion, and (3) a list of…

Using CamiTK for rapid prototyping of interactive computer assisted medical intervention applications.

PubMed

Promayon, Emmanuel; Fouard, Céline; Bailet, Mathieu; Deram, Aurélien; Fiard, Gaëlle; Hungr, Nikolai; Luboz, Vincent; Payan, Yohan; Sarrazin, Johan; Saubat, Nicolas; Selmi, Sonia Yuki; Voros, Sandrine; Cinquin, Philippe; Troccaz, Jocelyne

2013-01-01

Computer Assisted Medical Intervention (CAMI hereafter) is a complex multi-disciplinary field. CAMI research requires the collaboration of experts in several fields as diverse as medicine, computer science, mathematics, instrumentation, signal processing, mechanics, modeling, automatics, optics, etc. CamiTK is a modular framework that helps researchers and clinicians to collaborate together in order to prototype CAMI applications by regrouping the knowledge and expertise from each discipline. It is an open-source, cross-platform generic and modular tool written in C++ which can handle medical images, surgical navigation, biomedicals simulations and robot control. This paper presents the Computer Assisted Medical Intervention ToolKit (CamiTK) and how it is used in various applications in our research team.

Joint Common Architecture Demonstration (JCA Demo) Final Report

DTIC Science & Technology

2016-07-28

approach for implementing open systems [16], formerly known as the Modular Open Systems Approach (MOSA). OSA is a business and technical strategy to... TECHNICAL REPORT RDMR-AD-16-01 JOINT COMMON ARCHITECTURE DEMONSTRATION (JCA DEMO) FINAL REPORT Scott A. Wigginton... Modular Avionics .......................................................................... 5 E. Model-Based Engineering

Modular 3D-Printed Soil Gas Probes

NASA Astrophysics Data System (ADS)

Good, S. P.; Selker, J. S.; Al-Qqaili, F.; Lopez, M.; Kahel, L.

2016-12-01

ABSTRACT: Extraction of soil gas is required for a variety of applications in earth sciences and environmental engineering. However, commercially available probes can be costly and are typically limited to a single depth. Here, we present the open-source design and lab testing of a soil gas probe with modular capabilities that allow for the vertical stacking of gas extraction points at different depths in the soil column. The probe modules consist of a 3D printed spacer unit and hydrophobic gas permeable membrane made of high density Polyethylene with pore sizes 20-40 microns. Each of the modular spacer units contain both a gas extraction line and gas input line for the dilution of soil gases if needed. These 2-inch diameter probes can be installed in the field quickly with a hand auger and returned to at any frequency to extract soil gas from desired soil depths. The probes are tested through extraction of soil pore water vapors with distinct stable isotope ratios.

The Virtual Collaboration Environment: New Media for Crisis Response

DTIC Science & Technology

2011-05-01

openvce.net/forum-alternative-platforms and http://openvce.net/more), the open-source Drupal ®-based Proceedings of the 8th International ISCRAM... Drupal is a widely used modular content management system, with an active development community of its own. It provides a user management system and...authoring text documents (a facility felt to be lacking at the time in Drupal ). This wiki feature has itself been supplemented with experimental

Where Have All the Nunn-McCurdys Gone

DTIC Science & Technology

2015-12-01

trickier than coming up with root causes of problems. While opinions abound, it is difficult to ascertain that a given action or set of actions is...change that has been lauded by most defense experts as extremely positive. WSARA made sweeping changes that have strengthened ac- countability of...prior to MS B, and measures to ensure adequate competition, including competitive proto- typing, dual sourcing, and modular open architectures, among

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…

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.

Advanced capabilities for materials modelling with Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

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

2017-11-01

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

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

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

2017-10-24

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

Advanced capabilities for materials modelling with Quantum ESPRESSO.

PubMed

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

2017-09-27

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

The OPEnSampler: A Low-Cost, Low-Weight, Customizable and Modular Open Source 24-Unit Automatic Water Sampler

NASA Astrophysics Data System (ADS)

Nelke, M.; Selker, J. S.; Udell, C.

2017-12-01

Reliable automatic water samplers allow repetitive sampling of various water sources over long periods of time without requiring a researcher on site, reducing human error as well as the monetary and time costs of traveling to the field, particularly when the scale of the sample period is hours or days. The high fixed cost of buying a commercial sampler with little customizability can be a barrier to research requiring repetitive samples, such as the analysis of septic water pre- and post-treatment. DIY automatic samplers proposed in the past sacrifice maximum volume, customizability, or scope of applications, among other features, in exchange for a lower net cost. The purpose of this project was to develop a low-cost, highly customizable, robust water sampler that is capable of sampling many sources of water for various analytes. A lightweight aluminum-extrusion frame was designed and assembled, chosen for its mounting system, strength, and low cost. Water is drawn from two peristaltic pumps through silicone tubing and directed into 24 foil-lined 250mL bags using solenoid valves. A programmable Arduino Uno microcontroller connected to a circuit board communicates with a battery operated real-time clock, initiating sampling stages. Period and volume settings are programmable in-field by the user via serial commands. The OPEnSampler is an open design, allowing the user to decide what components to use and the modular theme of the frame allows fast mounting of new manufactured or 3D printed components. The 24-bag system weighs less than 10kg and the material cost is under $450. Up to 6L of sample water can be drawn at a rate of 100mL/minute in either direction. Faster flowrates are achieved by using more powerful peristaltic pumps. Future design changes could allow a greater maximum volume by filling the unused space with more containers and adding GSM communications to send real time status information.

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

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.

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.

GAMBIT: the global and modular beyond-the-standard-model inference tool

NASA Astrophysics Data System (ADS)

Athron, Peter; Balazs, Csaba; Bringmann, Torsten; Buckley, Andy; Chrząszcz, Marcin; Conrad, Jan; Cornell, Jonathan M.; Dal, Lars A.; Dickinson, Hugh; Edsjö, Joakim; Farmer, Ben; Gonzalo, Tomás E.; Jackson, Paul; Krislock, Abram; Kvellestad, Anders; Lundberg, Johan; McKay, James; Mahmoudi, Farvah; Martinez, Gregory D.; Putze, Antje; Raklev, Are; Ripken, Joachim; Rogan, Christopher; Saavedra, Aldo; Savage, Christopher; Scott, Pat; Seo, Seon-Hee; Serra, Nicola; Weniger, Christoph; White, Martin; Wild, Sebastian

2017-11-01

We describe the open-source global fitting package GAMBIT: the Global And Modular Beyond-the-Standard-Model Inference Tool. GAMBIT combines extensive calculations of observables and likelihoods in particle and astroparticle physics with a hierarchical model database, advanced tools for automatically building analyses of essentially any model, a flexible and powerful system for interfacing to external codes, a suite of different statistical methods and parameter scanning algorithms, and a host of other utilities designed to make scans faster, safer and more easily-extendible than in the past. Here we give a detailed description of the framework, its design and motivation, and the current models and other specific components presently implemented in GAMBIT. Accompanying papers deal with individual modules and present first GAMBIT results. GAMBIT can be downloaded from gambit.hepforge.org.

TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation.

PubMed

Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C; Wong, Willy; Daskalakis, Zafiris J; Farzan, Faranak

2016-01-01

Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal processing, this toolbox intends to promote the widespread utility and standardization of an emerging technology in brain research.

TMSEEG: A MATLAB-Based Graphical User Interface for Processing Electrophysiological Signals during Transcranial Magnetic Stimulation

PubMed Central

Atluri, Sravya; Frehlich, Matthew; Mei, Ye; Garcia Dominguez, Luis; Rogasch, Nigel C.; Wong, Willy; Daskalakis, Zafiris J.; Farzan, Faranak

2016-01-01

Concurrent recording of electroencephalography (EEG) during transcranial magnetic stimulation (TMS) is an emerging and powerful tool for studying brain health and function. Despite a growing interest in adaptation of TMS-EEG across neuroscience disciplines, its widespread utility is limited by signal processing challenges. These challenges arise due to the nature of TMS and the sensitivity of EEG to artifacts that often mask TMS-evoked potentials (TEP)s. With an increase in the complexity of data processing methods and a growing interest in multi-site data integration, analysis of TMS-EEG data requires the development of a standardized method to recover TEPs from various sources of artifacts. This article introduces TMSEEG, an open-source MATLAB application comprised of multiple algorithms organized to facilitate a step-by-step procedure for TMS-EEG signal processing. Using a modular design and interactive graphical user interface (GUI), this toolbox aims to streamline TMS-EEG signal processing for both novice and experienced users. Specifically, TMSEEG provides: (i) targeted removal of TMS-induced and general EEG artifacts; (ii) a step-by-step modular workflow with flexibility to modify existing algorithms and add customized algorithms; (iii) a comprehensive display and quantification of artifacts; (iv) quality control check points with visual feedback of TEPs throughout the data processing workflow; and (v) capability to label and store a database of artifacts. In addition to these features, the software architecture of TMSEEG ensures minimal user effort in initial setup and configuration of parameters for each processing step. This is partly accomplished through a close integration with EEGLAB, a widely used open-source toolbox for EEG signal processing. In this article, we introduce TMSEEG, validate its features and demonstrate its application in extracting TEPs across several single- and multi-pulse TMS protocols. As the first open-source GUI-based pipeline for TMS-EEG signal processing, this toolbox intends to promote the widespread utility and standardization of an emerging technology in brain research. PMID:27774054

Flutrack.org: Open-source and linked data for epidemiology.

PubMed

Chorianopoulos, Konstantinos; Talvis, Karolos

2016-12-01

Epidemiology has made advances, thanks to the availability of real-time surveillance data and by leveraging the geographic analysis of incidents. There are many health information systems that visualize the symptoms of influenza-like illness on a digital map, which is suitable for end-users, but it does not afford further processing and analysis. Existing systems have emphasized the collection, analysis, and visualization of surveillance data, but they have neglected a modular and interoperable design that integrates high-resolution geo-location with real-time data. As a remedy, we have built an open-source project and we have been operating an open service that detects flu-related symptoms and shares the data in real-time with anyone who wants to built upon this system. An analysis of a small number of precisely geo-located status updates (e.g. Twitter) correlates closely with the Google Flu Trends and the Centers for Disease Control and Prevention flu-positive reports. We suggest that public health information systems should embrace an open-source approach and offer linked data, in order to facilitate the development of an ecosystem of applications and services, and in order to be transparent to the general public interest. © The Author(s) 2015.

OFF, Open source Finite volume Fluid dynamics code: A free, high-order solver based on parallel, modular, object-oriented Fortran API

NASA Astrophysics Data System (ADS)

Zaghi, S.

2014-07-01

OFF, an open source (free software) code for performing fluid dynamics simulations, is presented. The aim of OFF is to solve, numerically, the unsteady (and steady) compressible Navier-Stokes equations of fluid dynamics by means of finite volume techniques: the research background is mainly focused on high-order (WENO) schemes for multi-fluids, multi-phase flows over complex geometries. To this purpose a highly modular, object-oriented application program interface (API) has been developed. In particular, the concepts of data encapsulation and inheritance available within Fortran language (from standard 2003) have been stressed in order to represent each fluid dynamics "entity" (e.g. the conservative variables of a finite volume, its geometry, etc…) by a single object so that a large variety of computational libraries can be easily (and efficiently) developed upon these objects. The main features of OFF can be summarized as follows: Programming LanguageOFF is written in standard (compliant) Fortran 2003; its design is highly modular in order to enhance simplicity of use and maintenance without compromising the efficiency; Parallel Frameworks Supported the development of OFF has been also targeted to maximize the computational efficiency: the code is designed to run on shared-memory multi-cores workstations and distributed-memory clusters of shared-memory nodes (supercomputers); the code's parallelization is based on Open Multiprocessing (OpenMP) and Message Passing Interface (MPI) paradigms; Usability, Maintenance and Enhancement in order to improve the usability, maintenance and enhancement of the code also the documentation has been carefully taken into account; the documentation is built upon comprehensive comments placed directly into the source files (no external documentation files needed): these comments are parsed by means of doxygen free software producing high quality html and latex documentation pages; the distributed versioning system referred as git has been adopted in order to facilitate the collaborative maintenance and improvement of the code; CopyrightsOFF is a free software that anyone can use, copy, distribute, study, change and improve under the GNU Public License version 3. The present paper is a manifesto of OFF code and presents the currently implemented features and ongoing developments. This work is focused on the computational techniques adopted and a detailed description of the main API characteristics is reported. OFF capabilities are demonstrated by means of one and two dimensional examples and a three dimensional real application.

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

PubMed

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

2014-01-01

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

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

PubMed

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

2009-09-30

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

STRAD Wheel: Web-Based Library for Visualizing Temporal Data.

PubMed

Fernondez-Prieto, Diana; Naranjo-Valero, Carol; Hernandez, Jose Tiberio; Hagen, Hans

2017-01-01

Recent advances in web development, including the introduction of HTML5, have opened a door for visualization researchers and developers to quickly access larger audiences worldwide. Open source libraries for the creation of interactive visualizations are becoming more specialized but also modular, which makes them easy to incorporate in domain-specific applications. In this context, the authors developed STRAD (Spatio-Temporal-Radar) Wheel, a web-based library that focuses on the visualization and interactive query of temporal data in a compact view with multiple temporal granularities. This article includes two application examples in urban planning to help illustrate the proposed visualization's use in practice.

Spatial Information Processing: Standards-Based Open Source Visualization Technology

NASA Astrophysics Data System (ADS)

Hogan, P.

2009-12-01

. Spatial information intelligence is a global issue that will increasingly affect our ability to survive as a species. Collectively we must better appreciate the complex relationships that make life on Earth possible. Providing spatial information in its native context can accelerate our ability to process that information. To maximize this ability to process information, three basic elements are required: data delivery (server technology), data access (client technology), and data processing (information intelligence). NASA World Wind provides open source client and server technologies based on open standards. The possibilities for data processing and data sharing are enhanced by this inclusive infrastructure for geographic information. It is interesting that this open source and open standards approach, unfettered by proprietary constraints, simultaneously provides for entirely proprietary use of this same technology. 1. WHY WORLD WIND? NASA World Wind began as a single program with specific functionality, to deliver NASA content. But as the possibilities for virtual globe technology became more apparent, we found that while enabling a new class of information technology, we were also getting in the way. Researchers, developers and even users expressed their desire for World Wind functionality in ways that would service their specific needs. They want it in their web pages. They want to add their own features. They want to manage their own data. They told us that only with this kind of flexibility, could their objectives and the potential for this technology be truly realized. World Wind client technology is a set of development tools, a software development kit (SDK) that allows a software engineer to create applications requiring geographic visualization technology. 2. MODULAR COMPONENTRY Accelerated evolution of a technology requires that the essential elements of that technology be modular components such that each can advance independent of the other elements. World Wind therefore changed its mission from providing a single information browser to enabling a whole class of 3D geographic applications. Instead of creating a single program, World Wind is a suite of components that can be selectively used in any number of programs. World Wind technology can be a part of any application, or it can be a window in a web page. Or it can be extended with additional functionalities by application and web developers. World Wind makes it possible to include virtual globe visualization and server technology in support of any objective. The world community can continually benefit from advances made in the technology by NASA in concert with the world community. 3. OPEN SOURCE AND OPEN STANDARDS NASA World Wind is NASA Open Source software. This means that the source code is fully accessible for anyone to freely use, even in association with proprietary technology. Imagery and other data provided by the World Wind servers reside in the public domain, including the data server technology itself. This allows others to deliver their own geospatial data and to provide custom solutions based on users specific needs.

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.

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

PubMed Central

Cladé, Thierry; Snyder, Joshua C.

2010-01-01

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

Iplt--image processing library and toolkit for the electron microscopy community.

PubMed

Philippsen, Ansgar; Schenk, Andreas D; Stahlberg, Henning; Engel, Andreas

2003-01-01

We present the foundation for establishing a modular, collaborative, integrated, open-source architecture for image processing of electron microscopy images, named iplt. It is designed around object oriented paradigms and implemented using the programming languages C++ and Python. In many aspects it deviates from classical image processing approaches. This paper intends to motivate developers within the community to participate in this on-going project. The iplt homepage can be found at http://www.iplt.org.

A high performance, cost-effective, open-source microscope for scanning two-photon microscopy that is modular and readily adaptable.

PubMed

Rosenegger, David G; Tran, Cam Ha T; LeDue, Jeffery; Zhou, Ning; Gordon, Grant R

2014-01-01

Two-photon laser scanning microscopy has revolutionized the ability to delineate cellular and physiological function in acutely isolated tissue and in vivo. However, there exist barriers for many laboratories to acquire two-photon microscopes. Additionally, if owned, typical systems are difficult to modify to rapidly evolving methodologies. A potential solution to these problems is to enable scientists to build their own high-performance and adaptable system by overcoming a resource insufficiency. Here we present a detailed hardware resource and protocol for building an upright, highly modular and adaptable two-photon laser scanning fluorescence microscope that can be used for in vitro or in vivo applications. The microscope is comprised of high-end componentry on a skeleton of off-the-shelf compatible opto-mechanical parts. The dedicated design enabled imaging depths close to 1 mm into mouse brain tissue and a signal-to-noise ratio that exceeded all commercial two-photon systems tested. In addition to a detailed parts list, instructions for assembly, testing and troubleshooting, our plan includes complete three dimensional computer models that greatly reduce the knowledge base required for the non-expert user. This open-source resource lowers barriers in order to equip more laboratories with high-performance two-photon imaging and to help progress our understanding of the cellular and physiological function of living systems.

A High Performance, Cost-Effective, Open-Source Microscope for Scanning Two-Photon Microscopy that Is Modular and Readily Adaptable

PubMed Central

Rosenegger, David G.; Tran, Cam Ha T.; LeDue, Jeffery; Zhou, Ning; Gordon, Grant R.

2014-01-01

Two-photon laser scanning microscopy has revolutionized the ability to delineate cellular and physiological function in acutely isolated tissue and in vivo. However, there exist barriers for many laboratories to acquire two-photon microscopes. Additionally, if owned, typical systems are difficult to modify to rapidly evolving methodologies. A potential solution to these problems is to enable scientists to build their own high-performance and adaptable system by overcoming a resource insufficiency. Here we present a detailed hardware resource and protocol for building an upright, highly modular and adaptable two-photon laser scanning fluorescence microscope that can be used for in vitro or in vivo applications. The microscope is comprised of high-end componentry on a skeleton of off-the-shelf compatible opto-mechanical parts. The dedicated design enabled imaging depths close to 1 mm into mouse brain tissue and a signal-to-noise ratio that exceeded all commercial two-photon systems tested. In addition to a detailed parts list, instructions for assembly, testing and troubleshooting, our plan includes complete three dimensional computer models that greatly reduce the knowledge base required for the non-expert user. This open-source resource lowers barriers in order to equip more laboratories with high-performance two-photon imaging and to help progress our understanding of the cellular and physiological function of living systems. PMID:25333934

Modular Integrated Stackable Layers (MISL) 1.1 Design Specification. Design Guideline Document

NASA Technical Reports Server (NTRS)

Yim, Hester J.

2012-01-01

This document establishes the design guideline of the Modular Instrumentation Data Acquisition (MI-DAQ) system in utilization of several designs available in EV. The MI- DAQ provides the options to the customers depending on their system requirements i.e. a 28V interface power supply, a low power battery operated system, a low power microcontroller, a higher performance microcontroller, a USB interface, a Ethernet interface, a wireless communication, various sensor interfaces, etc. Depending on customer's requirements, the each functional board can be stacked up from a bottom level of power supply to a higher level of stack to provide user interfaces. The stack up of boards are accomplished by a predefined and standardized power bus and data bus connections which are included in this document along with other physical and electrical guidelines. This guideline also provides information for a new design options. This specification is the product of a collaboration between NASA/JSC/EV and Texas A&M University. The goal of the collaboration is to open source the specification and allow outside entities to design, build, and market modules that are compatible with the specification. NASA has designed and is using numerous modules that are compatible to this specification. A limited number of these modules will also be released as open source designs to support the collaboration. The released designs are listed in the Applicable Documents.

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics

PubMed Central

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M.

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system. PMID:26710335

Ontology Alignment Repair through Modularization and Confidence-Based Heuristics.

PubMed

Santos, Emanuel; Faria, Daniel; Pesquita, Catia; Couto, Francisco M

2015-01-01

Ontology Matching aims at identifying a set of semantic correspondences, called an alignment, between related ontologies. In recent years, there has been a growing interest in efficient and effective matching methods for large ontologies. However, alignments produced for large ontologies are often logically incoherent. It was only recently that the use of repair techniques to improve the coherence of ontology alignments began to be explored. This paper presents a novel modularization technique for ontology alignment repair which extracts fragments of the input ontologies that only contain the necessary classes and relations to resolve all detectable incoherences. The paper presents also an alignment repair algorithm that uses a global repair strategy to minimize both the degree of incoherence and the number of mappings removed from the alignment, while overcoming the scalability problem by employing the proposed modularization technique. Our evaluation shows that our modularization technique produces significantly small fragments of the ontologies and that our repair algorithm produces more complete alignments than other current alignment repair systems, while obtaining an equivalent degree of incoherence. Additionally, we also present a variant of our repair algorithm that makes use of the confidence values of the mappings to improve alignment repair. Our repair algorithm was implemented as part of AgreementMakerLight, a free and open-source ontology matching system.

EnviroDIY ModularSensors: A Library to give Environmental Sensors a Common Interface of Functions for use with Arduino-Compatible Dataloggers

NASA Astrophysics Data System (ADS)

Aufdenkampe, A. K.; Damiano, S. G.; Hicks, S.; Horsburgh, J. S.

2017-12-01

EnviroDIY is a community for do-it-yourself environmental science and monitoring (https://envirodiy.org), largely focused on sharing ideas for developing Arduino-compatible open-source sensor stations, similar to the EnviroDIY Mayfly datalogger (http://envirodiy.org/mayfly/). Here we present the ModularSensors Arduino code library (https://github.com/EnviroDIY/ModularSensors), deisigned to give all sensors and variables a common interface of functions and returns and to make it very easy to iterate through and log data from many sensors and variables. This library was written primarily for the EnviroDIY Mayfly, but we have begun to test it on other Arduino based boards. We will show the large number of developed sensor interfaces, and examples of using this library code to stream near real time data to the new EnviroDIY Water Quality Data Portal (http://data.envirodiy.org/), a data and software system based on the Observations Data Model v2 (http://www.odm2.org).

SemantEco: a semantically powered modular architecture for integrating distributed environmental and ecological data

USGS Publications Warehouse

Patton, Evan W.; Seyed, Patrice; Wang, Ping; Fu, Linyun; Dein, F. Joshua; Bristol, R. Sky; McGuinness, Deborah L.

2014-01-01

We aim to inform the development of decision support tools for resource managers who need to examine large complex ecosystems and make recommendations in the face of many tradeoffs and conflicting drivers. We take a semantic technology approach, leveraging background ontologies and the growing body of linked open data. In previous work, we designed and implemented a semantically enabled environmental monitoring framework called SemantEco and used it to build a water quality portal named SemantAqua. Our previous system included foundational ontologies to support environmental regulation violations and relevant human health effects. In this work, we discuss SemantEco’s new architecture that supports modular extensions and makes it easier to support additional domains. Our enhanced framework includes foundational ontologies to support modeling of wildlife observation and wildlife health impacts, thereby enabling deeper and broader support for more holistically examining the effects of environmental pollution on ecosystems. We conclude with a discussion of how, through the application of semantic technologies, modular designs will make it easier for resource managers to bring in new sources of data to support more complex use cases.

Modular analysis of biological networks.

PubMed

Kaltenbach, Hans-Michael; Stelling, Jörg

2012-01-01

The analysis of complex biological networks has traditionally relied on decomposition into smaller, semi-autonomous units such as individual signaling pathways. With the increased scope of systems biology (models), rational approaches to modularization have become an important topic. With increasing acceptance of de facto modularity in biology, widely different definitions of what constitutes a module have sparked controversies. Here, we therefore review prominent classes of modular approaches based on formal network representations. Despite some promising research directions, several important theoretical challenges remain open on the way to formal, function-centered modular decompositions for dynamic biological networks.

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

PubMed

Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

2017-08-16

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

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.

Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models.

PubMed

Jardine, Bartholomew; Raymond, Gary M; Bassingthwaighte, James B

2015-01-01

The Modular Program Constructor (MPC) is an open-source Java based modeling utility, built upon JSim's Mathematical Modeling Language (MML) ( http://www.physiome.org/jsim/) that uses directives embedded in model code to construct larger, more complicated models quickly and with less error than manually combining models. A major obstacle in writing complex models for physiological processes is the large amount of time it takes to model the myriad processes taking place simultaneously in cells, tissues, and organs. MPC replaces this task with code-generating algorithms that take model code from several different existing models and produce model code for a new JSim model. This is particularly useful during multi-scale model development where many variants are to be configured and tested against data. MPC encodes and preserves information about how a model is built from its simpler model modules, allowing the researcher to quickly substitute or update modules for hypothesis testing. MPC is implemented in Java and requires JSim to use its output. MPC source code and documentation are available at http://www.physiome.org/software/MPC/.

U.S. Tsunami Information technology (TIM) Modernization:Developing a Maintainable and Extensible Open Source Earthquake and Tsunami Warning System

NASA Astrophysics Data System (ADS)

Hellman, S. B.; Lisowski, S.; Baker, B.; Hagerty, M.; Lomax, A.; Leifer, J. M.; Thies, D. A.; Schnackenberg, A.; Barrows, J.

2015-12-01

Tsunami Information technology Modernization (TIM) is a National Oceanic and Atmospheric Administration (NOAA) project to update and standardize the earthquake and tsunami monitoring systems currently employed at the U.S. Tsunami Warning Centers in Ewa Beach, Hawaii (PTWC) and Palmer, Alaska (NTWC). While this project was funded by NOAA to solve a specific problem, the requirements that the delivered system be both open source and easily maintainable have resulted in the creation of a variety of open source (OS) software packages. The open source software is now complete and this is a presentation of the OS Software that has been funded by NOAA for benefit of the entire seismic community. The design architecture comprises three distinct components: (1) The user interface, (2) The real-time data acquisition and processing system and (3) The scientific algorithm library. The system follows a modular design with loose coupling between components. We now identify the major project constituents. The user interface, CAVE, is written in Java and is compatible with the existing National Weather Service (NWS) open source graphical system AWIPS. The selected real-time seismic acquisition and processing system is open source SeisComp3 (sc3). The seismic library (libseismic) contains numerous custom written and wrapped open source seismic algorithms (e.g., ML/mb/Ms/Mwp, mantle magnitude (Mm), w-phase moment tensor, bodywave moment tensor, finite-fault inversion, array processing). The seismic library is organized in a way (function naming and usage) that will be familiar to users of Matlab. The seismic library extends sc3 so that it can be called by the real-time system, but it can also be driven and tested outside of sc3, for example, by ObsPy or Earthworm. To unify the three principal components we have developed a flexible and lightweight communication layer called SeismoEdex.

Solar heating and cooling diode module

DOEpatents

Maloney, Timothy J.

1986-01-01

A high efficiency solar heating system comprising a plurality of hollow modular units each for receiving a thermal storage mass, the units being arranged in stacked relation in the exterior frame of a building, each of the units including a port for filling the unit with the mass, a collector region and a storage region, each region having inner and outer walls, the outer wall of the collector region being oriented for exposure to sunlight for heating the thermal storage mass; the storage region having an opening therein and the collector region having a corresponding opening, the openings being joined for communicating the thermal storage mass between the storage and collector regions by thermosiphoning; the collector region being disposed substantially below and in parallel relation to the storage region in the modular unit; and the inner wall of the collector region of each successive modular unit in the stacked relation extending over the outer wall of the storage region of the next lower modular unit in the stacked relation for reducing heat loss from the system. Various modifications and alternatives are disclosed for both heating and cooling applications.

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

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.

PLACE: an open-source python package for laboratory automation, control, and experimentation.

PubMed

Johnson, Jami L; Tom Wörden, Henrik; van Wijk, Kasper

2015-02-01

In modern laboratories, software can drive the full experimental process from data acquisition to storage, processing, and analysis. The automation of laboratory data acquisition is an important consideration for every laboratory. When implementing a laboratory automation scheme, important parameters include its reliability, time to implement, adaptability, and compatibility with software used at other stages of experimentation. In this article, we present an open-source, flexible, and extensible Python package for Laboratory Automation, Control, and Experimentation (PLACE). The package uses modular organization and clear design principles; therefore, it can be easily customized or expanded to meet the needs of diverse laboratories. We discuss the organization of PLACE, data-handling considerations, and then present an example using PLACE for laser-ultrasound experiments. Finally, we demonstrate the seamless transition to post-processing and analysis with Python through the development of an analysis module for data produced by PLACE automation. © 2014 Society for Laboratory Automation and Screening.

An open-source laser electronics suite

NASA Astrophysics Data System (ADS)

Pisenti, Neal C.; Reschovsky, Benjamin J.; Barker, Daniel S.; Restelli, Alessandro; Campbell, Gretchen K.

2016-05-01

We present an integrated set of open-source electronics for controlling external-cavity diode lasers and other instruments in the laboratory. The complete package includes a low-noise circuit for driving high-voltage piezoelectric actuators, an ultra-stable current controller based on the design of, and a high-performance, multi-channel temperature controller capable of driving thermo-electric coolers or resistive heaters. Each circuit (with the exception of the temperature controller) is designed to fit in a Eurocard rack equipped with a low-noise linear power supply capable of driving up to 5 A at +/- 15 V. A custom backplane allows signals to be shared between modules, and a digital communication bus makes the entire rack addressable by external control software over TCP/IP. The modular architecture makes it easy for additional circuits to be designed and integrated with existing electronics, providing a low-cost, customizable alternative to commercial systems without sacrificing performance.

Amp: A modular approach to machine learning in atomistic simulations

NASA Astrophysics Data System (ADS)

Khorshidi, Alireza; Peterson, Andrew A.

2016-10-01

Electronic structure calculations, such as those employing Kohn-Sham density functional theory or ab initio wavefunction theories, have allowed for atomistic-level understandings of a wide variety of phenomena and properties of matter at small scales. However, the computational cost of electronic structure methods drastically increases with length and time scales, which makes these methods difficult for long time-scale molecular dynamics simulations or large-sized systems. Machine-learning techniques can provide accurate potentials that can match the quality of electronic structure calculations, provided sufficient training data. These potentials can then be used to rapidly simulate large and long time-scale phenomena at similar quality to the parent electronic structure approach. Machine-learning potentials usually take a bias-free mathematical form and can be readily developed for a wide variety of systems. Electronic structure calculations have favorable properties-namely that they are noiseless and targeted training data can be produced on-demand-that make them particularly well-suited for machine learning. This paper discusses our modular approach to atomistic machine learning through the development of the open-source Atomistic Machine-learning Package (Amp), which allows for representations of both the total and atom-centered potential energy surface, in both periodic and non-periodic systems. Potentials developed through the atom-centered approach are simultaneously applicable for systems with various sizes. Interpolation can be enhanced by introducing custom descriptors of the local environment. We demonstrate this in the current work for Gaussian-type, bispectrum, and Zernike-type descriptors. Amp has an intuitive and modular structure with an interface through the python scripting language yet has parallelizable fortran components for demanding tasks; it is designed to integrate closely with the widely used Atomic Simulation Environment (ASE), which makes it compatible with a wide variety of commercial and open-source electronic structure codes. We finally demonstrate that the neural network model inside Amp can accurately interpolate electronic structure energies as well as forces of thousands of multi-species atomic systems.

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.

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

PubMed Central

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

2014-01-01

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

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

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.

Modular thought in the circuit analysis

NASA Astrophysics Data System (ADS)

Wang, Feng

2018-04-01

Applied to solve the problem of modular thought, provides a whole for simplification's method, the complex problems have become of, and the study of circuit is similar to the above problems: the complex connection between components, make the whole circuit topic solution seems to be more complex, and actually components the connection between the have rules to follow, this article mainly tells the story of study on the application of the circuit modular thought. First of all, this paper introduces the definition of two-terminal network and the concept of two-terminal network equivalent conversion, then summarizes the common source resistance hybrid network modular approach, containing controlled source network modular processing method, lists the common module, typical examples analysis.

[Modularization by the open standard. (I)].

PubMed

Hirano, H

2000-10-01

We are proceeding with the project called "Open LA21 Project" in the course of the clinical laboratory automation toward the 21st century. With the modular system that realizes integration, downsizing, a reasonable price, and is the future course in the clinical testing automation system as well, we aim to establish common standards among manufacturers as the only way to create user friendly market environments where the proper competition exists among the manufacturers. The common standards which are in preparation by the participating companies as "Open module system standards" are the standards which are going to be made public. They are intended to guarantee connection, compatibility of the products in conformity with the standards. In this project, we intend to realize the modular system that integrates each field, such as chemistry, hematology, coagulation/fibrinolysis, immunology, urinalysis in an early stage, and contribute positively to restructuring and upgrading the "raison d'etre" of the 21st century clinical testing.

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/.

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.

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.

DSPSR: Digital Signal Processing Software for Pulsar Astronomy

NASA Astrophysics Data System (ADS)

van Straten, W.; Bailes, M.

2010-10-01

DSPSR, written primarily in C++, is an open-source, object-oriented, digital signal processing software library and application suite for use in radio pulsar astronomy. The library implements an extensive range of modular algorithms for use in coherent dedispersion, filterbank formation, pulse folding, and other tasks. The software is installed and compiled using the standard GNU configure and make system, and is able to read astronomical data in 18 different file formats, including FITS, S2, CPSR, CPSR2, PuMa, PuMa2, WAPP, ASP, and Mark5.

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

DTIC Science & Technology

2012-06-26

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

OSCAR4: a flexible architecture for chemical text-mining.

PubMed

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

2011-10-14

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

OpenWorm: an open-science approach to modeling Caenorhabditis elegans.

PubMed

Szigeti, Balázs; Gleeson, Padraig; Vella, Michael; Khayrulin, Sergey; Palyanov, Andrey; Hokanson, Jim; Currie, Michael; Cantarelli, Matteo; Idili, Giovanni; Larson, Stephen

2014-01-01

OpenWorm is an international collaboration with the aim of understanding how the behavior of Caenorhabditis elegans (C. elegans) emerges from its underlying physiological processes. The project has developed a modular simulation engine to create computational models of the worm. The modularity of the engine makes it possible to easily modify the model, incorporate new experimental data and test hypotheses. The modeling framework incorporates both biophysical neuronal simulations and a novel fluid-dynamics-based soft-tissue simulation for physical environment-body interactions. The project's open-science approach is aimed at overcoming the difficulties of integrative modeling within a traditional academic environment. In this article the rationale is presented for creating the OpenWorm collaboration, the tools and resources developed thus far are outlined and the unique challenges associated with the project are discussed.

Modular operads and the quantum open-closed homotopy algebra

NASA Astrophysics Data System (ADS)

Doubek, Martin; Jurčo, Branislav; Münster, Korbinian

2015-12-01

We verify that certain algebras appearing in string field theory are algebras over Feynman transform of modular operads which we describe explicitly. Equivalent description in terms of solutions of generalized BV master equations are explained from the operadic point of view.

Modularization of Courses.

ERIC Educational Resources Information Center

Eastern Arizona Coll., Thatcher.

Eastern Arizona College has developed a modularized system of instruction for five vocational and vocationally related courses--Introduction to Business, Business Mathematics, English, Drafting, and Electronics. Each course is divided into independent segments of instruction and students have open-entry and exit options. This document reviews the…

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

NASA Astrophysics Data System (ADS)

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

2009-12-01

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

Analyzing huge pathology images with open source software.

PubMed

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

2013-06-06

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

Analyzing huge pathology images with open source software

PubMed Central

2013-01-01

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

A Formal Theory for Modular ERDF Ontologies

NASA Astrophysics Data System (ADS)

Analyti, Anastasia; Antoniou, Grigoris; Damásio, Carlos Viegas

The success of the Semantic Web is impossible without any form of modularity, encapsulation, and access control. In an earlier paper, we extended RDF graphs with weak and strong negation, as well as derivation rules. The ERDF #n-stable model semantics of the extended RDF framework (ERDF) is defined, extending RDF(S) semantics. In this paper, we propose a framework for modular ERDF ontologies, called modular ERDF framework, which enables collaborative reasoning over a set of ERDF ontologies, while support for hidden knowledge is also provided. In particular, the modular ERDF stable model semantics of modular ERDF ontologies is defined, extending the ERDF #n-stable model semantics. Our proposed framework supports local semantics and different points of view, local closed-world and open-world assumptions, and scoped negation-as-failure. Several complexity results are provided.

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

NASA Astrophysics Data System (ADS)

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

2004-05-01

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

Brain modularity controls the critical behavior of spontaneous activity.

PubMed

Russo, R; Herrmann, H J; de Arcangelis, L

2014-03-13

The human brain exhibits a complex structure made of scale-free highly connected modules loosely interconnected by weaker links to form a small-world network. These features appear in healthy patients whereas neurological diseases often modify this structure. An important open question concerns the role of brain modularity in sustaining the critical behaviour of spontaneous activity. Here we analyse the neuronal activity of a model, successful in reproducing on non-modular networks the scaling behaviour observed in experimental data, on a modular network implementing the main statistical features measured in human brain. We show that on a modular network, regardless the strength of the synaptic connections or the modular size and number, activity is never fully scale-free. Neuronal avalanches can invade different modules which results in an activity depression, hindering further avalanche propagation. Critical behaviour is solely recovered if inter-module connections are added, modifying the modular into a more random structure.

Integrated genome browser: visual analytics platform for genomics.

PubMed

Freese, Nowlan H; Norris, David C; Loraine, Ann E

2016-07-15

Genome browsers that support fast navigation through vast datasets and provide interactive visual analytics functions can help scientists achieve deeper insight into biological systems. Toward this end, we developed Integrated Genome Browser (IGB), a highly configurable, interactive and fast open source desktop genome browser. Here we describe multiple updates to IGB, including all-new capabilities to display and interact with data from high-throughput sequencing experiments. To demonstrate, we describe example visualizations and analyses of datasets from RNA-Seq, ChIP-Seq and bisulfite sequencing experiments. Understanding results from genome-scale experiments requires viewing the data in the context of reference genome annotations and other related datasets. To facilitate this, we enhanced IGB's ability to consume data from diverse sources, including Galaxy, Distributed Annotation and IGB-specific Quickload servers. To support future visualization needs as new genome-scale assays enter wide use, we transformed the IGB codebase into a modular, extensible platform for developers to create and deploy all-new visualizations of genomic data. IGB is open source and is freely available from http://bioviz.org/igb aloraine@uncc.edu. © The Author 2016. Published by Oxford University Press.

Reader Response to Front Pages with Modular Format and Color [and] Newspaper Errors: Source Perception, Reporter Response and Some Causes. American Newspaper Publishers Association (ANPA) News Research Report No. 35.

ERIC Educational Resources Information Center

Click, J. W.; And Others

Two studies were conducted, the first to determine reader response to newspaper front pages with modular format and color, and the second to examine source perception and reporter response to errors in news stories. Results of the first study revealed that respondents in three cities preferred modular front pages to other modern format pages and…

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.

A simple object-oriented and open-source model for scientific and policy analyses of the global climate system – Hector v1.0

DOE PAGES

Hartin, Corinne A.; Patel, Pralit L.; Schwarber, Adria; ...

2015-04-01

Simple climate models play an integral role in the policy and scientific communities. They are used for climate mitigation scenarios within integrated assessment models, complex climate model emulation, and uncertainty analyses. Here we describe Hector v1.0, an open source, object-oriented, simple global climate carbon-cycle model. This model runs essentially instantaneously while still representing the most critical global-scale earth system processes. Hector has a three-part main carbon cycle: a one-pool atmosphere, land, and ocean. The model's terrestrial carbon cycle includes primary production and respiration fluxes, accommodating arbitrary geographic divisions into, e.g., ecological biomes or political units. Hector actively solves the inorganicmore » carbon system in the surface ocean, directly calculating air–sea fluxes of carbon and ocean pH. Hector reproduces the global historical trends of atmospheric [CO 2], radiative forcing, and surface temperatures. The model simulates all four Representative Concentration Pathways (RCPs) with equivalent rates of change of key variables over time compared to current observations, MAGICC (a well-known simple climate model), and models from the 5th Coupled Model Intercomparison Project. Hector's flexibility, open-source nature, and modular design will facilitate a broad range of research in various areas.« less

Demonstrating High-Accuracy Orbital Access Using Open-Source Tools

NASA Technical Reports Server (NTRS)

Gilbertson, Christian; Welch, Bryan

2017-01-01

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

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

NASA Astrophysics Data System (ADS)

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

2012-12-01

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

A modular approach to disease registry design: successful adoption of an internet-based rare disease registry.

PubMed

Bellgard, Matthew I; Macgregor, Andrew; Janon, Fred; Harvey, Adam; O'Leary, Peter; Hunter, Adam; Dawkins, Hugh

2012-10-01

There is a need to develop Internet-based rare disease registries to support health care stakeholders to deliver improved quality patient outcomes. Such systems should be architected to enable multiple-level access by a range of user groups within a region or across regional/country borders in a secure and private way. However, this functionality is currently not available in many existing systems. A new approach to the design of an Internet-based architecture for disease registries has been developed for patients with clinical and genetic data in geographical disparate locations. The system addresses issues of multiple-level access by key stakeholders, security and privacy. The system has been successfully adopted for specific rare diseases in Australia and is open source. The results of this work demonstrate that it is feasible to design an open source Internet-based disease registry system in a scalable and customizable fashion and designed to facilitate interoperability with other systems. © 2012 Wiley Periodicals, Inc.

TEA: A Code Calculating Thermochemical Equilibrium Abundances

NASA Astrophysics Data System (ADS)

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

2016-07-01

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

TEA: A CODE CALCULATING THERMOCHEMICAL EQUILIBRIUM ABUNDANCES

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

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

2016-07-01

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

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

Project-Based Module Development.

ERIC Educational Resources Information Center

Meel, R. M. van

A project management design for modularizing higher education at open universities was developed and tested. Literature in the fields of project management and development of modular curriculum materials was reviewed and used as a basis for developing a project-based approach to the process of developing modules for self-instruction. According to…

nodeGame: Real-time, synchronous, online experiments in the browser.

PubMed

Balietti, Stefano

2017-10-01

nodeGame is a free, open-source JavaScript/ HTML5 framework for conducting synchronous experiments online and in the lab directly in the browser window. It is specifically designed to support behavioral research along three dimensions: (i) larger group sizes, (ii) real-time (but also discrete time) experiments, and (iii) batches of simultaneous experiments. nodeGame has a modular source code, and defines an API (application programming interface) through which experimenters can create new strategic environments and configure the platform. With zero-install, nodeGame can run on a great variety of devices, from desktop computers to laptops, smartphones, and tablets. The current version of the software is 3.0, and extensive documentation is available on the wiki pages at http://nodegame.org .

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.

The Evolution of Medical Training Simulation in the U.S. Military.

PubMed

Linde, Amber S; Kunkler, Kevin

2016-01-01

The United States has been at war since 2003. During that time, training using Medical Simulation technology has been developed and integrated into military medical training for combat medics, nurses and surgeons. Efforts stemming from the Joint Programmatic Committee-1 (JPC-1) Medical Simulation and Training Portfolio has allowed for the improvement and advancement in military medical training by focusing on research in simulation training technology in order to achieve this. Based upon lessons learned capability gaps have been identified concerning the necessity to validate and enhance combat medial training simulators. These capability gaps include 1) Open Source/Open Architecture; 2) Modularity and Interoperability; and 3) Material and Virtual Reality (VR) Models. Using the capability gaps, JPC-1 has identified important research endeavors that need to be explored.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Anima: Modular Workflow System for Comprehensive Image Data Analysis

PubMed Central

Rantanen, Ville; Valori, Miko; Hautaniemi, Sampsa

2014-01-01

Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and pre-processing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis development, and it contains several features that are crucial in high-throughput image data analysis: programing language independence, batch processing, easily customized data processing, interoperability with other software via application programing interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environments. Anima is a fully open source and available with documentation at www.anduril.org/anima. PMID:25126541

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

ORBKIT: A modular python toolbox for cross-platform postprocessing of quantum chemical wavefunction data.

PubMed

Hermann, Gunter; Pohl, Vincent; Tremblay, Jean Christophe; Paulus, Beate; Hege, Hans-Christian; Schild, Axel

2016-06-15

ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several grid-independent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by user-written modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is open-source under GNU-LGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Development of a space universal modular architecture (SUMO)

NASA Astrophysics Data System (ADS)

Collins, Bernie F.

This concept paper proposes that the space community should develop and implement a universal standard for spacecraft modularity - to improve interoperability of spacecraft components. Pursuing a global industry consensus standard for open and modular spacecraft architecture will encourage trade, remove standards-related market barriers, and in the long run increase both value provided to customers and profitability of the space industrial sector. This concept paper sets out: (1) the goals for a SUMO standard and how it will benefit the space community; (2) background on spacecraft modularity and existing related standards; (3) the proposed technical scope of the current standardization effort; and (4) an approach for creating a SUMO standard.

FAST Modularization Framework for Wind Turbine Simulation: Full-System Linearization

DOE PAGES

Jonkman, Jason M.; Jonkman, Bonnie J.

2016-10-03

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well-established methods and tools for analyzing linear systems. Here, this paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

FAST modularization framework for wind turbine simulation: full-system linearization

NASA Astrophysics Data System (ADS)

Jonkman, J. M.; Jonkman, B. J.

2016-09-01

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well- established methods and tools for analyzing linear systems. This paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

Solar wind monitor—a school geophysics project

NASA Astrophysics Data System (ADS)

Robinson, Ian

2018-05-01

Described is an established geophysics project to construct a solar wind monitor based on a nT resolution fluxgate magnetometer. Low-cost and appropriate from school to university level it incorporates elements of astrophysics, geophysics, electronics, programming, computer networking and signal processing. The system monitors the earth’s field in real-time uploading data and graphs to a website every few minutes. Modular design encourages construction and testing by teams of students as well as expansion and refinement. The system has been tested running unattended for months at a time. Both the hardware design and software is published as open-source [1, 10].

OSCAR4: a flexible architecture for chemical text-mining

PubMed Central

2011-01-01

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

The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans

PubMed Central

Maia Chagas, Andre; Prieto-Godino, Lucia L.; Arrenberg, Aristides B.

2017-01-01

Small, genetically tractable species such as larval zebrafish, Drosophila, or Caenorhabditis elegans have become key model organisms in modern neuroscience. In addition to their low maintenance costs and easy sharing of strains across labs, one key appeal is the possibility to monitor single or groups of animals in a behavioural arena while controlling the activity of select neurons using optogenetic or thermogenetic tools. However, the purchase of a commercial solution for these types of experiments, including an appropriate camera system as well as a controlled behavioural arena, can be costly. Here, we present a low-cost and modular open-source alternative called ‘FlyPi’. Our design is based on a 3D-printed mainframe, a Raspberry Pi computer, and high-definition camera system as well as Arduino-based optical and thermal control circuits. Depending on the configuration, FlyPi can be assembled for well under €100 and features optional modules for light-emitting diode (LED)-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature stimulator for thermogenetics. The complete version with all modules costs approximately €200 or substantially less if the user is prepared to ‘shop around’. All functions of FlyPi can be controlled through a custom-written graphical user interface. To demonstrate FlyPi’s capabilities, we present its use in a series of state-of-the-art neurogenetics experiments. In addition, we demonstrate FlyPi’s utility as a medical diagnostic tool as well as a teaching aid at Neurogenetics courses held at several African universities. Taken together, the low cost and modular nature as well as fully open design of FlyPi make it a highly versatile tool in a range of applications, including the classroom, diagnostic centres, and research labs. PMID:28719603

The €100 lab: A 3D-printable open-source platform for fluorescence microscopy, optogenetics, and accurate temperature control during behaviour of zebrafish, Drosophila, and Caenorhabditis elegans.

PubMed

Maia Chagas, Andre; Prieto-Godino, Lucia L; Arrenberg, Aristides B; Baden, Tom

2017-07-01

Small, genetically tractable species such as larval zebrafish, Drosophila, or Caenorhabditis elegans have become key model organisms in modern neuroscience. In addition to their low maintenance costs and easy sharing of strains across labs, one key appeal is the possibility to monitor single or groups of animals in a behavioural arena while controlling the activity of select neurons using optogenetic or thermogenetic tools. However, the purchase of a commercial solution for these types of experiments, including an appropriate camera system as well as a controlled behavioural arena, can be costly. Here, we present a low-cost and modular open-source alternative called 'FlyPi'. Our design is based on a 3D-printed mainframe, a Raspberry Pi computer, and high-definition camera system as well as Arduino-based optical and thermal control circuits. Depending on the configuration, FlyPi can be assembled for well under €100 and features optional modules for light-emitting diode (LED)-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature stimulator for thermogenetics. The complete version with all modules costs approximately €200 or substantially less if the user is prepared to 'shop around'. All functions of FlyPi can be controlled through a custom-written graphical user interface. To demonstrate FlyPi's capabilities, we present its use in a series of state-of-the-art neurogenetics experiments. In addition, we demonstrate FlyPi's utility as a medical diagnostic tool as well as a teaching aid at Neurogenetics courses held at several African universities. Taken together, the low cost and modular nature as well as fully open design of FlyPi make it a highly versatile tool in a range of applications, including the classroom, diagnostic centres, and research labs.

LOVD: easy creation of a locus-specific sequence variation database using an "LSDB-in-a-box" approach.

PubMed

Fokkema, Ivo F A C; den Dunnen, Johan T; Taschner, Peter E M

2005-08-01

The completion of the human genome project has initiated, as well as provided the basis for, the collection and study of all sequence variation between individuals. Direct access to up-to-date information on sequence variation is currently provided most efficiently through web-based, gene-centered, locus-specific databases (LSDBs). We have developed the Leiden Open (source) Variation Database (LOVD) software approaching the "LSDB-in-a-Box" idea for the easy creation and maintenance of a fully web-based gene sequence variation database. LOVD is platform-independent and uses PHP and MySQL open source software only. The basic gene-centered and modular design of the database follows the recommendations of the Human Genome Variation Society (HGVS) and focuses on the collection and display of DNA sequence variations. With minimal effort, the LOVD platform is extendable with clinical data. The open set-up should both facilitate and promote functional extension with scripts written by the community. The LOVD software is freely available from the Leiden Muscular Dystrophy pages (www.DMD.nl/LOVD/). To promote the use of LOVD, we currently offer curators the possibility to set up an LSDB on our Leiden server. (c) 2005 Wiley-Liss, Inc.

Atomic force microscopy reveals the mechanical design of a modular protein

PubMed Central

Li, Hongbin; Oberhauser, Andres F.; Fowler, Susan B.; Clarke, Jane; Fernandez, Julio M.

2000-01-01

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering. PMID:10823913

Atomic force microscopy reveals the mechanical design of a modular protein.

PubMed

Li, H; Oberhauser, A F; Fowler, S B; Clarke, J; Fernandez, J M

2000-06-06

Tandem modular proteins underlie the elasticity of natural adhesives, cell adhesion proteins, and muscle proteins. The fundamental unit of elastic proteins is their individually folded modules. Here, we use protein engineering to construct multimodular proteins composed of Ig modules of different mechanical strength. We examine the mechanical properties of the resulting tandem modular proteins by using single protein atomic force microscopy. We show that by combining modules of known mechanical strength, we can generate proteins with novel elastic properties. Our experiments reveal the simple mechanical design of modular proteins and open the way for the engineering of elastic proteins with defined mechanical properties, which can be used in tissue and fiber engineering.

Youpi: YOUr processing PIpeline

NASA Astrophysics Data System (ADS)

Monnerville, Mathias; Sémah, Gregory

2012-03-01

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

Observations and Thermochemical Calculations for Hot-Jupiter Atmospheres

NASA Astrophysics Data System (ADS)

Blecic, Jasmina; Harrington, Joseph; Bowman, M. Oliver; Cubillos, Patricio; Stemm, Madison

2015-01-01

I present Spitzer eclipse observations for WASP-14b and WASP-43b, an open source tool for thermochemical equilibrium calculations, and components of an open source tool for atmospheric parameter retrieval from spectroscopic data. WASP-14b is a planet that receives high irradiation from its host star, yet, although theory does not predict it, the planet hosts a thermal inversion. The WASP-43b eclipses have signal-to-noise ratios of ~25, one of the largest among exoplanets. To assess these planets' atmospheric composition and thermal structure, we developed an open-source Bayesian Atmospheric Radiative Transfer (BART) code. My dissertation tasks included developing a Thermochemical Equilibrium Abundances (TEA) code, implementing the eclipse geometry calculation in BART's radiative transfer module, and generating parameterized pressure and temperature profiles so the radiative-transfer module can be driven by the statistical module.To initialize the radiative-transfer calculation in BART, TEA calculates the equilibrium abundances of gaseous molecular species at a given temperature and pressure. It uses the Gibbs-free-energy minimization method with an iterative Lagrangian optimization scheme. Given elemental abundances, TEA calculates molecular abundances for a particular temperature and pressure or a list of temperature-pressure pairs. The code is tested against the original method developed by White at al. (1958), the analytic method developed by Burrows and Sharp (1999), and the Newton-Raphson method implemented in the open-source Chemical Equilibrium with Applications (CEA) code. TEA, written in Python, is modular, documented, and available to the community via the open-source development site GitHub.com.Support for this work was provided by NASA Headquarters under the NASA Earth and Space Science Fellowship Program, grant NNX12AL83H, by NASA through an award issued by JPL/Caltech, and through the Science Mission Directorate's Planetary Atmospheres Program, grant NNX12AI69G.

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems

PubMed Central

Stefanini, Fabio; Neftci, Emre O.; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS. PMID:25232314

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.

DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

PubMed Central

Gouws, André; Woods, Will; Millman, Rebecca; Morland, Antony; Green, Gary

2008-01-01

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data. PMID:19352444

Creative computing with Landlab: an open-source toolkit for building, coupling, and exploring two-dimensional numerical models of Earth-surface dynamics

NASA Astrophysics Data System (ADS)

Hobley, Daniel E. J.; Adams, Jordan M.; Nudurupati, Sai Siddhartha; Hutton, Eric W. H.; Gasparini, Nicole M.; Istanbulluoglu, Erkan; Tucker, Gregory E.

2017-01-01

The ability to model surface processes and to couple them to both subsurface and atmospheric regimes has proven invaluable to research in the Earth and planetary sciences. However, creating a new model typically demands a very large investment of time, and modifying an existing model to address a new problem typically means the new work is constrained to its detriment by model adaptations for a different problem. Landlab is an open-source software framework explicitly designed to accelerate the development of new process models by providing (1) a set of tools and existing grid structures - including both regular and irregular grids - to make it faster and easier to develop new process components, or numerical implementations of physical processes; (2) a suite of stable, modular, and interoperable process components that can be combined to create an integrated model; and (3) a set of tools for data input, output, manipulation, and visualization. A set of example models built with these components is also provided. Landlab's structure makes it ideal not only for fully developed modelling applications but also for model prototyping and classroom use. Because of its modular nature, it can also act as a platform for model intercomparison and epistemic uncertainty and sensitivity analyses. Landlab exposes a standardized model interoperability interface, and is able to couple to third-party models and software. Landlab also offers tools to allow the creation of cellular automata, and allows native coupling of such models to more traditional continuous differential equation-based modules. We illustrate the principles of component coupling in Landlab using a model of landform evolution, a cellular ecohydrologic model, and a flood-wave routing model.

PyNCS: a microkernel for high-level definition and configuration of neuromorphic electronic systems.

PubMed

Stefanini, Fabio; Neftci, Emre O; Sheik, Sadique; Indiveri, Giacomo

2014-01-01

Neuromorphic hardware offers an electronic substrate for the realization of asynchronous event-based sensory-motor systems and large-scale spiking neural network architectures. In order to characterize these systems, configure them, and carry out modeling experiments, it is often necessary to interface them to workstations. The software used for this purpose typically consists of a large monolithic block of code which is highly specific to the hardware setup used. While this approach can lead to highly integrated hardware/software systems, it hampers the development of modular and reconfigurable infrastructures thus preventing a rapid evolution of such systems. To alleviate this problem, we propose PyNCS, an open-source front-end for the definition of neural network models that is interfaced to the hardware through a set of Python Application Programming Interfaces (APIs). The design of PyNCS promotes modularity, portability and expandability and separates implementation from hardware description. The high-level front-end that comes with PyNCS includes tools to define neural network models as well as to create, monitor and analyze spiking data. Here we report the design philosophy behind the PyNCS framework and describe its implementation. We demonstrate its functionality with two representative case studies, one using an event-based neuromorphic vision sensor, and one using a set of multi-neuron devices for carrying out a cognitive decision-making task involving state-dependent computation. PyNCS, already applicable to a wide range of existing spike-based neuromorphic setups, will accelerate the development of hybrid software/hardware neuromorphic systems, thanks to its code flexibility. The code is open-source and available online at https://github.com/inincs/pyNCS.

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D

PubMed Central

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron

2017-01-01

Abstract Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. PMID:28814063

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

PubMed

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

2018-02-01

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

iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

PubMed

Liluashvili, Vaja; Kalayci, Selim; Fluder, Eugene; Wilson, Manda; Gabow, Aaron; Gümüs, Zeynep H

2017-08-01

Visualizations of biomolecular networks assist in systems-level data exploration in many cellular processes. Data generated from high-throughput experiments increasingly inform these networks, yet current tools do not adequately scale with concomitant increase in their size and complexity. We present an open source software platform, interactome-CAVE (iCAVE), for visualizing large and complex biomolecular interaction networks in 3D. Users can explore networks (i) in 3D using a desktop, (ii) in stereoscopic 3D using 3D-vision glasses and a desktop, or (iii) in immersive 3D within a CAVE environment. iCAVE introduces 3D extensions of known 2D network layout, clustering, and edge-bundling algorithms, as well as new 3D network layout algorithms. Furthermore, users can simultaneously query several built-in databases within iCAVE for network generation or visualize their own networks (e.g., disease, drug, protein, metabolite). iCAVE has modular structure that allows rapid development by addition of algorithms, datasets, or features without affecting other parts of the code. Overall, iCAVE is the first freely available open source tool that enables 3D (optionally stereoscopic or immersive) visualizations of complex, dense, or multi-layered biomolecular networks. While primarily designed for researchers utilizing biomolecular networks, iCAVE can assist researchers in any field. © The Authors 2017. Published by Oxford University Press.

Non-additive dissipation in open quantum networks out of equilibrium

NASA Astrophysics Data System (ADS)

Mitchison, Mark T.; Plenio, Martin B.

2018-03-01

We theoretically study a simple non-equilibrium quantum network whose dynamics can be expressed and exactly solved in terms of a time-local master equation. Specifically, we consider a pair of coupled fermionic modes, each one locally exchanging energy and particles with an independent, macroscopic thermal reservoir. We show that the generator of the asymptotic master equation is not additive, i.e. it cannot be expressed as a sum of contributions describing the action of each reservoir alone. Instead, we identify an additional interference term that generates coherences in the energy eigenbasis, associated with the current of conserved particles flowing in the steady state. Notably, non-additivity arises even for wide-band reservoirs coupled arbitrarily weakly to the system. Our results shed light on the non-trivial interplay between multiple thermal noise sources in modular open quantum systems.

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review

PubMed Central

Zolfo, Maria; Diro, Ermias

2017-01-01

Background Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. Objective The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. Methods First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. Results The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. Conclusions There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. PMID:29133283

Modular Heat Exchanger With Integral Heat Pipe

NASA Technical Reports Server (NTRS)

Schreiber, Jeffrey G.

1992-01-01

Modular heat exchanger with integral heat pipe transports heat from source to Stirling engine. Alternative to heat exchangers depending on integrities of thousands of brazed joints, contains only 40 brazed tubes.

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.

Modular Filter and Source-Management Upgrade of RADAC

NASA Technical Reports Server (NTRS)

Lanzi, R. James; Smith, Donna C.

2007-01-01

In an upgrade of the Range Data Acquisition Computer (RADAC) software, a modular software object library was developed to implement required functionality for filtering of flight-vehicle-tracking data and management of tracking-data sources. (The RADAC software is used to process flight-vehicle metric data for realtime display in the Wallops Flight Facility Range Control Center and Mobile Control Center.)

Integrating Innovation: Keeping the Leading Edge

DTIC Science & Technology

2015-08-01

access inside Army com- mand posts. Commercial innovation also can be built directly into our con- tract structure. Just as today’s smartphones ...moving to publish detailed guidance this year on how gov- ernment and industry partners will comply with the Modular Open Systems Architecture...which outlines design principles and interface characteristics allowing for modular hardware While the Army cannot predict the future or design

SPLASSH: Open source software for camera-based high-speed, multispectral in-vivo optical image acquisition

PubMed Central

Sun, Ryan; Bouchard, Matthew B.; Hillman, Elizabeth M. C.

2010-01-01

Camera-based in-vivo optical imaging can provide detailed images of living tissue that reveal structure, function, and disease. High-speed, high resolution imaging can reveal dynamic events such as changes in blood flow and responses to stimulation. Despite these benefits, commercially available scientific cameras rarely include software that is suitable for in-vivo imaging applications, making this highly versatile form of optical imaging challenging and time-consuming to implement. To address this issue, we have developed a novel, open-source software package to control high-speed, multispectral optical imaging systems. The software integrates a number of modular functions through a custom graphical user interface (GUI) and provides extensive control over a wide range of inexpensive IEEE 1394 Firewire cameras. Multispectral illumination can be incorporated through the use of off-the-shelf light emitting diodes which the software synchronizes to image acquisition via a programmed microcontroller, allowing arbitrary high-speed illumination sequences. The complete software suite is available for free download. Here we describe the software’s framework and provide details to guide users with development of this and similar software. PMID:21258475

Open-source image reconstruction of super-resolution structured illumination microscopy data in ImageJ

PubMed Central

Müller, Marcel; Mönkemöller, Viola; Hennig, Simon; Hübner, Wolfgang; Huser, Thomas

2016-01-01

Super-resolved structured illumination microscopy (SR-SIM) is an important tool for fluorescence microscopy. SR-SIM microscopes perform multiple image acquisitions with varying illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution structured illumination microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses. PMID:26996201

Integrating personalized medical test contents with XML and XSL-FO.

PubMed

Toddenroth, Dennis; Dugas, Martin; Frankewitsch, Thomas

2011-03-01

In 2004 the adoption of a modular curriculum at the medical faculty in Muenster led to the introduction of centralized examinations based on multiple-choice questions (MCQs). We report on how organizational challenges of realizing faculty-wide personalized tests were addressed by implementation of a specialized software module to automatically generate test sheets from individual test registrations and MCQ contents. Key steps of the presented method for preparing personalized test sheets are (1) the compilation of relevant item contents and graphical media from a relational database with database queries, (2) the creation of Extensible Markup Language (XML) intermediates, and (3) the transformation into paginated documents. The software module by use of an open source print formatter consistently produced high-quality test sheets, while the blending of vectorized textual contents and pixel graphics resulted in efficient output file sizes. Concomitantly the module permitted an individual randomization of item sequences to prevent illicit collusion. The automatic generation of personalized MCQ test sheets is feasible using freely available open source software libraries, and can be efficiently deployed on a faculty-wide scale.

Haptic/graphic rehabilitation: integrating a robot into a virtual environment library and applying it to stroke therapy.

PubMed

Sharp, Ian; Patton, James; Listenberger, Molly; Case, Emily

2011-08-08

Recent research that tests interactive devices for prolonged therapy practice has revealed new prospects for robotics combined with graphical and other forms of biofeedback. Previous human-robot interactive systems have required different software commands to be implemented for each robot leading to unnecessary developmental overhead time each time a new system becomes available. For example, when a haptic/graphic virtual reality environment has been coded for one specific robot to provide haptic feedback, that specific robot would not be able to be traded for another robot without recoding the program. However, recent efforts in the open source community have proposed a wrapper class approach that can elicit nearly identical responses regardless of the robot used. The result can lead researchers across the globe to perform similar experiments using shared code. Therefore modular "switching out"of one robot for another would not affect development time. In this paper, we outline the successful creation and implementation of a wrapper class for one robot into the open-source H3DAPI, which integrates the software commands most commonly used by all robots.

Toward a Wireless Open Source Instrument: Functional Near-infrared Spectroscopy in Mobile Neuroergonomics and BCI Applications

PubMed Central

von Lühmann, Alexander; Herff, Christian; Heger, Dominic; Schultz, Tanja

2015-01-01

Brain-Computer Interfaces (BCIs) and neuroergonomics research have high requirements regarding robustness and mobility. Additionally, fast applicability and customization are desired. Functional Near-Infrared Spectroscopy (fNIRS) is an increasingly established technology with a potential to satisfy these conditions. EEG acquisition technology, currently one of the main modalities used for mobile brain activity assessment, is widely spread and open for access and thus easily customizable. fNIRS technology on the other hand has either to be bought as a predefined commercial solution or developed from scratch using published literature. To help reducing time and effort of future custom designs for research purposes, we present our approach toward an open source multichannel stand-alone fNIRS instrument for mobile NIRS-based neuroimaging, neuroergonomics and BCI/BMI applications. The instrument is low-cost, miniaturized, wireless and modular and openly documented on www.opennirs.org. It provides features such as scalable channel number, configurable regulated light intensities, programmable gain and lock-in amplification. In this paper, the system concept, hardware, software and mechanical implementation of the lightweight stand-alone instrument are presented and the evaluation and verification results of the instrument's hardware and physiological fNIRS functionality are described. Its capability to measure brain activity is demonstrated by qualitative signal assessments and a quantitative mental arithmetic based BCI study with 12 subjects. PMID:26617510

Development of a Commercially Viable, Modular Autonomous Robotic Systems for Converting any Vehicle to Autonomous Control

NASA Technical Reports Server (NTRS)

Parish, David W.; Grabbe, Robert D.; Marzwell, Neville I.

1994-01-01

A Modular Autonomous Robotic System (MARS), consisting of a modular autonomous vehicle control system that can be retrofit on to any vehicle to convert it to autonomous control and support a modular payload for multiple applications is being developed. The MARS design is scalable, reconfigurable, and cost effective due to the use of modern open system architecture design methodologies, including serial control bus technology to simplify system wiring and enhance scalability. The design is augmented with modular, object oriented (C++) software implementing a hierarchy of five levels of control including teleoperated, continuous guidepath following, periodic guidepath following, absolute position autonomous navigation, and relative position autonomous navigation. The present effort is focused on producing a system that is commercially viable for routine autonomous patrolling of known, semistructured environments, like environmental monitoring of chemical and petroleum refineries, exterior physical security and surveillance, perimeter patrolling, and intrafacility transport applications.

ConKit: a python interface to contact predictions.

PubMed

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

2017-07-15

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

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.

The Open AUC Project.

PubMed

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

2010-02-01

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

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

Static Aeroelastic Analysis with an Inviscid Cartesian Method

NASA Technical Reports Server (NTRS)

Rodriguez, David L.; Aftosmis, Michael J.; Nemec, Marian; Smith, Stephen C.

2014-01-01

An embedded-boundary Cartesian-mesh flow solver is coupled with a three degree-offreedom structural model to perform static, aeroelastic analysis of complex aircraft geometries. The approach solves the complete system of aero-structural equations using a modular, loosely-coupled strategy which allows the lower-fidelity structural model to deform the highfidelity CFD model. The approach uses an open-source, 3-D discrete-geometry engine to deform a triangulated surface geometry according to the shape predicted by the structural model under the computed aerodynamic loads. The deformation scheme is capable of modeling large deflections and is applicable to the design of modern, very-flexible transport wings. The interface is modular so that aerodynamic or structural analysis methods can be easily swapped or enhanced. This extended abstract includes a brief description of the architecture, along with some preliminary validation of underlying assumptions and early results on a generic 3D transport model. The final paper will present more concrete cases and validation of the approach. Preliminary results demonstrate convergence of the complete aero-structural system and investigate the accuracy of the approximations used in the formulation of the structural model.

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

Krishnamurthy, Dheepak

This paper is an overview of Power System Simulation Toolbox (psst). psst is an open-source Python application for the simulation and analysis of power system models. psst simulates the wholesale market operation by solving a DC Optimal Power Flow (DCOPF), Security Constrained Unit Commitment (SCUC) and a Security Constrained Economic Dispatch (SCED). psst also includes models for the various entities in a power system such as Generator Companies (GenCos), Load Serving Entities (LSEs) and an Independent System Operator (ISO). psst features an open modular object oriented architecture that will make it useful for researchers to customize, expand, experiment beyond solvingmore » traditional problems. psst also includes a web based Graphical User Interface (GUI) that allows for user friendly interaction and for implementation on remote High Performance Computing (HPCs) clusters for parallelized operations. This paper also provides an illustrative application of psst and benchmarks with standard IEEE test cases to show the advanced features and the performance of toolbox.« less

An open source GIS-based tool to integrate the fragmentation mechanism in rockfall propagation

NASA Astrophysics Data System (ADS)

Matas, Gerard; Lantada, Nieves; Gili, Josep A.; Corominas, Jordi

2015-04-01

Rockfalls are frequent instability processes in road cuts, open pit mines and quarries, steep slopes and cliffs. Even though the stability of rock slopes can be determined using analytical approaches, the assessment of large rock cliffs require simplifying assumptions due to the difficulty of working with a large amount of joints, the scattering of both the orientations and strength parameters. The attitude and persistency of joints within the rock mass define the size of kinematically unstable rock volumes. Furthermore the rock block will eventually split in several fragments during its propagation downhill due its impact with the ground surface. Knowledge of the size, energy, trajectory… of each block resulting from fragmentation is critical in determining the vulnerability of buildings and protection structures. The objective of this contribution is to present a simple and open source tool to simulate the fragmentation mechanism in rockfall propagation models and in the calculation of impact energies. This tool includes common modes of motion for falling boulders based on the previous literature. The final tool is being implemented in a GIS (Geographic Information Systems) using open source Python programming. The tool under development will be simple, modular, compatible with any GIS environment, open source, able to model rockfalls phenomena correctly. It could be used in any area susceptible to rockfalls with a previous adjustment of the parameters. After the adjustment of the model parameters to a given area, a simulation could be performed to obtain maps of kinetic energy, frequency, stopping density and passing heights. This GIS-based tool and the analysis of the fragmentation laws using data collected from recent rockfall have being developed within the RockRisk Project (2014-2016). This project is funded by the Spanish Ministerio de Economía y Competitividad and entitled "Rockfalls in cliffs: risk quantification and its prevention"(BIA2013-42582-P).

Numerical simulations of human tibia osteosynthesis using modular plates based on Nitinol staples.

PubMed

Tarniţă, Daniela; Tarniţă, D N; Popa, D; Grecu, D; Tarniţă, Roxana; Niculescu, D; Cismaru, F

2010-01-01

The shape memory alloys exhibit a number of remarkable properties, which open new possibilities in engineering and more specifically in biomedical engineering. The most important alloy used in biomedical applications is NiTi. This alloy combines the characteristics of the shape memory effect and superelasticity with excellent corrosion resistance, wear characteristics, mechanical properties and a good biocompatibility. These properties make it an ideal biological engineering material, especially in orthopedic surgery and orthodontics. In this work, modular plates for the osteosynthesis of the long bones fractures are presented. The proposed modular plates are realized from identical modules, completely interchangeable, made of titanium or stainless steel having as connecting elements U-shaped staples made of Nitinol. Using computed tomography (CT) images to provide three-dimensional geometric details and SolidWorks software package, the three dimensional virtual models of the tibia bone and of the modular plates are obtained. The finite element models of the tibia bone and of the modular plate are generated. For numerical simulation, VisualNastran software is used. Finally, displacements diagram, von Misses strain diagram, for the modular plate and for the fractured tibia and modular plate ensemble are obtained.

Bethe/Gauge correspondence in odd dimension: modular double, non-perturbative corrections and open topological strings

NASA Astrophysics Data System (ADS)

Sciarappa, Antonio

2016-10-01

Bethe/Gauge correspondence as it is usually stated is ill-defined in five dimensions and needs a "non-perturbative" completion; a related problem also appears in three dimensions. It has been suggested that this problem, probably due to incompleteness of Omega background regularization in odd dimension, may be solved if we consider gauge theory on compact S 5 and S 3 geometries. We will develop this idea further by giving a full Bethe/Gauge correspondence dictionary on S 5 and S 3 focussing mainly on the eigenfunctions of (open and closed) relativistic 2-particle Toda chain and its quantized spectral curve: these are most properly written in terms of non-perturbatively completed NS open topological strings. A key ingredient is Faddeev's modular double structure which is naturally implemented by the S 5 and S 3 geometries.

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

PubMed

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

2006-11-13

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

GALARIO: a GPU accelerated library for analysing radio interferometer observations

NASA Astrophysics Data System (ADS)

Tazzari, Marco; Beaujean, Frederik; Testi, Leonardo

2018-06-01

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

Modular approach to achieving the next-generation X-ray light source

NASA Astrophysics Data System (ADS)

Biedron, S. G.; Milton, S. V.; Freund, H. P.

2001-12-01

A modular approach to the next-generation light source is described. The "modules" include photocathode, radio-frequency, electron guns and their associated drive-laser systems, linear accelerators, bunch-compression systems, seed laser systems, planar undulators, two-undulator harmonic generation schemes, high-gain harmonic generation systems, nonlinear higher harmonics, and wavelength shifting. These modules will be helpful in distributing the next-generation light source to many more laboratories than the current single-pass, high-gain free-electron laser designs permit, due to both monetary and/or physical space constraints.

Split green fluorescent protein as a modular binding partner for protein crystallization

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

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.

2013-12-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was testedmore » by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization.« less

Open-Source Electronic Health Record Systems for Low-Resource Settings: Systematic Review.

PubMed

Syzdykova, Assel; Malta, André; Zolfo, Maria; Diro, Ermias; Oliveira, José Luis

2017-11-13

Despite the great impact of information and communication technologies on clinical practice and on the quality of health services, this trend has been almost exclusive to developed countries, whereas countries with poor resources suffer from many economic and social issues that have hindered the real benefits of electronic health (eHealth) tools. As a component of eHealth systems, electronic health records (EHRs) play a fundamental role in patient management and effective medical care services. Thus, the adoption of EHRs in regions with a lack of infrastructure, untrained staff, and ill-equipped health care providers is an important task. However, the main barrier to adopting EHR software in low- and middle-income countries is the cost of its purchase and maintenance, which highlights the open-source approach as a good solution for these underserved areas. The aim of this study was to conduct a systematic review of open-source EHR systems based on the requirements and limitations of low-resource settings. First, we reviewed existing literature on the comparison of available open-source solutions. In close collaboration with the University of Gondar Hospital, Ethiopia, we identified common limitations in poor resource environments and also the main requirements that EHRs should support. Then, we extensively evaluated the current open-source EHR solutions, discussing their strengths and weaknesses, and their appropriateness to fulfill a predefined set of features relevant for low-resource settings. The evaluation methodology allowed assessment of several key aspects of available solutions that are as follows: (1) integrated applications, (2) configurable reports, (3) custom reports, (4) custom forms, (5) interoperability, (6) coding systems, (7) authentication methods, (8) patient portal, (9) access control model, (10) cryptographic features, (11) flexible data model, (12) offline support, (13) native client, (14) Web client,(15) other clients, (16) code-based language, (17) development activity, (18) modularity, (19) user interface, (20) community support, and (21) customization. The quality of each feature is discussed for each of the evaluated solutions and a final comparison is presented. There is a clear demand for open-source, reliable, and flexible EHR systems in low-resource settings. In this study, we have evaluated and compared five open-source EHR systems following a multidimensional methodology that can provide informed recommendations to other implementers, developers, and health care professionals. We hope that the results of this comparison can guide decision making when needing to adopt, install, and maintain an open-source EHR solution in low-resource settings. ©Assel Syzdykova, André Malta, Maria Zolfo, Ermias Diro, José Luis Oliveira. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 13.11.2017.

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

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

Totally Integrated Munitions Enterprise ''Affordable Munitions Production for the 21st Century''

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

Burleson, R.R.; Poggio, M.E.; Rosenberg, S.J.

2000-09-13

The U.S. Army faces several munitions manufacturing issues: downsizing of the organic production base, timely fielding of affordable smart munitions, and munitions replenishment during national emergencies. Totally Integrated Munitions Enterprise (TIME) is addressing these complex issues via the development and demonstration of an integrated enterprise. The enterprise will include the tools, network, and open modular architecture controllers to enable accelerated acquisition, shortened concept to volume production, lower life cycle costs, capture of critical manufacturing processes, and communication of process parameters between remote sites to rapidly spin-off production for replenishment by commercial sources. TIME addresses the enterprise as a system, integratingmore » design, engineering, manufacturing, administration, and logistics.« less

Totally Integrated Munitions Enterprise ''Affordable Munitions Production for the 21st Century''

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

Burleson, R.R.; Poggio, M.E.; Rosenberg, S.J.

2000-07-14

The U.S. Army faces several munitions manufacturing issues: downsizing of the organic production base, timely fielding of affordable smart munitions, and munitions replenishment during national emergencies. TIME is addressing these complex issues via the development and demonstration of an integrated enterprise. The enterprise will include the tools, network, and open modular architecture controller to enable accelerated acquisition, shortened concept to volume production, lower life cycle costs, capture of critical manufacturing processes, and communication of process parameters between remote sites to rapidly spin-off production for replenishment by commercial sources. TIME addresses the enterprise as a system, integrating design, engineering, manufacturing, administration,more » and logistics.« less

Totally Integrated Munitions Enterprise ''Affordable Munitions Production for the 21st Century''

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

Burleson, R.R.; Poggio, M.E.; Rosenberg, S.J.

2000-08-18

The U.S. Army faces several munitions manufacturing issues: downsizing of the organic production base, timely fielding of affordable smart munitions, and munitions replenishment during national emergencies. Totally Integrated Munitions Enterprise (TIME) is addressing these complex issues via the development and demonstration of an integrated enterprise. The enterprise will include the tools, network, and open modular architecture controllers to enable accelerated acquisition, shortened concept to volume production, lower life cycle costs, capture of critical manufacturing processes, and communication of process parameters between remote sites to rapidly spin-off production for replenishment by commercial sources. TIME addresses the enterprise as a system, integratingmore » design, engineering, manufacturing, administration, and logistics.« less

AN OVERVIEW OF THE INTEROPERABILITY ROADMAP FOR COM/.NET-BASED CAPE-OPEN

EPA Science Inventory

The CAPE-OPEN standard interfaces have been designed to permit flexibility and modularization of process simulation environments (PMEs) in order to use process modeling components such as unit operation or thermodynamic property models across a range of tolls employed in the life...

Next Generation Space Interconnect Standard (NGSIS): a modular open standards approach for high performance interconnects for space

NASA Astrophysics Data System (ADS)

Collier, Charles Patrick

2017-04-01

The Next Generation Space Interconnect Standard (NGSIS) effort is a Government-Industry collaboration effort to define a set of standards for interconnects between space system components with the goal of cost effectively removing bandwidth as a constraint for future space systems. The NGSIS team has selected the ANSI/VITA 65 OpenVPXTM standard family for the physical baseline. The RapidIO protocol has been selected as the basis for the digital data transport. The NGSIS standards are developed to provide sufficient flexibility to enable users to implement a variety of system configurations, while meeting goals for interoperability and robustness for space. The NGSIS approach and effort represents a radical departure from past approaches to achieve a Modular Open System Architecture (MOSA) for space systems and serves as an exemplar for the civil, commercial, and military Space communities as well as a broader high reliability terrestrial market.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

PubMed

Neinstein, Aaron; Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-03-01

Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management

PubMed Central

Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-01-01

Objective Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. Materials and Methods An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Results Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application (“app”), Blip, to visualize the data. Tidepool’s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. Discussion By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. Conclusion The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool’s open source, cloud model for health data interoperability is applicable to other healthcare use cases. PMID:26338218

IgSimulator: a versatile immunosequencing simulator.

PubMed

Safonova, Yana; Lapidus, Alla; Lill, Jennie

2015-10-01

The recent introduction of next-generation sequencing technologies to antibody studies have resulted in a growing number of immunoinformatics tools for antibody repertoire analysis. However, benchmarking these newly emerging tools remains problematic since the gold standard datasets that are needed to validate these tools are typically not available. Since simulating antibody repertoires is often the only feasible way to benchmark new immunoinformatics tools, we developed the IgSimulator tool that addresses various complications in generating realistic antibody repertoires. IgSimulator's code has modular structure and can be easily adapted to new requirements to simulation. IgSimulator is open source and freely available as a C++ and Python program running on all Unix-compatible platforms. The source code is available from yana-safonova.github.io/ig_simulator. safonova.yana@gmail.com Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

cellPACK: A Virtual Mesoscope to Model and Visualize Structural Systems Biology

PubMed Central

Johnson, Graham T.; Autin, Ludovic; Al-Alusi, Mostafa; Goodsell, David S.; Sanner, Michel F.; Olson, Arthur J.

2014-01-01

cellPACK assembles computational models of the biological mesoscale, an intermediate scale (10−7–10−8m) between molecular and cellular biology. cellPACK’s modular architecture unites existing and novel packing algorithms to generate, visualize and analyze comprehensive 3D models of complex biological environments that integrate data from multiple experimental systems biology and structural biology sources. cellPACK is currently available as open source code, with tools for validation of models and with recipes and models for five biological systems: blood plasma, cytoplasm, synaptic vesicles, HIV and a mycoplasma cell. We have applied cellPACK to model distributions of HIV envelope protein to test several hypotheses for consistency with experimental observations. Biologists, educators, and outreach specialists can interact with cellPACK models, develop new recipes and perform packing experiments through scripting and graphical user interfaces at http://cellPACK.org. PMID:25437435

The Effects of Race Conditions When Implementing Single-Source Redundant Clock Trees in Triple Modular Redundant Synchronous Architectures

NASA Technical Reports Server (NTRS)

Berg, Melanie D.; Kim, Hak S.; Phan, Anthony M.; Seidleck, Christina M.; Label, Kenneth A.; Pellish, Jonathan A.; Campola, Michael J.

2016-01-01

We present the challenges that arise when using redundant clock domains due to their time-skew. Radiation data show that a singular clock domain provides an improved triple modular redundant (TMR) scheme over redundant clocks.

Distance Education and Open Learning--Implications for Professional Development and Retraining.

ERIC Educational Resources Information Center

Scriven, Bruce

1991-01-01

Discusses the increasing need for professional development and retraining in Australia, especially for inservice teacher education, and describes new methods that may be more effective than traditional methods. Highlights include open learning; the modularization of courses and programs; the adaptation of instructional materials; and distance…

Big Software for SmallSats: Adapting CFS to CubeSat Missions

NASA Technical Reports Server (NTRS)

Cudmore, Alan P.; Crum, Gary; Sheikh, Salman; Marshall, James

2015-01-01

Expanding capabilities and mission objectives for SmallSats and CubeSats is driving the need for reliable, reusable, and robust flight software. While missions are becoming more complicated and the scientific goals more ambitious, the level of acceptable risk has decreased. Design challenges are further compounded by budget and schedule constraints that have not kept pace. NASA's Core Flight Software System (cFS) is an open source solution which enables teams to build flagship satellite level flight software within a CubeSat schedule and budget. NASA originally developed cFS to reduce mission and schedule risk for flagship satellite missions by increasing code reuse and reliability. The Lunar Reconnaissance Orbiter, which launched in 2009, was the first of a growing list of Class B rated missions to use cFS. Large parts of cFS are now open source, which has spurred adoption outside of NASA. This paper reports on the experiences of two teams using cFS for current CubeSat missions. The performance overheads of cFS are quantified, and the reusability of code between missions is discussed. The analysis shows that cFS is well suited to use on CubeSats and demonstrates the portability and modularity of cFS code.

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

PubMed

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

2014-10-01

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

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

PubMed Central

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

2015-01-01

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

Launching GUPPI: the Green Bank Ultimate Pulsar Processing Instrument

NASA Astrophysics Data System (ADS)

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

2008-08-01

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

OpenPET Hardware, Firmware, Software, and Board Design Files

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

Abu-Nimeh, Faisal; Choong, Woon-Sengq; Moses, William W.

OpenPET is an open source, flexible, high-performance, and modular data acquisition system for a variety of applications. The OpenPET electronics are capable of reading analog voltage or current signals from a wide variety of sensors. The electronics boards make extensive use of field programmable gate arrays (FPGAs) to provide flexibility and scalability. Firmware and software for the FPGAs and computer are used to control and acquire data from the system. The command and control flow is similar to the data flow, however, the commands are initiated from the computer similar to a tree topology (i.e., from top-to-bottom). Each node inmore » the tree discovers its parent and children, and all addresses are configured accordingly. A user (or a script) initiates a command from the computer. This command will be translated and encoded to the corresponding child (e.g., SB, MB, DB, etc.). Consecutively, each node will pass the command to its corresponding child(ren) by looking at the destination address. Finally, once the command reaches its desired destination(s) the corresponding node(s) execute(s) the command and send(s) a reply, if required. All the firmware, software, and the electronics board design files are distributed through the OpenPET website (http://openpet.lbl.gov).« less

OpenROCS: a software tool to control robotic observatories

NASA Astrophysics Data System (ADS)

Colomé, Josep; Sanz, Josep; Vilardell, Francesc; Ribas, Ignasi; Gil, Pere

2012-09-01

We present the Open Robotic Observatory Control System (OpenROCS), an open source software platform developed for the robotic control of telescopes. It acts as a software infrastructure that executes all the necessary processes to implement responses to the system events that appear in the routine and non-routine operations associated to data-flow and housekeeping control. The OpenROCS software design and implementation provides a high flexibility to be adapted to different observatory configurations and event-action specifications. It is based on an abstract model that is independent of the specific hardware or software and is highly configurable. Interfaces to the system components are defined in a simple manner to achieve this goal. We give a detailed description of the version 2.0 of this software, based on a modular architecture developed in PHP and XML configuration files, and using standard communication protocols to interface with applications for hardware monitoring and control, environment monitoring, scheduling of tasks, image processing and data quality control. We provide two examples of how it is used as the core element of the control system in two robotic observatories: the Joan Oró Telescope at the Montsec Astronomical Observatory (Catalonia, Spain) and the SuperWASP Qatar Telescope at the Roque de los Muchachos Observatory (Canary Islands, Spain).

Commissioning and field tests of a van-mounted system for the detection of radioactive sources and Special Nuclear Material

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

Cester, D.; Lunardon, M.; Stevanato, L.

2015-07-01

MODES SNM project aimed to carry out technical research in order to develop a prototype for a mobile, modular detection system for radioactive sources and Special Nuclear Materials (SNM). Its main goal was to deliver a tested prototype of a modular mobile system capable of passively detecting weak or shielded radioactive sources with accuracy higher than that of currently available systems. By the end of the project all the objectives have been successfully achieved. Results from the laboratory commissioning and the field tests will be presented. (authors)

Battery with modular air cathode and anode cage

DOEpatents

Niksa, Marilyn J.; Pohto, Gerald R.; Lakatos, Leslie K.; Wheeler, Douglas J.; Niksa, Andrew J.; Schue, Thomas J.

1987-01-01

A battery assembly of the consumable metal anode type has now been constructed for ready assembly as well as disassembly. In a non-conductive and at least substantially inert cell body, space is provided for receiving an open-structured, non-consumable anode cage. The cage has an open top for facilitating insertion of an anode. A modular cathode is used, comprising a peripheral current conductor frame clamped about a grid reinforced air cathode in sheet form. The air cathode may be double gridded. The cathode frame can be sealed, during assembly, with electrolyte-resistant-sealant as well as with adhesive. The resulting cathode module can be assembled outside the cell body and readily inserted therein, or can later be easily removed therefrom.

Battery with modular air cathode and anode cage

DOEpatents

Niksa, Marilyn J.; Pohto, Gerald R.; Lakatos, Leslie K.; Wheeler, Douglas J.; Niksa, Andrew J.; Schue, Thomas J.; Turk, Thomas R.

1988-01-01

A battery assembly of the consumable metal anode type has now been constructed for ready assembly as well as disassembly. In a non-conductive and at least substantially inert cell body, space is provided for receiving an open-structured, non-consumable anode cage. The cage has an open top for facilitating insertion of an anode. A modular cathode is used, comprising a peripheral current conductor frame clamped about a grid reinforced air cathode in sheet form. The air cathode may be double gridded. The cathode frame can be sealed, during assembly, with electrolyte-resistant-sealant as well as with adhesive. The resulting cathode module can be assembled outside the cell body and readily inserted therein, or can later be easily removed therefrom.

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

Microbial contamination of enteral feeding products in thermoneutral and hyperthermal ICU environments.

PubMed

Perry, Jeffery; Stankorb, Susan M; Salgueiro, Marybeth

2015-02-01

Temperature is known to affect bacterial growth, but current safety recommendations for enteral formula are based on studies conducted in thermoneutral environments, which are not representative of select burn intensive care units (ICUs) that are kept therapeutically hyperthermal. This project evaluated microbial growth in 3 enteral feeding systems: closed, open, and open with modular additives (modular tube feeding [MTF]) exposed to 2 different environments. Product for each of the 3 systems was prepared and hung in both a thermoneutral (23.3°C) and a hyperthermal (32.5°C) ICU room. At baseline, 4 hours, and 8 hours, samples were plated and incubated overnight and the number of colony-forming units (CFUs) counted. In the thermoneutral and hyperthermal environments, there was no evidence of microbial growth in the open or closed feeding systems at any time point. The MTF exhibited baseline contamination with a median of 10 CFUs (95% CI, 8-16) and significant growth over time to 54 CFUs (95% CI, 20-230) by 8 hours in the thermoneutral setting. In the hyperthermal environment, the MTF showed baseline contamination of 390 CFUs (95% CI, 40-1600) and significant growth over time, with 30% of samples exhibiting contamination levels exceeding Food and Drug Administration standards by 4 hours and CFUs being too numerous to count by 8 hours. CFUs in enteral formula did not differ between open and closed feeding systems in either environment for up to 8 hours; however, the addition of modulars to open systems may result in an unacceptable risk of contamination in hyperthermal environments. © 2014 American Society for Parenteral and Enteral Nutrition.

[Modularization by the open standard. (II)].

PubMed

Muto, M; Takaha, Y; Chiba, N

2000-10-01

In recent years, accompanied by the marvelous development and spread of Laboratory Automation System(LAS), the NCCLS is now proposing five international standards for laboratory automation. We have based our laboratory on these "NCCLS standards of laboratory automation", we take these standards ahead first, and we now propose an open standard called "Open LA 21", to establish more detailed standard replacing the NCCLS laboratory automation standards.

A Modular Set of Mixed Reality Simulators for Blind and Guided Procedures

DTIC Science & Technology

2017-08-01

Form Factor, Modular, DoD CVA Sim: Learning Outcome Study This between-groups study will compare performance scores on the CVA simulator to determine...simulation.health.ufl.edu/research/ra_sim.wmv. Preliminary data from a new study of the CVA simulator indicates that an integrated tutor may be non-inferior to a human...instructor, opening the possibility of self- study and self-debriefing which in turn facilitate competency-based, instead of time-based simulation

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

PubMed Central

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

2013-01-01

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

EEG Recording and Online Signal Processing on Android: A Multiapp Framework for Brain-Computer Interfaces on Smartphone

PubMed Central

Debener, Stefan; Emkes, Reiner; Volkening, Nils; Fudickar, Sebastian; Bleichner, Martin G.

2017-01-01

Objective Our aim was the development and validation of a modular signal processing and classification application enabling online electroencephalography (EEG) signal processing on off-the-shelf mobile Android devices. The software application SCALA (Signal ProCessing and CLassification on Android) supports a standardized communication interface to exchange information with external software and hardware. Approach In order to implement a closed-loop brain-computer interface (BCI) on the smartphone, we used a multiapp framework, which integrates applications for stimulus presentation, data acquisition, data processing, classification, and delivery of feedback to the user. Main Results We have implemented the open source signal processing application SCALA. We present timing test results supporting sufficient temporal precision of audio events. We also validate SCALA with a well-established auditory selective attention paradigm and report above chance level classification results for all participants. Regarding the 24-channel EEG signal quality, evaluation results confirm typical sound onset auditory evoked potentials as well as cognitive event-related potentials that differentiate between correct and incorrect task performance feedback. Significance We present a fully smartphone-operated, modular closed-loop BCI system that can be combined with different EEG amplifiers and can easily implement other paradigms. PMID:29349070

A Low-cost data-logging platform for long-term field sensor deployment in caves

NASA Astrophysics Data System (ADS)

Cruz, M. A.; Myre, J. M.; Covington, M. D.

2014-12-01

Active karst systems are notoriously inhospitable environments for humans and equipment. Caves require equipment to cope with high humidity, high velocity flows, submersion, sediment loads, and harassment from local fauna. Equipment taken into caves is often considered "consumable" due to the extreme nature of cave environments and the difficulty of transport. Further, because many interesting monitoring locations within caves can be considered remote, it is ideal for electronic monitoring platforms to require minimal maintenance of parts and power supplies. To partially address the challenge of scientifically monitoring such environments, we have developed an arduino based platform for environmental monitoring of cave systems. The arduino is a general purpose open source microcontroller that is easily programmed with only a basic knowledge of the C programming language. The arduino is capable of controlling digital and analog electronics in a modular fashion. Using this capability, we have created a platform for monitoring CO2 levels in cave systems that costs one-tenth of a comparable commercial system while using a fraction of the power. The modular nature of the arduino system allows the incorporation of additional environmental sensors in the future.

EEG Recording and Online Signal Processing on Android: A Multiapp Framework for Brain-Computer Interfaces on Smartphone.

PubMed

Blum, Sarah; Debener, Stefan; Emkes, Reiner; Volkening, Nils; Fudickar, Sebastian; Bleichner, Martin G

2017-01-01

Our aim was the development and validation of a modular signal processing and classification application enabling online electroencephalography (EEG) signal processing on off-the-shelf mobile Android devices. The software application SCALA (Signal ProCessing and CLassification on Android) supports a standardized communication interface to exchange information with external software and hardware. In order to implement a closed-loop brain-computer interface (BCI) on the smartphone, we used a multiapp framework, which integrates applications for stimulus presentation, data acquisition, data processing, classification, and delivery of feedback to the user. We have implemented the open source signal processing application SCALA. We present timing test results supporting sufficient temporal precision of audio events. We also validate SCALA with a well-established auditory selective attention paradigm and report above chance level classification results for all participants. Regarding the 24-channel EEG signal quality, evaluation results confirm typical sound onset auditory evoked potentials as well as cognitive event-related potentials that differentiate between correct and incorrect task performance feedback. We present a fully smartphone-operated, modular closed-loop BCI system that can be combined with different EEG amplifiers and can easily implement other paradigms.

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.

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.

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

PubMed Central

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

2006-01-01

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

Modular minimally invasive extracorporeal circulation systems; can they become the standard practice for performing cardiac surgery?

PubMed

Anastasiadis, K; Antonitsis, P; Argiriadou, H; Deliopoulos, A; Grosomanidis, V; Tossios, P

2015-04-01

Minimally invasive extracorporeal circulation (MiECC) has been developed in an attempt to integrate all advances in cardiopulmonary bypass technology in one closed circuit that shows improved biocompatibility and minimizes the systemic detrimental effects of CPB. Despite well-evidenced clinical advantages, penetration of MiECC technology into clinical practice is hampered by concerns raised by perfusionists and surgeons regarding air handling together with blood and volume management during CPB. We designed a modular MiECC circuit, bearing an accessory circuit for immediate transition to an open system that can be used in every adult cardiac surgical procedure, offering enhanced safety features. We challenged this modular circuit in a series of 50 consecutive patients. Our results showed that the modular AHEPA circuit design offers 100% technical success rate in a cohort of random, high-risk patients who underwent complex procedures, including reoperation and valve and aortic surgery, together with emergency cases. This pilot study applies to the real world and prompts for further evaluation of modular MiECC systems through multicentre trials. © The Author(s) 2015.

Modular open RF architecture: extending VICTORY to RF systems

NASA Astrophysics Data System (ADS)

Melber, Adam; Dirner, Jason; Johnson, Michael

2015-05-01

Radio frequency products spanning multiple functions have become increasingly critical to the warfighter. Military use of the electromagnetic spectrum now includes communications, electronic warfare (EW), intelligence, and mission command systems. Due to the urgent needs of counterinsurgency operations, various quick reaction capabilities (QRCs) have been fielded to enhance warfighter capability. Although these QRCs were highly successfully in their respective missions, they were designed independently resulting in significant challenges when integrated on a common platform. This paper discusses how the Modular Open RF Architecture (MORA) addresses these challenges by defining an open architecture for multifunction missions that decomposes monolithic radio systems into high-level components with welldefined functions and interfaces. The functional decomposition maximizes hardware sharing while minimizing added complexity and cost due to modularization. MORA achieves significant size, weight and power (SWaP) savings by allowing hardware such as power amplifiers and antennas to be shared across systems. By separating signal conditioning from the processing that implements the actual radio application, MORA exposes previously inaccessible architecture points, providing system integrators with the flexibility to insert third-party capabilities to address technical challenges and emerging requirements. MORA leverages the Vehicular Integration for Command, Control, Communication, Computers, Intelligence, Surveillance, and Reconnaissance (C4ISR)/EW Interoperability (VICTORY) framework. This paper concludes by discussing how MORA, VICTORY and other standards such as OpenVPX are being leveraged by the U.S. Army Research, Development, and Engineering Command (RDECOM) Communications Electronics Research, Development, and Engineering Center (CERDEC) to define a converged architecture enabling rapid technology insertion, interoperability and reduced SWaP.

The new generation of OpenGL support in ROOT

NASA Astrophysics Data System (ADS)

Tadel, M.

2008-07-01

OpenGL has been promoted to become the main 3D rendering engine of the ROOT framework. This required a major re-modularization of OpenGL support on all levels, from basic window-system specific interface to medium-level object-representation and top-level scene management. This new architecture allows seamless integration of external scene-graph libraries into the ROOT OpenGL viewer as well as inclusion of ROOT 3D scenes into external GUI and OpenGL-based 3D-rendering frameworks. Scene representation was removed from inside of the viewer, allowing scene-data to be shared among several viewers and providing for a natural implementation of multi-view canvas layouts. The object-graph traversal infrastructure allows free mixing of 3D and 2D-pad graphics and makes implementation of ROOT canvas in pure OpenGL possible. Scene-elements representing ROOT objects trigger automatic instantiation of user-provided rendering-objects based on the dictionary information and class-naming convention. Additionally, a finer, per-object control over scene-updates is available to the user, allowing overhead-free maintenance of dynamic 3D scenes and creation of complex real-time animations. User-input handling was modularized as well, making it easy to support application-specific scene navigation, selection handling and tool management.

Development and comparison of Bayesian modularization method in uncertainty assessment of hydrological models

NASA Astrophysics Data System (ADS)

Li, L.; Xu, C.-Y.; Engeland, K.

2012-04-01

With respect to model calibration, parameter estimation and analysis of uncertainty sources, different approaches have been used in hydrological models. Bayesian method is one of the most widely used methods for uncertainty assessment of hydrological models, which incorporates different sources of information into a single analysis through Bayesian theorem. However, none of these applications can well treat the uncertainty in extreme flows of hydrological models' simulations. This study proposes a Bayesian modularization method approach in uncertainty assessment of conceptual hydrological models by considering the extreme flows. It includes a comprehensive comparison and evaluation of uncertainty assessments by a new Bayesian modularization method approach and traditional Bayesian models using the Metropolis Hasting (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions are used in combination with traditional Bayesian: the AR (1) plus Normal and time period independent model (Model 1), the AR (1) plus Normal and time period dependent model (Model 2) and the AR (1) plus multi-normal model (Model 3). The results reveal that (1) the simulations derived from Bayesian modularization method are more accurate with the highest Nash-Sutcliffe efficiency value, and (2) the Bayesian modularization method performs best in uncertainty estimates of entire flows and in terms of the application and computational efficiency. The study thus introduces a new approach for reducing the extreme flow's effect on the discharge uncertainty assessment of hydrological models via Bayesian. Keywords: extreme flow, uncertainty assessment, Bayesian modularization, hydrological model, WASMOD

New Approach to Road Construction in Oil-Producing Regions of Western Siberia

NASA Astrophysics Data System (ADS)

Piirainen, V. Y.; Estrin, Y.

2017-10-01

This article presents, as a polemic exercise, a new approach to road construction in marshland areas of oil and gas producing regions of Western Siberia. The approach is based on the use of novel modular elements that can be assembled into an integral structure by means of topological interlocking. The use of modern superlight concrete in conjunction with the new design systems based on the modular principle opens up new avenues to solving problems of road construction in regions with unstable, boggy soils.

The Ensembl Web Site: Mechanics of a Genome Browser

PubMed Central

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V.

2004-01-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (∼2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species. PMID:15123591

The Ensembl Web site: mechanics of a genome browser.

PubMed

Stalker, James; Gibbins, Brian; Meidl, Patrick; Smith, James; Spooner, William; Hotz, Hans-Rudolf; Cox, Antony V

2004-05-01

The Ensembl Web site (http://www.ensembl.org/) is the principal user interface to the data of the Ensembl project, and currently serves >500,000 pages (approximately 2.5 million hits) per week, providing access to >80 GB (gigabyte) of data to users in more than 80 countries. Built atop an open-source platform comprising Apache/mod_perl and the MySQL relational database management system, it is modular, extensible, and freely available. It is being actively reused and extended in several different projects, and has been downloaded and installed in companies and academic institutions worldwide. Here, we describe some of the technical features of the site, with particular reference to its dynamic configuration that enables it to handle disparate data from multiple species.

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.

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

Standard Modular Hydropower Technology Acceleration Workshop: Summary Report

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

Smith, Brennan T.; DeNeale, Scott T.; Witt, Adam M.

In support of the Department of Energy (DOE) funded Standard Modular Hydropower (SMH) Technology Acceleration project, Oak Ridge National Laboratory (ORNL) staff convened with five small hydropower technology entrepreneurs on June 14 and 15, 2017 to discuss gaps, challenges, and opportunities for small modular hydropower development. The workshop was designed to walk through SMH concepts, discuss the SMH research vision, assess how each participant’s technology aligns with SMH concepts and research, and identify future pathways for mutually beneficial collaboration that leverages ORNL expertise and entrepreneurial industry experience. The goal coming out of the workshop is to advance standardized, scalable, modularmore » hydropower technologies and development approaches with sustained and open dialogue among diverse stakeholder groups.« less

AOI 1— COMPUTATIONAL ENERGY SCIENCES:MULTIPHASE FLOW RESEARCH High-fidelity multi-phase radiation module for modern coal combustion systems

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

Modest, Michael

The effects of radiation in particle-laden flows were the object of the present research. The presence of particles increases optical thickness substantially, making the use of the “optically thin” approximation in most cases a very poor assumption. However, since radiation fluxes peak at intermediate optical thicknesses, overall radiative effects may not necessarily be stronger than in gas combustion. Also, the spectral behavior of particle radiation properties is much more benign, making spectral models simpler (and making the assumption of a gray radiator halfway acceptable, at least for fluidized beds when gas radiation is not large). On the other hand, particlesmore » scatter radiation, making the radiative transfer equation (RTE) much more di fficult to solve. The research carried out in this project encompassed three general areas: (i) assessment of relevant radiation properties of particle clouds encountered in fluidized bed and pulverized coal combustors, (ii) development of proper spectral models for gas–particulate mixtures for various types of two-phase combustion flows, and (iii) development of a Radiative Transfer Equation (RTE) solution module for such applications. The resulting models were validated against artificial cases since open literature experimental data were not available. The final models are in modular form tailored toward maximum portability, and were incorporated into two research codes: (i) the open-source CFD code OpenFOAM, which we have extensively used in our previous work, and (ii) the open-source multi-phase flow code MFIX, which is maintained by NETL.« less

An Open Educational Resource Supports a Diversity of Inquiry-Based Learning

ERIC Educational Resources Information Center

Schmidt-Jones, Catherine Anne

2012-01-01

There have been numerous calls for research that demonstrates how open education resources (OERs) are actually being used. This case study sought to shed light on the users of a well-visited set of modular music-education materials published at Connexions. Respondents to a voluntary survey included teachers, students, self-directed learners, music…

A new software for deformation source optimization, the Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

Vasyura-Bathke, H.; Dutta, R.; Jonsson, S.; Mai, P. M.

2017-12-01

Modern studies of crustal deformation and the related source estimation, including magmatic and tectonic sources, increasingly use non-linear optimization strategies to estimate geometric and/or kinematic source parameters and often consider both jointly, geodetic and seismic data. Bayesian inference is increasingly being used for estimating posterior distributions of deformation source model parameters, given measured/estimated/assumed data and model uncertainties. For instance, some studies consider uncertainties of a layered medium and propagate these into source parameter uncertainties, while others use informative priors to reduce the model parameter space. In addition, innovative sampling algorithms have been developed to efficiently explore the high-dimensional parameter spaces. Compared to earlier studies, these improvements have resulted in overall more robust source model parameter estimates that include uncertainties. However, the computational burden of these methods is high and estimation codes are rarely made available along with the published results. Even if the codes are accessible, it is usually challenging to assemble them into a single optimization framework as they are typically coded in different programing languages. Therefore, further progress and future applications of these methods/codes are hampered, while reproducibility and validation of results has become essentially impossible. In the spirit of providing open-access and modular codes to facilitate progress and reproducible research in deformation source estimations, we undertook the effort of developing BEAT, a python package that comprises all the above-mentioned features in one single programing environment. The package builds on the pyrocko seismological toolbox (www.pyrocko.org), and uses the pymc3 module for Bayesian statistical model fitting. BEAT is an open-source package (https://github.com/hvasbath/beat), and we encourage and solicit contributions to the project. Here, we present our strategy for developing BEAT and show application examples; especially the effect of including the model prediction uncertainty of the velocity model in following source optimizations: full moment tensor, Mogi source, moderate strike-slip earth-quake.

Engineering Design Handbook: Timing Systems and Components

DTIC Science & Technology

1975-12-01

23-1 23-2 Modular Components 23-2 23—3 Integrated Circuits 23—2 23—4 Matching Techniques 23-5 23-5 DC and AC Systems 23-7 23-6 Hybrid...Assembly Illustrating Modular Design . . 23—4 23-3 Characteristics of the Source 23—6 23—4 Characteristics of the Load 23—6 23—5 Matching Source and...4-1 INTRODUCTION There is a continuous demand for increased precision and accuracy in frequency control. Today fast time pulses are used in

Innovation: Attracting and Retaining the Best of the Private Sector

DTIC Science & Technology

2014-01-01

The recommendations seek to open up Innovation: Attracting and Retaining the the Best of the Private Sector Task Group 6 Report FY14-02 what is a...industry structure changes, the Task Group recommends the following: • Require the adoption of an open architecture, modular approach to new mission...essential platforms; and • Take steps to open a closed supply chain; re-examine industry structure and encourage new entrants. With regard to messaging

Modular optical detector system

DOEpatents

Horn, Brent A [Livermore, CA; Renzi, Ronald F [Tracy, CA

2006-02-14

A modular optical detector system. The detector system is designed to detect the presence of molecules or molecular species by inducing fluorescence with exciting radiation and detecting the emitted fluorescence. Because the system is capable of accurately detecting and measuring picomolar concentrations it is ideally suited for use with microchemical analysis systems generally and capillary chromatographic systems in particular. By employing a modular design, the detector system provides both the ability to replace various elements of the detector system without requiring extensive realignment or recalibration of the components as well as minimal user interaction with the system. In addition, the modular concept provides for the use and addition of a wide variety of components, including optical elements (lenses and filters), light sources, and detection means, to fit particular needs.

A modular approach to detection and identification of defects in rough lumber

Treesearch

Sang Mook Lee; A. Lynn Abbott; Daniel L. Schmoldt

2001-01-01

This paper describes a prototype scanning system that can automatically identify several important defects on rough hardwood lumber. The scanning system utilizes 3 laser sources and an embedded-processor camera to capture and analyze profile and gray-scale images. The modular approach combines the detection of wane (the curved sides of a board, possibly containing...

Flexible weapons architecture design

NASA Astrophysics Data System (ADS)

Pyant, William C., III

Present day air-delivered weapons are of a closed architecture, with little to no ability to tailor the weapon for the individual engagement. The closed architectures require weaponeers to make the target fit the weapon instead of fitting the individual weapons to a target. The concept of a flexible weapons aims to modularize weapons design using an open architecture shell into which different modules are inserted to achieve the desired target fractional damage while reducing cost and civilian casualties. This thesis shows that the architecture design factors of damage mechanism, fusing, weapons weight, guidance, and propulsion are significant in enhancing weapon performance objectives, and would benefit from modularization. Additionally, this thesis constructs an algorithm that can be used to design a weapon set for a particular target class based on these modular components.

A new free and open source tool for space plasma modeling.

NASA Astrophysics Data System (ADS)

Honkonen, I. J.

2014-12-01

I will present a new distributed memory parallel, free and open source computational model for studying space plasma. The model is written in C++ with emphasis on good software development practices and code readability without sacrificing serial or parallel performance. As such the model could be especially useful for education, for learning both (magneto)hydrodynamics (MHD) and computational model development. By using latest features of the C++ standard (2011) it has been possible to develop a very modular program which improves not only the readability of code but also the testability of the model and decreases the effort required to make changes to various parts of the program. Major parts of the model, functionality not directly related to (M)HD, have been outsourced to other freely available libraries which has reduced the development time of the model significantly. I will present an overview of the code architecture as well as details of different parts of the model and will show examples of using the model including preparing input files and plotting results. A multitude of 1-, 2- and 3-dimensional test cases are included in the software distribution and the results of, for example, Kelvin-Helmholtz, bow shock, blast wave and reconnection tests, will be presented.

Design of the Familial Hypercholesterolaemia Australasia Network Registry: Creating Opportunities for Greater International Collaboration.

PubMed

Bellgard, Matthew I; Walker, Caroline E; Napier, Kathryn R; Lamont, Leanne; Hunter, Adam A; Render, Lee; Radochonski, Maciej; Pang, Jing; Pedrotti, Annette; Sullivan, David R; Kostner, Karam; Bishop, Warrick; George, Peter M; O'Brien, Richard C; Clifton, Peter M; Bockxmeer, Frank M Van; Nicholls, Stephen J; Hamilton-Craig, Ian; Dawkins, Hugh Js; Watts, Gerald F

2017-10-01

Familial Hypercholesterolemia (FH) is the most common and serious monogenic disorder of lipoprotein metabolism that leads to premature coronary heart disease. There are over 65,000 people estimated to have FH in Australia, but many remain undiagnosed. Patients with FH are often under-treated, but with early detection, cascade family testing and adequate treatment, patient outcomes can improve. Patient registries are key tools for providing new information on FH and enhancing care worldwide. The development and design of the FH Australasia Network Registry is a crucial component in the comprehensive model of care for FH, which aims to provide a standardized, high-quality and cost-effective system of care that is likely to have the highest impact on patient outcomes. Informed by stakeholder engagement, the FH Australasia Network Registry was collaboratively developed by government, patient and clinical networks and research groups. The open-source, web-based Rare Disease Registry Framework was the architecture chosen for this registry owing to its open-source standards, modular design, interoperability, scalability and security features; all these are key components required to meet the ever changing clinical demands across regions. This paper provides a high level blueprint for other countries and jurisdictions to help inform and map out the critical features of an FH registry to meet their particular health system needs.

ProteoWizard: open source software for rapid proteomics tools development.

PubMed

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

2008-11-01

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

An open source, wireless capable miniature microscope system

NASA Astrophysics Data System (ADS)

Liberti, William A., III; Perkins, L. Nathan; Leman, Daniel P.; Gardner, Timothy J.

2017-08-01

Objective. Fluorescence imaging through head-mounted microscopes in freely behaving animals is becoming a standard method to study neural circuit function. Flexible, open-source designs are needed to spur evolution of the method. Approach. We describe a miniature microscope for single-photon fluorescence imaging in freely behaving animals. The device is made from 3D printed parts and off-the-shelf components. These microscopes weigh less than 1.8 g, can be configured to image a variety of fluorophores, and can be used wirelessly or in conjunction with active commutators. Microscope control software, based in Swift for macOS, provides low-latency image processing capabilities for closed-loop, or BMI, experiments. Main results. Miniature microscopes were deployed in the songbird premotor region HVC (used as a proper name), in singing zebra finches. Individual neurons yield temporally precise patterns of calcium activity that are consistent over repeated renditions of song. Several cells were tracked over timescales of weeks and months, providing an opportunity to study learning related changes in HVC. Significance. 3D printed miniature microscopes, composed completely of consumer grade components, are a cost-effective, modular option for head-mounting imaging. These easily constructed and customizable tools provide access to cell-type specific neural ensembles over timescales of weeks.

An open-source data storage and visualization back end for experimental data.

PubMed

Nielsen, Kenneth; Andersen, Thomas; Jensen, Robert; Nielsen, Jane H; Chorkendorff, Ib

2014-04-01

In this article, a flexible free and open-source software system for data logging and presentation will be described. The system is highly modular and adaptable and can be used in any laboratory in which continuous and/or ad hoc measurements require centralized storage. A presentation component for the data back end has furthermore been written that enables live visualization of data on any device capable of displaying Web pages. The system consists of three parts: data-logging clients, a data server, and a data presentation Web site. The logging of data from independent clients leads to high resilience to equipment failure, whereas the central storage of data dramatically eases backup and data exchange. The visualization front end allows direct monitoring of acquired data to see live progress of long-duration experiments. This enables the user to alter experimental conditions based on these data and to interfere with the experiment if needed. The data stored consist both of specific measurements and of continuously logged system parameters. The latter is crucial to a variety of automation and surveillance features, and three cases of such features are described: monitoring system health, getting status of long-duration experiments, and implementation of instant alarms in the event of failure.

X-ray optics for the LAMAR facility, an overview. [Large Area Modular Array of Reflectors

NASA Technical Reports Server (NTRS)

Gorenstein, P.

1979-01-01

The paper surveys the Large Area Modular Array of Reflectors (LAMAR), the concept of which is based on meeting two major requirements in X-ray astronomy, large collecting area and moderately good or better angular resolution for avoiding source confusion and imaging source fields. It is shown that the LAMAR provides the same sensitivity and signal to noise in imaging as a single large telescope having the same area and angular resolution but is a great deal less costly to develop, construct, and integrate into a space mission. Attention is also given to the LAMAR modular nature which will allow for an evolutionary development from a modest size array on Spacelab to a Shuttle launched free flyer. Finally, consideration is given to manufacturing methods which show promise of making LAMAR meet the criteria of good angular resolution, relatively low cost, and capability for fast volume production.

Using a Modular Open Systems Approach in Defense Acquisitions: Implications for the Contracting Process

DTIC Science & Technology

2006-01-30

He has taught contract management courses for the UCLA Government Contracts Certificate program and is also a senior faculty member for the Keller...standards for its key interfaces, and has been subjected to successful validation and verification tests to ensure the openness of its key interfaces...widely supported and consensus based standards for its key interfaces, and is subject to validation and verification tests to ensure the openness of its

Nuclear reactor

DOEpatents

Pennell, William E.; Rowan, William J.

1977-01-01

A nuclear reactor in which the core components, including fuel-rod assemblies, control-rod assemblies, fertile rod-assemblies, and removable shielding assemblies, are supported by a plurality of separate inlet modular units. These units are referred to as inlet module units to distinguish them from the modules of the upper internals of the reactor. The modular units are supported, each removable independently of the others, in liners in the supporting structure for the lower internals of the reactor. The core assemblies are removably supported in integral receptacles or sockets of the modular units. The liners, units, sockets and assmblies have inlet openings for entry of the fluid. The modular units are each removably mounted in the liners with fluid seals interposed between the opening in the liner and inlet module into which the fluid enters and the upper and lower portion of the liner. Each assembly is similarly mounted in a corresponding receptacle with fluid seals interposed between the openings where the fluid enters and the lower portion of the receptacle or fitting closely in these regions. As fluid flows along each core assembly a pressure drop is produced along the fluid so that the fluid which emerges from each core assembly is at a lower pressure than the fluid which enters the core assembly. However because of the seals interposed in the mountings of the units and assemblies the pressures above and below the units and assemblies are balanced and the units are held in the liners and the assemblies are held in the receptacles by their weights as they have a higher specific gravity than the fluid. The low-pressure spaces between each module and its liner and between each core assembly and its module is vented to the low-pressure regions of the vessel to assure that fluid which leaks through the seals does not accumulate and destroy the hydraulic balance.

A modular (almost) automatic set-up for elastic multi-tenants cloud (micro)infrastructures

NASA Astrophysics Data System (ADS)

Amoroso, A.; Astorino, F.; Bagnasco, S.; Balashov, N. A.; Bianchi, F.; Destefanis, M.; Lusso, S.; Maggiora, M.; Pellegrino, J.; Yan, L.; Yan, T.; Zhang, X.; Zhao, X.

2017-10-01

An auto-installing tool on an usb drive can allow for a quick and easy automatic deployment of OpenNebula-based cloud infrastructures remotely managed by a central VMDIRAC instance. A single team, in the main site of an HEP Collaboration or elsewhere, can manage and run a relatively large network of federated (micro-)cloud infrastructures, making an highly dynamic and elastic use of computing resources. Exploiting such an approach can lead to modular systems of cloud-bursting infrastructures addressing complex real-life scenarios.

Human Impacts and Climate Change Influence Nestedness and Modularity in Food-Web and Mutualistic Networks.

PubMed

Takemoto, Kazuhiro; Kajihara, Kosuke

2016-01-01

Theoretical studies have indicated that nestedness and modularity-non-random structural patterns of ecological networks-influence the stability of ecosystems against perturbations; as such, climate change and human activity, as well as other sources of environmental perturbations, affect the nestedness and modularity of ecological networks. However, the effects of climate change and human activities on ecological networks are poorly understood. Here, we used a spatial analysis approach to examine the effects of climate change and human activities on the structural patterns of food webs and mutualistic networks, and found that ecological network structure is globally affected by climate change and human impacts, in addition to current climate. In pollination networks, for instance, nestedness increased and modularity decreased in response to increased human impacts. Modularity in seed-dispersal networks decreased with temperature change (i.e., warming), whereas food web nestedness increased and modularity declined in response to global warming. Although our findings are preliminary owing to data-analysis limitations, they enhance our understanding of the effects of environmental change on ecological communities.

A disposable power source in resource-limited environments: A paper-based biobattery generating electricity from wastewater.

PubMed

Fraiwan, Arwa; Kwan, Landen; Choi, Seokheun

2016-11-15

We report a novel paper-based biobattery which generates power from microorganism-containing liquid derived from renewable and sustainable wastewater which is readily accessible in the local environment. The device fuses the art of origami and the technology of microbial fuel cells (MFCs) and has the potential to shift the paradigm for flexible and stackable paper-based batteries by enabling exceptional electrical characteristics and functionalities. 3D, modular, and retractable battery stack is created from (i) 2D paper sheets through high degrees of folding and (ii) multifunctional layers sandwiched for MFC device configuration. The stack is based on ninja star-shaped origami design formed by eight MFC modular blades, which is retractable from sharp shuriken (closed) to round frisbee (opened). The microorganism-containing wastewater is added into an inlet of the closed battery stack and it is transported into each MFC module through patterned fluidic pathways in the paper layers. During operation, the battery stack is transformed into the round frisbee to connect eight MFC modules in series for improving the power output and simultaneously expose all air-cathodes to the air for their cathodic reactions. The device generates desired values of electrical current and potential for powering an LED for more than 20min. Copyright © 2016 Elsevier B.V. All rights reserved.

Towards a Food Safety Knowledge Base Applicable in Crisis Situations and Beyond

PubMed Central

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

2015-01-01

In case of contamination in the food chain, fast action is required in order to reduce the numbers of affected people. In such situations, being able to predict the fate of agents in foods would help risk assessors and decision makers in assessing the potential effects of a specific contamination event and thus enable them to deduce the appropriate mitigation measures. One efficient strategy supporting this is using model based simulations. However, application in crisis situations requires ready-to-use and easy-to-adapt models to be available from the so-called food safety knowledge bases. Here, we illustrate this concept and its benefits by applying the modular open source software tools PMM-Lab and FoodProcess-Lab. As a fictitious sample scenario, an intentional ricin contamination at a beef salami production facility was modelled. Predictive models describing the inactivation of ricin were reviewed, relevant models were implemented with PMM-Lab, and simulations on residual toxin amounts in the final product were performed with FoodProcess-Lab. Due to the generic and modular modelling concept implemented in these tools, they can be applied to simulate virtually any food safety contamination scenario. Apart from the application in crisis situations, the food safety knowledge base concept will also be useful in food quality and safety investigations. PMID:26247028

Towards a Food Safety Knowledge Base Applicable in Crisis Situations and Beyond.

PubMed

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

2015-01-01

In case of contamination in the food chain, fast action is required in order to reduce the numbers of affected people. In such situations, being able to predict the fate of agents in foods would help risk assessors and decision makers in assessing the potential effects of a specific contamination event and thus enable them to deduce the appropriate mitigation measures. One efficient strategy supporting this is using model based simulations. However, application in crisis situations requires ready-to-use and easy-to-adapt models to be available from the so-called food safety knowledge bases. Here, we illustrate this concept and its benefits by applying the modular open source software tools PMM-Lab and FoodProcess-Lab. As a fictitious sample scenario, an intentional ricin contamination at a beef salami production facility was modelled. Predictive models describing the inactivation of ricin were reviewed, relevant models were implemented with PMM-Lab, and simulations on residual toxin amounts in the final product were performed with FoodProcess-Lab. Due to the generic and modular modelling concept implemented in these tools, they can be applied to simulate virtually any food safety contamination scenario. Apart from the application in crisis situations, the food safety knowledge base concept will also be useful in food quality and safety investigations.

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.

EvolQG - An R package for evolutionary quantitative genetics

PubMed Central

Melo, Diogo; Garcia, Guilherme; Hubbe, Alex; Assis, Ana Paula; Marroig, Gabriel

2016-01-01

We present an open source package for performing evolutionary quantitative genetics analyses in the R environment for statistical computing. Evolutionary theory shows that evolution depends critically on the available variation in a given population. When dealing with many quantitative traits this variation is expressed in the form of a covariance matrix, particularly the additive genetic covariance matrix or sometimes the phenotypic matrix, when the genetic matrix is unavailable and there is evidence the phenotypic matrix is sufficiently similar to the genetic matrix. Given this mathematical representation of available variation, the \\textbf{EvolQG} package provides functions for calculation of relevant evolutionary statistics; estimation of sampling error; corrections for this error; matrix comparison via correlations, distances and matrix decomposition; analysis of modularity patterns; and functions for testing evolutionary hypotheses on taxa diversification. PMID:27785352

A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC.

PubMed

Song, Qingfeng; Chen, Dairui; Long, Stephen P; Zhu, Xin-Guang

2017-01-01

Windows Intuitive Model of Vegetation response to Atmosphere and Climate Change (WIMOVAC) has been used widely as a generic modular mechanistically rich model of plant production. It can predict the responses of leaf and canopy carbon balance, as well as production in different environmental conditions, in particular those relevant to global change. Here, we introduce an open source Java user-friendly version of WIMOVAC. This software is platform independent and can be easily downloaded to a laptop and used without any prior programming skills. In this article, we describe the structure, equations and user guide and illustrate some potential applications of WIMOVAC. © 2016 The Authors Plant, Cell & Environment Published by John Wiley & Sons Ltd.

Best kept secrets ... Source Data Systems, Inc. (SDS).

PubMed

Andrew, W F

1991-03-01

The SDS/MEDNET system is a cost-effective option for small- to medium-size hospitals (up to 400 beds). The parameter-driven system lets users control operations with only occasional SDS assistance. A full application set, available for modular selection to reduce upfront costs while facilitating steady growth and protecting client investment, is adaptable to multi-facility environments. The industry-standard, Intel-based multi-user processors, network communications and protocols assure high efficiency, low-cost solutions independent of any one hardware vendor. Sustained growth in both client base and product offerings point to a high level of responsiveness and healthcare industry commitment. Corporate emphasis on user involvement and open systems integration assures clients of leading-edge capabilities. SDS/MEDNET will be a strong contender in selected marketing environments.

The OpenEarth Framework (OEF) for the 3D Visualization of Integrated Earth Science Data

NASA Astrophysics Data System (ADS)

Nadeau, David; Moreland, John; Baru, Chaitan; Crosby, Chris

2010-05-01

Data integration is increasingly important as we strive to combine data from disparate sources and assemble better models of the complex processes operating at the Earth's surface and within its interior. These data are often large, multi-dimensional, and subject to differing conventions for data structures, file formats, coordinate spaces, and units of measure. When visualized, these data require differing, and sometimes conflicting, conventions for visual representations, dimensionality, symbology, and interaction. All of this makes the visualization of integrated Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data integration and visualization suite of applications and libraries being developed by the GEON project at the University of California, San Diego, USA. Funded by the NSF, the project is leveraging virtual globe technology from NASA's WorldWind to create interactive 3D visualization tools that combine and layer data from a wide variety of sources to create a holistic view of features at, above, and beneath the Earth's surface. The OEF architecture is open, cross-platform, modular, and based upon Java. The OEF's modular approach to software architecture yields an array of mix-and-match software components for assembling custom applications. Available modules support file format handling, web service communications, data management, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats used in the field. Each one imports data into a general-purpose common data model supporting multidimensional regular and irregular grids, topography, feature geometry, and more. Data within these data models may be manipulated, combined, reprojected, and visualized. The OEF's visualization features support a variety of conventional and new visualization techniques for looking at topography, tomography, point clouds, imagery, maps, and feature geometry. 3D data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery, maps, and data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers within a common 3D coordinate space. Data management within the OEF handles and hides the inevitable quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Heuristics are used to extract necessary metadata used to guide data and visual operations. Derived data representations are computed to better support fluid interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization makes use of 3D graphics hardware support found on today's computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

A Novel Multilevel DC - AC Converter from Green Energy Power Generators Using Step-Square Waving and PWM Technique

NASA Astrophysics Data System (ADS)

Fajingbesi, F. E.; Midi, N. S.; Khan, S.

2017-06-01

Green energy sources or renewable energy system generally utilize modular approach in their design. This sort of power sources are generally in DC form or in single cases AC. Due to high fluctuation in the natural origin of this energy (wind & solar) source they are stored as DC. DC power however are difficult to transfer over long distances hence DC to AC converters and storage system are very important in green energy system design. In this work we have designed a novel multilevel DC to AC converter that takes into account the modular design of green energy systems. A power conversion efficiency of 99% with reduced total harmonic distortion (THD) was recorded from our simulated system design.

Open Source Dataturbine (OSDT) Android Sensorpod in Environmental Observing Systems

NASA Astrophysics Data System (ADS)

Fountain, T. R.; Shin, P.; Tilak, S.; Trinh, T.; Smith, J.; Kram, S.

2014-12-01

The OSDT Android SensorPod is a custom-designed mobile computing platform for assembling wireless sensor networks for environmental monitoring applications. Funded by an award from the Gordon and Betty Moore Foundation, the OSDT SensorPod represents a significant technological advance in the application of mobile and cloud computing technologies to near-real-time applications in environmental science, natural resources management, and disaster response and recovery. It provides a modular architecture based on open standards and open-source software that allows system developers to align their projects with industry best practices and technology trends, while avoiding commercial vendor lock-in to expensive proprietary software and hardware systems. The integration of mobile and cloud-computing infrastructure represents a disruptive technology in the field of environmental science, since basic assumptions about technology requirements are now open to revision, e.g., the roles of special purpose data loggers and dedicated site infrastructure. The OSDT Android SensorPod was designed with these considerations in mind, and the resulting system exhibits the following characteristics - it is flexible, efficient and robust. The system was developed and tested in the three science applications: 1) a fresh water limnology deployment in Wisconsin, 2) a near coastal marine science deployment at the UCSD Scripps Pier, and 3) a terrestrial ecological deployment in the mountains of Taiwan. As part of a public education and outreach effort, a Facebook page with daily ocean pH measurements from the UCSD Scripps pier was developed. Wireless sensor networks and the virtualization of data and network services is the future of environmental science infrastructure. The OSDT Android SensorPod was designed and developed to harness these new technology developments for environmental monitoring applications.

Data Fusion and Visualization with the OpenEarth Framework (OEF)

NASA Astrophysics Data System (ADS)

Nadeau, D. R.; Baru, C.; Fouch, M. J.; Crosby, C. J.

2010-12-01

Data fusion is an increasingly important problem to solve as we strive to integrate data from multiple sources and build better models of the complex processes operating at the Earth’s surface and its interior. These data are often large, multi-dimensional, and subject to differing conventions for file formats, data structures, coordinate spaces, units of measure, and metadata organization. When visualized, these data require differing, and often conflicting, conventions for visual representations, dimensionality, icons, color schemes, labeling, and interaction. These issues make the visualization of fused Earth science data particularly difficult. The OpenEarth Framework (OEF) is an open-source data fusion and visualization suite of software being developed at the Supercomputer Center at the University of California, San Diego. Funded by the NSF, the project is leveraging virtual globe technology from NASA’s WorldWind to create interactive 3D visualization tools that combine layered data from a variety of sources to create a holistic view of features at, above, and beneath the Earth’s surface. The OEF architecture is cross-platform, multi-threaded, modular, and based upon Java. The OEF’s modular approach yields a collection of compatible mix-and-match components for assembling custom applications. Available modules support file format handling, web service communications, data management, data filtering, user interaction, and 3D visualization. File parsers handle a variety of formal and de facto standard file formats. Each one imports data into a general-purpose data representation that supports multidimensional grids, topography, points, lines, polygons, images, and more. From there these data then may be manipulated, merged, filtered, reprojected, and visualized. Visualization features support conventional and new visualization techniques for looking at topography, tomography, maps, and feature geometry. 3D grid data such as seismic tomography may be sliced by multiple oriented cutting planes and isosurfaced to create 3D skins that trace feature boundaries within the data. Topography may be overlaid with satellite imagery along with data such as gravity and magnetics measurements. Multiple data sets may be visualized simultaneously using overlapping layers and a common 3D+time coordinate space. Data management within the OEF handles and hides the quirks of differing file formats, web protocols, storage structures, coordinate spaces, and metadata representations. Derived data are computed automatically to support interaction and visualization while the original data is left unchanged in its original form. Data is cached for better memory and network efficiency, and all visualization is accelerated by 3D graphics hardware found on today’s computers. The OpenEarth Framework project is currently prototyping the software for use in the visualization, and integration of continental scale geophysical data being produced by EarthScope-related research in the Western US. The OEF is providing researchers with new ways to display and interrogate their data and is anticipated to be a valuable tool for future EarthScope-related research.

Research Notes - An Introduction to Openness and Evolvability Assessment

DTIC Science & Technology

2016-08-01

importance of different business and technical characteristics that combine to achieve an open solution. The complexity of most large-scale systems of...process characteristic)  Granularity of the architecture (size of functional blocks)  Modularity (cohesion and coupling)  Support for multiple...Description)  OV-3 (Operational Information Exchange Matrix)  SV-1 (Systems Interface Description)  TV-1 ( Technical Standards Profile). Note that there

Rapid prototyping prosthetic hand acting by a low-cost shape-memory-alloy actuator.

PubMed

Soriano-Heras, Enrique; Blaya-Haro, Fernando; Molino, Carlos; de Agustín Del Burgo, José María

2018-06-01

The purpose of this article is to develop a new concept of modular and operative prosthetic hand based on rapid prototyping and a novel shape-memory-alloy (SMA) actuator, thus minimizing the manufacturing costs. An underactuated mechanism was needed for the design of the prosthesis to use only one input source. Taking into account the state of the art, an underactuated mechanism prosthetic hand was chosen so as to implement the modifications required for including the external SMA actuator. A modular design of a new prosthesis was developed which incorporated a novel SMA actuator for the index finger movement. The primary objective of the prosthesis is achieved, obtaining a modular and functional low-cost prosthesis based on additive manufacturing executed by a novel SMA actuator. The external SMA actuator provides a modular system which allows implementing it in different systems. This paper combines rapid prototyping and a novel SMA actuator to develop a new concept of modular and operative low-cost prosthetic hand.

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.

MANTA--an open-source, high density electrophysiology recording suite for MATLAB.

PubMed

Englitz, B; David, S V; Sorenson, M D; Shamma, S A

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

MANTA—an open-source, high density electrophysiology recording suite for MATLAB

PubMed Central

Englitz, B.; David, S. V.; Sorenson, M. D.; Shamma, S. A.

2013-01-01

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point. PMID:23653593

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

NASA Astrophysics Data System (ADS)

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

2004-12-01

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

Navy Expeditionary Technology Transition Program (NETTP)

DTIC Science & Technology

2012-03-02

water vapor from feed air using a zeolite membrane •Temperature/Humidity levels can be met in warm, humid climates without reheating •Allows higher...UNCLASSIFIED, Distribution Unlimited Modular Thermal Hub •Small, efficient absorption cooling •Energy source: Combustion, low- grade waste heat, solar... thermal energy •Reversible operation enables space cooling and heating, and water heating •Modular cooling and heating unit •Monolithic packaging offers

Characteristics of detectors for prevention of nuclear radiation terrorism

NASA Astrophysics Data System (ADS)

Kolesnikov, S. V.; Ryabeva, E. V.; Samosadny, V. T.

2017-01-01

There is description of one type of detectors in use for the task of nuclear terrorism cases prevention to determine the direction to the radioactive source and geometrical structure of radiation field. This type is a modular detector with anisotropic sensitivity. The principle of work of a modular detecting device is the simultaneous operation of several detecting modules with anisotropic sensitivity to gamma radiation.

A modular optically powered floating high voltage generator.

PubMed

Antonini, P; Borsato, E; Carugno, G; Pegoraro, M; Zotto, P

2013-02-01

The feasibility of fully floating high voltage (HV) generation was demonstrated producing a prototype of a modular HV system. The primary power source is provided by a high efficiency semiconductor power cell illuminated by a laser system ensuring the floating nature of each module. The HV is then generated by dc-dc conversion and a HV multiplier. The possibility of series connection among modules was verified.

Space Ultrareliable Modular Computer (SUMC) instruction simulator

NASA Technical Reports Server (NTRS)

Curran, R. T.

1972-01-01

The design principles, description, functional operation, and recommended expansion and enhancements are presented for the Space Ultrareliable Modular Computer interpretive simulator. Included as appendices are the user's manual, program module descriptions, target instruction descriptions, simulator source program listing, and a sample program printout. In discussing the design and operation of the simulator, the key problems involving host computer independence and target computer architectural scope are brought into focus.

Kinota: An Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring

NASA Astrophysics Data System (ADS)

Miles, B.; Chepudira, K.; LaBar, W.

2017-12-01

The Open Geospatial Consortium (OGC) SensorThings API (STA) specification, ratified in 2016, is a next-generation open standard for enabling real-time communication of sensor data. Building on over a decade of OGC Sensor Web Enablement (SWE) Standards, STA offers a rich data model that can represent a range of sensor and phenomena types (e.g. fixed sensors sensing fixed phenomena, fixed sensors sensing moving phenomena, mobile sensors sensing fixed phenomena, and mobile sensors sensing moving phenomena) and is data agnostic. Additionally, and in contrast to previous SWE standards, STA is developer-friendly, as is evident from its convenient JSON serialization, and expressive OData-based query language (with support for geospatial queries); with its Message Queue Telemetry Transport (MQTT), STA is also well-suited to efficient real-time data publishing and discovery. All these attributes make STA potentially useful for use in environmental monitoring sensor networks. Here we present Kinota(TM), an Open-Source NoSQL implementation of OGC SensorThings for large-scale high-resolution real-time environmental monitoring. Kinota, which roughly stands for Knowledge from Internet of Things Analyses, relies on Cassandra its underlying data store, which is a horizontally scalable, fault-tolerant open-source database that is often used to store time-series data for Big Data applications (though integration with other NoSQL or rational databases is possible). With this foundation, Kinota can scale to store data from an arbitrary number of sensors collecting data every 500 milliseconds. Additionally, Kinota architecture is very modular allowing for customization by adopters who can choose to replace parts of the existing implementation when desirable. The architecture is also highly portable providing the flexibility to choose between cloud providers like azure, amazon, google etc. The scalable, flexible and cloud friendly architecture of Kinota makes it ideal for use in next-generation large-scale and high-resolution real-time environmental monitoring networks used in domains such as hydrology, geomorphology, and geophysics, as well as management applications such as flood early warning, and regulatory enforcement.

Cranial airways and the integration between the inner and outer facial skeleton in humans.

PubMed

Bastir, Markus; Rosas, Antonio

2013-10-01

The cranial airways are in the center of the human face. Therefore variation in the size and shape of these central craniofacial structures could have important consequences for the surrounding midfacial morphology during development and evolution. Yet such interactions are unclear because one school of thought, based on experimental and developmental evidence, suggests a relative independence (modularity) of these two facial compartments, whereas another one assumes tight morphological integration. This study uses geometric morphometrics of modern humans (N = 263) and 40 three-dimensional-landmarks of the skeletal nasopharynx and nasal cavity and outer midfacial skeleton to analyze these questions in terms of modularity. The sizes of all facial compartments were all strongly correlated. Shape integration was high between the cranial airways and the outer midfacial skeleton and between the latter and the anterior airway openings (skeletal regions close to and including piriform aperture). However, no shape integration was detected between outer midface and posterior airway openings (nasopharynx and choanae). Similarly, no integration was detected between posterior and anterior airway openings. This may reflect functional modularization of nasal cavity compartments related to respiratory physiology and differential developmental interactions with the face. Airway size likely relates to the energetics of the organism, whereas airways shape might be more indicative of respiratory physiology and climate. Although this hypothesis should be addressed in future steps, here we suggest that selection on morphofunctional characteristics of the cranial airways could have cascading effects for the variation, development, and evolution of the human face. Copyright © 2013 Wiley Periodicals, Inc.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

Extended spectrum SWIR camera with user-accessible Dewar

NASA Astrophysics Data System (ADS)

Benapfl, Brendan; Miller, John Lester; Vemuri, Hari; Grein, Christoph; Sivananthan, Siva

2017-02-01

Episensors has developed a series of extended short wavelength infrared (eSWIR) cameras based on high-Cd concentration Hg1-xCdxTe absorbers. The cameras have a bandpass extending to 3 microns cutoff wavelength, opening new applications relative to traditional InGaAs-based cameras. Applications and uses are discussed and examples given. A liquid nitrogen pour-filled version was initially developed. This was followed by a compact Stirling-cooled version with detectors operating at 200 K. Each camera has unique sensitivity and performance characteristics. The cameras' size, weight and power specifications are presented along with images captured with band pass filters and eSWIR sources to demonstrate spectral response beyond 1.7 microns. The soft seal Dewars of the cameras are designed for accessibility, and can be opened and modified in a standard laboratory environment. This modular approach allows user flexibility for swapping internal components such as cold filters and cold stops. The core electronics of the Stirlingcooled camera are based on a single commercial field programmable gate array (FPGA) that also performs on-board non-uniformity corrections, bad pixel replacement, and directly drives any standard HDMI display.

3D printed Lego®-like modular microfluidic devices based on capillary driving.

PubMed

Nie, Jing; Gao, Qing; Qiu, Jing-Jiang; Sun, Miao; Liu, An; Shao, Lei; Fu, Jian-Zhong; Zhao, Peng; He, Yong

2018-03-12

The field of how to rapidly assemble microfluidics with modular components continuously attracts researchers' attention, however, extra efforts must be devoted to solving the problems of leaking and aligning between individual modules. This paper presents a novel type of modular microfluidic device, driven by capillary force. There is no necessity for a strict seal or special alignment, and its open structures make it easy to integrate various stents and reactants. The key rationale for this method is to print different functional modules with a low-cost three-dimensional (3D) printer, then fill the channels with capillary materials and assemble them with plugs like Lego ® bricks. This rapidly reconstructed modular microfluidic device consists of a variety of common functional modules and other personalized modules, each module having a unified standard interface for easy assembly. As it can be printed by a desktop 3D printer, the manufacturing process is simple and efficient, with controllable regulation of the flow channel scale. Through diverse combinations of different modules, a variety of different functions can be achieved, without duplicating the manufacturing process. A single module can also be taken out for testing and analysis. What's more, combined with basic circuit components, it can serve as a low-cost Lego ® -like modular microfluidic circuits. As a proof of concept, the modular microfluidic device has been successfully demonstrated and used for stent degradation and cell cultures, revealing the potential use of this method in both chemical and biological research.

Note: Hollow cathode lamp with integral, high optical efficiency isolation valve: a modular vacuum ultraviolet source.

PubMed

Roberts, F Sloan; Anderson, Scott L

2013-12-01

The design and operating conditions of a hollow cathode discharge lamp for the generation of vacuum ultraviolet radiation, suitable for ultrahigh vacuum (UHV) application, are described in detail. The design is easily constructed, and modular, allowing it to be adapted to different experimental requirements. A thin isolation valve is built into one of the differential pumping stages, isolating the discharge section from the UHV section, both for vacuum safety and to allow lamp maintenance without venting the UHV chamber. The lamp has been used both for ultraviolet photoelectron spectroscopy of surfaces and as a "soft" photoionization source for gas-phase mass spectrometry.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.

PubMed

Egea, Jose A; Henriques, David; Cokelaer, Thomas; Villaverde, Alejandro F; MacNamara, Aidan; Danciu, Diana-Patricia; Banga, Julio R; Saez-Rodriguez, Julio

2014-05-10

Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods.

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

PubMed Central

2014-01-01

Background Optimization is the key to solving many problems in computational biology. Global optimization methods, which provide a robust methodology, and metaheuristics in particular have proven to be the most efficient methods for many applications. Despite their utility, there is a limited availability of metaheuristic tools. Results We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics. The toolbox includes the enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Additionally, the R version includes BayesFit for parameter estimation by Bayesian inference. The eSS and VNS methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/~gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to BioConductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology where it outperforms other state-of-the-art methods. Conclusions MEIGO provides a free, open-source platform for optimization that can be applied to multiple domains of systems biology and bioinformatics. It includes efficient state of the art metaheuristics, and its open and modular structure allows the addition of further methods. PMID:24885957

Human life support during interplanetary travel and domicile. II - Generic Modular Flow Schematic modeling

NASA Technical Reports Server (NTRS)

Farral, Joseph F.; Seshan, P. K.; Rohatgi, Naresh K.

1991-01-01

This paper describes the Generic Modular Flow Schematic (GMFS) architecture capable of encompassing all functional elements of a physical/chemical life support system (LSS). The GMFS can be implemented to synthesize, model, analyze, and quantitatively compare many configurations of LSSs, from a simple, completely open-loop to a very complex closed-loop. The GMFS model is coded in ASPEN, a state-of-the-art chemical process simulation program, to accurately compute the material, heat, and power flow quantities for every stream in each of the subsystem functional elements (SFEs) in the chosen configuration of a life support system. The GMFS approach integrates the various SFEs and subsystems in a hierarchical and modular fashion facilitating rapid substitutions and reconfiguration of a life support system. The comprehensive ASPEN material and energy balance output is transferred to a systems and technology assessment spreadsheet for rigorous system analysis and trade studies.

Applying representational state transfer (REST) architecture to archetype-based electronic health record systems

PubMed Central

2013-01-01

Background The openEHR project and the closely related ISO 13606 standard have defined structures supporting the content of Electronic Health Records (EHRs). However, there is not yet any finalized openEHR specification of a service interface to aid application developers in creating, accessing, and storing the EHR content. The aim of this paper is to explore how the Representational State Transfer (REST) architectural style can be used as a basis for a platform-independent, HTTP-based openEHR service interface. Associated benefits and tradeoffs of such a design are also explored. Results The main contribution is the formalization of the openEHR storage, retrieval, and version-handling semantics and related services into an implementable HTTP-based service interface. The modular design makes it possible to prototype, test, replicate, distribute, cache, and load-balance the system using ordinary web technology. Other contributions are approaches to query and retrieval of the EHR content that takes caching, logging, and distribution into account. Triggering on EHR change events is also explored. A final contribution is an open source openEHR implementation using the above-mentioned approaches to create LiU EEE, an educational EHR environment intended to help newcomers and developers experiment with and learn about the archetype-based EHR approach and enable rapid prototyping. Conclusions Using REST addressed many architectural concerns in a successful way, but an additional messaging component was needed to address some architectural aspects. Many of our approaches are likely of value to other archetype-based EHR implementations and may contribute to associated service model specifications. PMID:23656624

Applying representational state transfer (REST) architecture to archetype-based electronic health record systems.

PubMed

Sundvall, Erik; Nyström, Mikael; Karlsson, Daniel; Eneling, Martin; Chen, Rong; Örman, Håkan

2013-05-09

The openEHR project and the closely related ISO 13606 standard have defined structures supporting the content of Electronic Health Records (EHRs). However, there is not yet any finalized openEHR specification of a service interface to aid application developers in creating, accessing, and storing the EHR content.The aim of this paper is to explore how the Representational State Transfer (REST) architectural style can be used as a basis for a platform-independent, HTTP-based openEHR service interface. Associated benefits and tradeoffs of such a design are also explored. The main contribution is the formalization of the openEHR storage, retrieval, and version-handling semantics and related services into an implementable HTTP-based service interface. The modular design makes it possible to prototype, test, replicate, distribute, cache, and load-balance the system using ordinary web technology. Other contributions are approaches to query and retrieval of the EHR content that takes caching, logging, and distribution into account. Triggering on EHR change events is also explored.A final contribution is an open source openEHR implementation using the above-mentioned approaches to create LiU EEE, an educational EHR environment intended to help newcomers and developers experiment with and learn about the archetype-based EHR approach and enable rapid prototyping. Using REST addressed many architectural concerns in a successful way, but an additional messaging component was needed to address some architectural aspects. Many of our approaches are likely of value to other archetype-based EHR implementations and may contribute to associated service model specifications.

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data

PubMed Central

Jaitly, Navdeep; Mayampurath, Anoop; Littlefield, Kyle; Adkins, Joshua N; Anderson, Gordon A; Smith, Richard D

2009-01-01

Background Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. Results With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. Conclusion Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs. Decon2LS source code, installer, and tutorials may be downloaded free of charge at . PMID:19292916

Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data.

PubMed

Jaitly, Navdeep; Mayampurath, Anoop; Littlefield, Kyle; Adkins, Joshua N; Anderson, Gordon A; Smith, Richard D

2009-03-17

Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form of proteins, peptides, and metabolites. Interpreting this data involves inferring the masses and abundances of biomolecules injected into the instrument. Because of the inherent complexity of mass spectral patterns produced by these biomolecules, the analysis is significantly enhanced by using visualization capabilities to inspect and confirm results. In this paper we describe Decon2LS, an open-source software package for automated processing and visualization of high-resolution MS data. Drawing extensively on algorithms developed over the last ten years for ICR2LS, Decon2LS packages the algorithms as a rich set of modular, reusable processing classes for performing diverse functions such as reading raw data, routine peak finding, theoretical isotope distribution modelling, and deisotoping. Because the source code is openly available, these functionalities can now be used to build derivative applications in relatively fast manner. In addition, Decon2LS provides an extensive set of visualization tools, such as high performance chart controls. With a variety of options that include peak processing, deisotoping, isotope composition, etc, Decon2LS supports processing of multiple raw data formats. Deisotoping can be performed on an individual scan, an individual dataset, or on multiple datasets using batch processing. Other processing options include creating a two dimensional view of mass and liquid chromatography (LC) elution time features, generating spectrum files for tandem MS data, creating total intensity chromatograms, and visualizing theoretical peptide profiles. Application of Decon2LS to deisotope different datasets obtained across different instruments yielded a high number of features that can be used to identify and quantify peptides in the biological sample. Decon2LS is an efficient software package for discovering and visualizing features in proteomics studies that require automated interpretation of mass spectra. Besides being easy to use, fast, and reliable, Decon2LS is also open-source, which allows developers in the proteomics and bioinformatics communities to reuse and refine the algorithms to meet individual needs.Decon2LS source code, installer, and tutorials may be downloaded free of charge at http://http:/ncrr.pnl.gov/software/.

Estimation of Solar Radiation on Building Roofs in Mountainous Areas

NASA Astrophysics Data System (ADS)

Agugiaro, G.; Remondino, F.; Stevanato, G.; De Filippi, R.; Furlanello, C.

2011-04-01

The aim of this study is estimating solar radiation on building roofs in complex mountain landscape areas. A multi-scale solar radiation estimation methodology is proposed that combines 3D data ranging from regional scale to the architectural one. Both the terrain and the nearby building shadowing effects are considered. The approach is modular and several alternative roof models, obtained by surveying and modelling techniques at varying level of detail, can be embedded in a DTM, e.g. that of an Alpine valley surrounded by mountains. The solar radiation maps obtained from raster models at different resolutions are compared and evaluated in order to obtain information regarding the benefits and disadvantages tied to each roof modelling approach. The solar radiation estimation is performed within the open-source GRASS GIS environment using r.sun and its ancillary modules.

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.

The Exoplanet Characterization ToolKit (ExoCTK)

NASA Astrophysics Data System (ADS)

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

2018-01-01

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

ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging

PubMed Central

Ovesný, Martin; Křížek, Pavel; Borkovec, Josef; Švindrych, Zdeněk; Hagen, Guy M.

2014-01-01

Summary: ThunderSTORM is an open-source, interactive and modular plug-in for ImageJ designed for automated processing, analysis and visualization of data acquired by single-molecule localization microscopy methods such as photo-activated localization microscopy and stochastic optical reconstruction microscopy. ThunderSTORM offers an extensive collection of processing and post-processing methods so that users can easily adapt the process of analysis to their data. ThunderSTORM also offers a set of tools for creation of simulated data and quantitative performance evaluation of localization algorithms using Monte Carlo simulations. Availability and implementation: ThunderSTORM and the online documentation are both freely accessible at https://code.google.com/p/thunder-storm/ Contact: guy.hagen@lf1.cuni.cz Supplementary information: Supplementary data are available at Bioinformatics online. PMID:24771516

The role of 3-D interactive visualization in blind surveys of H I in galaxies

NASA Astrophysics Data System (ADS)

Punzo, D.; van der Hulst, J. M.; Roerdink, J. B. T. M.; Oosterloo, T. A.; Ramatsoku, M.; Verheijen, M. A. W.

2015-09-01

Upcoming H I surveys will deliver large datasets, and automated processing using the full 3-D information (two positional dimensions and one spectral dimension) to find and characterize H I objects is imperative. In this context, visualization is an essential tool for enabling qualitative and quantitative human control on an automated source finding and analysis pipeline. We discuss how Visual Analytics, the combination of automated data processing and human reasoning, creativity and intuition, supported by interactive visualization, enables flexible and fast interaction with the 3-D data, helping the astronomer to deal with the analysis of complex sources. 3-D visualization, coupled to modeling, provides additional capabilities helping the discovery and analysis of subtle structures in the 3-D domain. The requirements for a fully interactive visualization tool are: coupled 1-D/2-D/3-D visualization, quantitative and comparative capabilities, combined with supervised semi-automated analysis. Moreover, the source code must have the following characteristics for enabling collaborative work: open, modular, well documented, and well maintained. We review four state of-the-art, 3-D visualization packages assessing their capabilities and feasibility for use in the case of 3-D astronomical data.

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design.

PubMed

Wood, Christopher W; Heal, Jack W; Thomson, Andrew R; Bartlett, Gail J; Ibarra, Amaurys Á; Brady, R Leo; Sessions, Richard B; Woolfson, Derek N

2017-10-01

The rational design of biomolecules is becoming a reality. However, further computational tools are needed to facilitate and accelerate this, and to make it accessible to more users. Here we introduce ISAMBARD, a tool for structural analysis, model building and rational design of biomolecules. ISAMBARD is open-source, modular, computationally scalable and intuitive to use. These features allow non-experts to explore biomolecular design in silico. ISAMBARD addresses a standing issue in protein design, namely, how to introduce backbone variability in a controlled manner. This is achieved through the generalization of tools for parametric modelling, describing the overall shape of proteins geometrically, and without input from experimentally determined structures. This will allow backbone conformations for entire folds and assemblies not observed in nature to be generated de novo, that is, to access the 'dark matter of protein-fold space'. We anticipate that ISAMBARD will find broad applications in biomolecular design, biotechnology and synthetic biology. A current stable build can be downloaded from the python package index (https://pypi.python.org/pypi/isambard/) with development builds available on GitHub (https://github.com/woolfson-group/) along with documentation, tutorial material and all the scripts used to generate the data described in this paper. d.n.woolfson@bristol.ac.uk or chris.wood@bristol.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management.

PubMed

Kang, Wenjun; Kadri, Sabah; Puranik, Rutika; Wurst, Michelle N; Patil, Sushant A; Mujacic, Ibro; Benhamed, Sonia; Niu, Nifang; Zhen, Chao Jie; Ameti, Bekim; Long, Bradley C; Galbo, Filipo; Montes, David; Iracheta, Crystal; Gamboa, Venessa L; Lopez, Daisy; Yourshaw, Michael; Lawrence, Carolyn A; Aisner, Dara L; Fitzpatrick, Carrie; McNerney, Megan E; Wang, Y Lynn; Andrade, Jorge; Volchenboum, Samuel L; Furtado, Larissa V; Ritterhouse, Lauren L; Segal, Jeremy P

2018-04-24

Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory, a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. The System for Informatics in the Molecular Pathology Laboratory was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of the system, its clinical validation at the Genomic and Molecular Pathology Division at the University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing. Copyright © 2018. Published by Elsevier Inc.

Mining collections of compounds with Screening Assistant 2

PubMed Central

2012-01-01

Background High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. Results We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Conclusions Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/. PMID:23327565

Mining collections of compounds with Screening Assistant 2.

PubMed

Guilloux, Vincent Le; Arrault, Alban; Colliandre, Lionel; Bourg, Stéphane; Vayer, Philippe; Morin-Allory, Luc

2012-08-31

High-throughput screening assays have become the starting point of many drug discovery programs for large pharmaceutical companies as well as academic organisations. Despite the increasing throughput of screening technologies, the almost infinite chemical space remains out of reach, calling for tools dedicated to the analysis and selection of the compound collections intended to be screened. We present Screening Assistant 2 (SA2), an open-source JAVA software dedicated to the storage and analysis of small to very large chemical libraries. SA2 stores unique molecules in a MySQL database, and encapsulates several chemoinformatics methods, among which: providers management, interactive visualisation, scaffold analysis, diverse subset creation, descriptors calculation, sub-structure / SMART search, similarity search and filtering. We illustrate the use of SA2 by analysing the composition of a database of 15 million compounds collected from 73 providers, in terms of scaffolds, frameworks, and undesired properties as defined by recently proposed HTS SMARTS filters. We also show how the software can be used to create diverse libraries based on existing ones. Screening Assistant 2 is a user-friendly, open-source software that can be used to manage collections of compounds and perform simple to advanced chemoinformatics analyses. Its modular design and growing documentation facilitate the addition of new functionalities, calling for contributions from the community. The software can be downloaded at http://sa2.sourceforge.net/.

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.

Design of a portable, intrinsically safe multichannel acquisition system for high-resolution, real-time processing HD-sEMG.

PubMed

Barone, Umberto; Merletti, Roberto

2013-08-01

A compact and portable system for real-time, multichannel, HD-sEMG acquisition is presented. The device is based on a modular, multiboard approach for scalability and to optimize power consumption for battery operating mode. The proposed modular approach allows us to configure the number of sEMG channels from 64 to 424. A plastic-optical-fiber-based 10/100 Ethernet link is implemented on a field-programmable gate array (FPGA)-based board for real-time, safety data transmission toward a personal computer or laptop for data storage and offline analysis. The high-performance A/D conversion stage, based on 24-bit ADC, allows us to automatically serialize the samples and transmits them on a single SPI bus connecting a sequence of up to 14 ADC chips in chain mode. The prototype is configured to work with 64 channels and a sample frequency of 2.441 ksps (derived from 25-MHz clock source), corresponding to a real data throughput of 3 Mbps. The prototype was assembled to demonstrate the available features (e.g., scalability) and evaluate the expected performances. The analog front end board could be dynamically configured to acquire sEMG signals in monopolar or single differential mode by means of FPGA I/O interface. The system can acquire continuously 64 channels for up to 5 h with a lightweight battery pack of 7.5 Vdc/2200 mAh. A PC-based application was also developed, by means of the open source Qt Development Kit from Nokia, for prototype characterization, sEMG measurements, and real-time visualization of 2-D maps.

miRMaid: a unified programming interface for microRNA data resources

PubMed Central

2010-01-01

Background MicroRNAs (miRNAs) are endogenous small RNAs that play a key role in post-transcriptional regulation of gene expression in animals and plants. The number of known miRNAs has increased rapidly over the years. The current release (version 14.0) of miRBase, the central online repository for miRNA annotation, comprises over 10.000 miRNA precursors from 115 different species. Furthermore, a large number of decentralized online resources are now available, each contributing with important miRNA annotation and information. Results We have developed a software framework, designated here as miRMaid, with the goal of integrating miRNA data resources in a uniform web service interface that can be accessed and queried by researchers and, most importantly, by computers. miRMaid is built around data from miRBase and is designed to follow the official miRBase data releases. It exposes miRBase data as inter-connected web services. Third-party miRNA data resources can be modularly integrated as miRMaid plugins or they can loosely couple with miRMaid as individual entities in the World Wide Web. miRMaid is available as a public web service but is also easily installed as a local application. The software framework is freely available under the LGPL open source license for academic and commercial use. Conclusion miRMaid is an intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources. Furthermore, miRMaid constitutes a basic framework for further programming in which microRNA-interested bioinformaticians can readily develop their own tools and data sources. PMID:20074352

A Comprehensive Data Architecture for Multi-Disciplinary Marine Mammal Research

NASA Astrophysics Data System (ADS)

Palacios, D. M.; Follett, T.; Winsor, M.; Mate, B. R.

2016-02-01

The Oregon State University Marine Mammal Institute (MMI) comprises five research laboratories, each with specific research objectives, technological approaches, and data requirements. Among the types of data under management are individual photo-ID and field observations, telemetry (e.g., locations, dive characteristics, temperature, acoustics), genetics (and relatedness), stable isotope and toxicology assays, and remotely sensed environmental data. Coordinating data management that facilitates collaboration and comparative exploration among different researchers has been a longstanding challenge for our groups as well as for the greater wildlife research community. Research data are commonly stored locally in flat files or spreadsheets, with copies made and analyses performed with various packages without any common standards for interoperability, becoming a potential source of error. Database design, where it exists, is frequently arrived at ad-hoc. New types of data are generally tacked on when technological advances present them. A data management solution that can address these issues should meet the following requirements: be scalable, modular (i.e., able to incorporate new types of data as they arise), incorporate spatiotemporal dimensions, and be compliant with existing data standards such as DarwinCore. The MMI has developed a data architecture that allows the incorporation of any type of animal-associated data into a modular and portable format that can be integrated with any other dataset sharing the core format. It allows browsing, querying and visualization across any of the attributes that can be associated with individual animals, groups, sensors, or environmental datasets. We have implemented this architecture in an open-source geo-enabled relational database system (PostgreSQL, PostGIS), and have designed a suite of software tools (Python, R) to load, preprocess, visualize, analyze, and export data. This architecture could benefit organizations with similar data challenges.

Using CellML with OpenCMISS to Simulate Multi-Scale Physiology

PubMed Central

Nickerson, David P.; Ladd, David; Hussan, Jagir R.; Safaei, Soroush; Suresh, Vinod; Hunter, Peter J.; Bradley, Christopher P.

2014-01-01

OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also discussed. PMID:25601911

Teleoperated Modular Robots for Lunar Operations

NASA Technical Reports Server (NTRS)

Globus, Al; Hornby, Greg; Larchev, Greg; Hancher, Matt; Cannon, Howard; Lohn, Jason

2004-01-01

Solar system exploration is currently carried out by special purpose robots exquisitely designed for the anticipated tasks. However, all contingencies for in situ resource utilization (ISRU), human habitat preparation, and exploration will be difficult to anticipate. Furthermore, developing the necessary special purpose mechanisms for deployment and other capabilities is difficult and error prone. For example, the Galileo high gain antenna never opened, severely restricting the quantity of data returned by the spacecraft. Also, deployment hardware is used only once. To address these problems, we are developing teleoperated modular robots for lunar missions, including operations in transit from Earth. Teleoperation of lunar systems from Earth involves a three second speed-of-light delay, but experiment suggests that interactive operations are feasible.' Modular robots typically consist of many identical modules that pass power and data between them and can be reconfigured for different tasks providing great flexibility, inherent redundancy and graceful degradation as modules fail. Our design features a number of different hub, link, and joint modules to simplify the individual modules, lower structure cost, and provide specialized capabilities. Modular robots are well suited for space applications because of their extreme flexibility, inherent redundancy, high-density packing, and opportunities for mass production. Simple structural modules can be manufactured from lunar regolith in situ using molds or directed solar sintering. Software to direct and control modular robots is difficult to develop. We have used genetic algorithms to evolve both the morphology and control system for walking modular robots3 We are currently using evolvable system technology to evolve controllers for modular robots in the ISS glove box. Development of lunar modular robots will require software and physical simulators, including regolith simulation, to enable design and test of robot software and hardware, particularly automation software. Ready access to these simulators could provide opportunities for contest-driven development ala RoboCup (http://www.robocup.org/). Licensing of module designs could provide opportunities in the toy market and for spin-off applications.

Single-channel kinetics of BK (Slo1) channels

PubMed Central

Geng, Yanyan; Magleby, Karl L.

2014-01-01

Single-channel kinetics has proven a powerful tool to reveal information about the gating mechanisms that control the opening and closing of ion channels. This introductory review focuses on the gating of large conductance Ca2+- and voltage-activated K+ (BK or Slo1) channels at the single-channel level. It starts with single-channel current records and progresses to presentation and analysis of single-channel data and the development of gating mechanisms in terms of discrete state Markov (DSM) models. The DSM models are formulated in terms of the tetrameric modular structure of BK channels, consisting of a central transmembrane pore-gate domain (PGD) attached to four surrounding transmembrane voltage sensing domains (VSD) and a large intracellular cytosolic domain (CTD), also referred to as the gating ring. The modular structure and data analysis shows that the Ca2+ and voltage dependent gating considered separately can each be approximated by 10-state two-tiered models with five closed states on the upper tier and five open states on the lower tier. The modular structure and joint Ca2+ and voltage dependent gating are consistent with a 50 state two-tiered model with 25 closed states on the upper tier and 25 open states on the lower tier. Adding an additional tier of brief closed (flicker states) to the 10-state or 50-state models improved the description of the gating. For fixed experimental conditions a channel would gate in only a subset of the potential number of states. The detected number of states and the correlations between adjacent interval durations are consistent with the tiered models. The examined models can account for the single-channel kinetics and the bursting behavior of gating. Ca2+ and voltage activate BK channels by predominantly increasing the effective opening rate of the channel with a smaller decrease in the effective closing rate. Ca2+ and depolarization thus activate by mainly destabilizing the closed states. PMID:25653620

Watershed Modeling Applications with the Open-Access Modular Distributed Watershed Educational Toolbox (MOD-WET) and Introductory Hydrology Textbook

NASA Astrophysics Data System (ADS)

Huning, L. S.; Margulis, S. A.

2014-12-01

Traditionally, introductory hydrology courses focus on hydrologic processes as independent or semi-independent concepts that are ultimately integrated into a watershed model near the end of the term. When an "off-the-shelf" watershed model is introduced in the curriculum, this approach can result in a potential disconnect between process-based hydrology and the inherent interconnectivity of processes within the water cycle. In order to curb this and reduce the learning curve associated with applying hydrologic concepts to complex real-world problems, we developed the open-access Modular Distributed Watershed Educational Toolbox (MOD-WET). The user-friendly, MATLAB-based toolbox contains the same physical equations for hydrological processes (i.e. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) that are presented in the companion e-textbook (http://aqua.seas.ucla.edu/margulis_intro_to_hydro_textbook.html) and taught in the classroom. The modular toolbox functions can be used by students to study individual hydrologic processes. These functions are integrated together to form a simple spatially-distributed watershed model, which reinforces a holistic understanding of how hydrologic processes are interconnected and modeled. Therefore when watershed modeling is introduced, students are already familiar with the fundamental building blocks that have been unified in the MOD-WET model. Extensive effort has been placed on the development of a highly modular and well-documented code that can be run on a personal computer within the commonly-used MATLAB environment. MOD-WET was designed to: 1) increase the qualitative and quantitative understanding of hydrological processes at the basin-scale and demonstrate how they vary with watershed properties, 2) emphasize applications of hydrologic concepts rather than computer programming, 3) elucidate the underlying physical processes that can often be obscured with a complicated "off-the-shelf" watershed model in an introductory hydrology course, and 4) reduce the learning curve associated with analyzing meaningful real-world problems. The open-access MOD-WET and e-textbook have already been successfully incorporated within our undergraduate curriculum.

Biomechanical, Physiological, and Agility Performance of Soldiers Carrying Loads: A Comparison of the Modular Lightweight Load Carrying Equipment and a Lightning Packs, LLC, Prototype

DTIC Science & Technology

2016-12-27

2015 Approved for public release; distribution is unlimited U.S. Army Natick Soldier Research, Development and Engineering Center...is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and...MODULAR LIGHTWEIGHT LOAD CARRYING EQUIPMENT) HUMAN FACTORS ENGINEERING U.S. Army Natick Soldier Research, Development and Engineering Center ATTN

Synthetic Aperture Imaging Polarimeter: Postprint

DTIC Science & Technology

2010-02-01

mechanical design of the SAlP prototype revol .... es around the concept of a modular array. The modular aspect allows for the array to be built in...imagery of source . The top row images are of the actual fringe pattern incident on the SAlP prototype array. These pictures were taken through the...processed images associated with each of the inputs. The results demonstrated that the SAlP prototype array works in conjunction with the algorithm

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

PubMed

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

2015-06-16

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

VoIP attacks detection engine based on neural network

NASA Astrophysics Data System (ADS)

Safarik, Jakub; Slachta, Jiri

2015-05-01

The security is crucial for any system nowadays, especially communications. One of the most successful protocols in the field of communication over IP networks is Session Initiation Protocol. It is an open-source project used by different kinds of applications, both open-source and proprietary. High penetration and text-based principle made SIP number one target in IP telephony infrastructure, so security of SIP server is essential. To keep up with hackers and to detect potential malicious attacks, security administrator needs to monitor and evaluate SIP traffic in the network. But monitoring and following evaluation could easily overwhelm the security administrator in networks, typically in networks with a number of SIP servers, users and logically or geographically separated networks. The proposed solution lies in automatic attack detection systems. The article covers detection of VoIP attacks through a distributed network of nodes. Then the gathered data analyze aggregation server with artificial neural network. Artificial neural network means multilayer perceptron network trained with a set of collected attacks. Attack data could also be preprocessed and verified with a self-organizing map. The source data is detected by distributed network of detection nodes. Each node contains a honeypot application and traffic monitoring mechanism. Aggregation of data from each node creates an input for neural networks. The automatic classification on a centralized server with low false positive detection reduce the cost of attack detection resources. The detection system uses modular design for easy deployment in final infrastructure. The centralized server collects and process detected traffic. It also maintains all detection nodes.

Note: Hollow cathode lamp with integral, high optical efficiency isolation valve: A modular vacuum ultraviolet source

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

Sloan Roberts, F.; Anderson, Scott L.

2013-12-15

The design and operating conditions of a hollow cathode discharge lamp for the generation of vacuum ultraviolet radiation, suitable for ultrahigh vacuum (UHV) application, are described in detail. The design is easily constructed, and modular, allowing it to be adapted to different experimental requirements. A thin isolation valve is built into one of the differential pumping stages, isolating the discharge section from the UHV section, both for vacuum safety and to allow lamp maintenance without venting the UHV chamber. The lamp has been used both for ultraviolet photoelectron spectroscopy of surfaces and as a “soft” photoionization source for gas-phase massmore » spectrometry.« less

Boiler using combustible fluid

DOEpatents

Baumgartner, H.; Meier, J.G.

1974-07-03

A fluid fuel boiler is described comprising a combustion chamber, a cover on the combustion chamber having an opening for introducing a combustion-supporting gaseous fluid through said openings, means to impart rotation to the gaseous fluid about an axis of the combustion chamber, a burner for introducing a fluid fuel into the chamber mixed with the gaseous fluid for combustion thereof, the cover having a generally frustro-conical configuration diverging from the opening toward the interior of the chamber at an angle of between 15/sup 0/ and 55/sup 0/; means defining said combustion chamber having means defining a plurality of axial hot gas flow paths from a downstream portion of the combustion chamber to flow hot gases into an upstream portion of the combustion chamber, and means for diverting some of the hot gas flow along paths in a direction circumferentially of the combustion chamber, with the latter paths being immersed in the water flow path thereby to improve heat transfer and terminating in a gas outlet, the combustion chamber comprising at least one modular element, joined axially to the frustro-conical cover and coaxial therewith. The modular element comprises an inner ring and means of defining the circumferential, radial, and spiral flow paths of the hot gases.

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.

Acceptance and Commitment Therapy modules: Differential impact on treatment processes and outcomes.

PubMed

Villatte, Jennifer L; Vilardaga, Roger; Villatte, Matthieu; Plumb Vilardaga, Jennifer C; Atkins, David C; Hayes, Steven C

2016-02-01

A modular, transdiagnostic approach to treatment design and implementation may increase the public health impact of evidence-based psychosocial interventions. Such an approach relies on algorithms for selecting and implementing treatment components intended to have a specific therapeutic effect, yet there is little evidence for how components function independent of their treatment packages when employed in clinical service settings. This study aimed to demonstrate the specificity of treatment effects for two components of Acceptance and Commitment Therapy (ACT), a promising candidate for modularization. A randomized, nonconcurrent, multiple-baseline across participants design was used to examine component effects on treatment processes and outcomes in 15 adults seeking mental health treatment. The ACT OPEN module targeted acceptance and cognitive defusion; the ACT ENGAGED module targeted values-based activation and persistence. According to Tau-U analyses, both modules produced significant improvements in psychiatric symptoms, quality of life, and targeted therapeutic processes. ACT ENGAGED demonstrated greater improvements in quality of life and values-based activation. ACT OPEN showed greater improvements in symptom severity, acceptance, and defusion. Both modules improved awareness and non-reactivity, which were mutually targeted, though using distinct intervention procedures. Both interventions demonstrated high treatment acceptability, completion, and patient satisfaction. Treatment effects were maintained at 3-month follow up. ACT components should be considered for inclusion in a modular approach to implementing evidence-based psychosocial interventions for adults. Copyright © 2015 Elsevier Ltd. All rights reserved.

A networked modular hardware and software system for MRI-guided robotic prostate interventions

NASA Astrophysics Data System (ADS)

Su, Hao; Shang, Weijian; Harrington, Kevin; Camilo, Alex; Cole, Gregory; Tokuda, Junichi; Hata, Nobuhiko; Tempany, Clare; Fischer, Gregory S.

2012-02-01

Magnetic resonance imaging (MRI) provides high resolution multi-parametric imaging, large soft tissue contrast, and interactive image updates making it an ideal modality for diagnosing prostate cancer and guiding surgical tools. Despite a substantial armamentarium of apparatuses and systems has been developed to assist surgical diagnosis and therapy for MRI-guided procedures over last decade, the unified method to develop high fidelity robotic systems in terms of accuracy, dynamic performance, size, robustness and modularity, to work inside close-bore MRI scanner still remains a challenge. In this work, we develop and evaluate an integrated modular hardware and software system to support the surgical workflow of intra-operative MRI, with percutaneous prostate intervention as an illustrative case. Specifically, the distinct apparatuses and methods include: 1) a robot controller system for precision closed loop control of piezoelectric motors, 2) a robot control interface software that connects the 3D Slicer navigation software and the robot controller to exchange robot commands and coordinates using the OpenIGTLink open network communication protocol, and 3) MRI scan plane alignment to the planned path and imaging of the needle as it is inserted into the target location. A preliminary experiment with ex-vivo phantom validates the system workflow, MRI-compatibility and shows that the robotic system has a better than 0.01mm positioning accuracy.

The development of a lightweight modular compliant surface bio-inspired robot

NASA Astrophysics Data System (ADS)

Stone, David L.; Cranney, John

2004-09-01

The DARPA Sponsored Compliant Surface Robotics (CSR) program pursues development of a high mobility, lightweight, modular, morphable robot for military forces in the field and for other industrial uses. The USTLAB effort builds on proof of concept feasibility studies and demonstration of a 4, 6, or 8 wheeled modular vehicle with articulated leg-wheel assemblies. In Phase I, basic open plant stability was proven for climbing over obstacles of ~18 inches high and traversing ~75 degree inclines (up, down, or sideways) in a platform of approximately 15 kilograms. At the completion of Phase II, we have completed mechanical and electronics engineering design and achieved changes which currently enable future work in active articulation, enabling autonomous reconfiguration for a wide variety of terrains, including upside down operations (in case of flip over), and we have reduced platform weight by one third. Currently the vehicle weighs 10 kilograms and will grow marginally as additional actuation, MEMS based organic sensing, payload, and autonomous processing is added. The CSR vehicle"s modular spider-like configuration facilitates adaptation to many uses and compliance over rugged terrain. The developmental process and the vehicle characteristics will be discussed.

Tentacle: distributed quantification of genes in metagenomes.

PubMed

Boulund, Fredrik; Sjögren, Anders; Kristiansson, Erik

2015-01-01

In metagenomics, microbial communities are sequenced at increasingly high resolution, generating datasets with billions of DNA fragments. Novel methods that can efficiently process the growing volumes of sequence data are necessary for the accurate analysis and interpretation of existing and upcoming metagenomes. Here we present Tentacle, which is a novel framework that uses distributed computational resources for gene quantification in metagenomes. Tentacle is implemented using a dynamic master-worker approach in which DNA fragments are streamed via a network and processed in parallel on worker nodes. Tentacle is modular, extensible, and comes with support for six commonly used sequence aligners. It is easy to adapt Tentacle to different applications in metagenomics and easy to integrate into existing workflows. Evaluations show that Tentacle scales very well with increasing computing resources. We illustrate the versatility of Tentacle on three different use cases. Tentacle is written for Linux in Python 2.7 and is published as open source under the GNU General Public License (v3). Documentation, tutorials, installation instructions, and the source code are freely available online at: http://bioinformatics.math.chalmers.se/tentacle.

NASA's Earth Science Gateway: A Platform for Interoperable Services in Support of the GEOSS Architecture

NASA Astrophysics Data System (ADS)

Alameh, N.; Bambacus, M.; Cole, M.

2006-12-01

Nasa's Earth Science as well as interdisciplinary research and applications activities require access to earth observations, analytical models and specialized tools and services, from diverse distributed sources. Interoperability and open standards for geospatial data access and processing greatly facilitate such access among the information and processing compo¬nents related to space¬craft, airborne, and in situ sensors; predictive models; and decision support tools. To support this mission, NASA's Geosciences Interoperability Office (GIO) has been developing the Earth Science Gateway (ESG; online at http://esg.gsfc.nasa.gov) by adapting and deploying a standards-based commercial product. Thanks to extensive use of open standards, ESG can tap into a wide array of online data services, serve a variety of audiences and purposes, and adapt to technology and business changes. Most importantly, the use of open standards allow ESG to function as a platform within a larger context of distributed geoscience processing, such as the Global Earth Observing System of Systems (GEOSS). ESG shares the goals of GEOSS to ensure that observations and products shared by users will be accessible, comparable, and understandable by relying on common standards and adaptation to user needs. By maximizing interoperability, modularity, extensibility and scalability, ESG's architecture fully supports the stated goals of GEOSS. As such, ESG's role extends beyond that of a gateway to NASA science data to become a shared platform that can be leveraged by GEOSS via: A modular and extensible architecture Consensus and community-based standards (e.g. ISO and OGC standards) A variety of clients and visualization techniques, including WorldWind and Google Earth A variety of services (including catalogs) with standard interfaces Data integration and interoperability Mechanisms for user involvement and collaboration Mechanisms for supporting interdisciplinary and domain-specific applications ESG has played a key role in recent GEOSS Service Network (GSN) demos and workshops, acting not only as a service and data catalog and discovery client, but also as a portrayal and visualization client to distributed data.

A modular synthesis of dithiocarbamate pendant unnatural α-amino acids

EPA Science Inventory

Unnatural α-amino acids containing dithiocarbamate side chains were synthesized by a one-pot reaction of in-situ generated dithiocarbamate anions with sulfamidates. A wide range of these anions participated in the highly regio- and stereo-selective ring opening of sulfamidates to...

Flexible ultrasonic pipe inspection apparatus

DOEpatents

Jenkins, C.F.; Howard, B.D.

1994-01-01

Pipe crawlers, pipe inspection {open_quotes}rabbits{close_quotes} and similar vehicles are widely used for inspecting the interior surfaces of piping systems, storage tanks and process vessels for damaged or flawed structural features. This paper describes the design of a flexible, modular ultrasonic pipe inspection apparatus.

The Evolution of Academic Library Architecture: A Summary.

ERIC Educational Resources Information Center

Toombs, Kenneth E.

1992-01-01

Reviews the history of architectural developments in academic libraries. Highlights include natural lighting and the invention of the incandescent bulb; compact shelving; open versus closed stacks; modular construction methods; central air conditioning and controlled environments; interior arrangements; access to handicapped users and staff; and…

Enantioselective total synthesis of hyperforin.

PubMed

Sparling, Brian A; Moebius, David C; Shair, Matthew D

2013-01-16

A modular, 18-step total synthesis of hyperforin is described. The natural product was quickly accessed using latent symmetry elements, whereby a group-selective, Lewis acid-catalyzed epoxide-opening cascade cyclization was used to furnish the bicyclo[3.3.1]nonane core and set two key quaternary stereocenters.

A geothermal AMTEC system

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

Schuller, M.J.; LeMire, R.A.; Horner-Richardson, K.

1995-12-31

The Phillips Laboratory Power and Thermal Management Division (PL/VTP), with the support of ORION International Technologies, is investigating new methods of advanced thermal to electric power conversion for space and terrestrial applications. The alkali metal thermal-to-electric converter (AMTEC), manufactured primarily by Advanced Modular Power Systems (AMPS) of Ann Arbor, MI, has reached a level of technological maturity which would allow its use in a constant, unattended thermal source, such as a geothermal field. Approximately 95,000 square miles in the western United States has hot dry rock with thermal gradients of 60 C/km and higher. Several places in the United Statesmore » and the world have thermal gradients of 500 C/km. Such heat sources represent an excellent thermal source for a system of modular power units using AMTEC devices to convert the heat to electricity. AMTEC cells using sodium as a working fluid require heat input at temperatures between 500 and 1,000 C to generate power. The present state of the art is capable of 15% efficiency with 800 C heat input and has demonstrated 18% efficiency for single cells. This paper discusses the basics of AMTEC operation, current drilling technology as a cost driver, design of modular AMTEC power units, heat rejection technologies, materials considerations, and estimates of power production from a geothermal AMTEC concept.« less

Targeting multiple heterogeneous hardware platforms with OpenCL

NASA Astrophysics Data System (ADS)

Fox, Paul A.; Kozacik, Stephen T.; Humphrey, John R.; Paolini, Aaron; Kuller, Aryeh; Kelmelis, Eric J.

2014-06-01

The OpenCL API allows for the abstract expression of parallel, heterogeneous computing, but hardware implementations have substantial implementation differences. The abstractions provided by the OpenCL API are often insufficiently high-level to conceal differences in hardware architecture. Additionally, implementations often do not take advantage of potential performance gains from certain features due to hardware limitations and other factors. These factors make it challenging to produce code that is portable in practice, resulting in much OpenCL code being duplicated for each hardware platform being targeted. This duplication of effort offsets the principal advantage of OpenCL: portability. The use of certain coding practices can mitigate this problem, allowing a common code base to be adapted to perform well across a wide range of hardware platforms. To this end, we explore some general practices for producing performant code that are effective across platforms. Additionally, we explore some ways of modularizing code to enable optional optimizations that take advantage of hardware-specific characteristics. The minimum requirement for portability implies avoiding the use of OpenCL features that are optional, not widely implemented, poorly implemented, or missing in major implementations. Exposing multiple levels of parallelism allows hardware to take advantage of the types of parallelism it supports, from the task level down to explicit vector operations. Static optimizations and branch elimination in device code help the platform compiler to effectively optimize programs. Modularization of some code is important to allow operations to be chosen for performance on target hardware. Optional subroutines exploiting explicit memory locality allow for different memory hierarchies to be exploited for maximum performance. The C preprocessor and JIT compilation using the OpenCL runtime can be used to enable some of these techniques, as well as to factor in hardware-specific optimizations as necessary.

Open Trial of Modular Cognitive-Behavioral Therapy in the Treatment of Anxiety Among Late Adolescents with Autism Spectrum Disorder.

PubMed

Wise, Jillian M; Cepeda, Sandra L; Ordaz, D Luis; McBride, Nicole M; Cavitt, Mark A; Howie, Flora R; Scalli, Leanne; Ehrenreich-May, Jill; Wood, Jeffrey J; Lewin, Adam B; Storch, Eric A

2018-05-31

Given the high rates of comorbid anxiety and autism spectrum disorder (ASD) in the adolescent and young adult population, effective treatment protocols to address anxiety symptoms are of importance to help promote greater independence across settings. While research supports the use of cognitive-behavioral therapy (CBT) across younger age groups with ASD, the literature is limited on interventions benefitting adolescents and young adults with comorbid anxiety disorders and ASD. Therefore, this open trial utilized a modified CBT manual for seven participants between the ages of 16 and 20 years, consisting of a 16-week modularized CBT treatment, including psychoeducation, cognitive therapy, and exposure therapy. Measures of anxiety and depression were completed at baseline and post-treatment. Findings demonstrated significant reductions on clinician-rated measures of anxiety. While findings are encouraging, additional studies examining the efficacy of CBT for this population with ASD and clinical anxiety are necessary to further identify beneficial treatment components.

Advances in X-Ray Simulator Technology

DTIC Science & Technology

1995-07-01

d’Etudes de Gramat ; I. Vitkovitsky, Logicon RDA INTRODUCTION DNA’s future x-ray simulators are based upon inductive energy storage, a technology which...switch. SYRINX, a proposed design to be built by the Centre d’Etudes de Gramat (CEG) in France would employ a modular approach, possibly with a...called SYRINX, would be built at the Centred’ Etudes de Gramat (CEG). It would employ a modular.long conduction time current source to drive a PRS

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

OVAS: an open-source variant analysis suite with inheritance modelling.

PubMed

Mozere, Monika; Tekman, Mehmet; Kari, Jameela; Bockenhauer, Detlef; Kleta, Robert; Stanescu, Horia

2018-02-08

The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functionally important variants has now shifted towards identifying the critical differences between normal variants and disease-causing ones. The ever-increasing reliance on cloud-based services for sequence analysis and the non-transparent methods they utilize has prompted the need for more in-situ services that can provide a safer and more accessible environment to process patient data, especially in circumstances where continuous internet usage is limited. To address these issues, we herein propose our standalone Open-source Variant Analysis Sequencing (OVAS) pipeline; consisting of three key stages of processing that pertain to the separate modes of annotation, filtering, and interpretation. Core annotation performs variant-mapping to gene-isoforms at the exon/intron level, append functional data pertaining the type of variant mutation, and determine hetero/homozygosity. An extensive inheritance-modelling module in conjunction with 11 other filtering components can be used in sequence ranging from single quality control to multi-file penetrance model specifics such as X-linked recessive or mosaicism. Depending on the type of interpretation required, additional annotation is performed to identify organ specificity through gene expression and protein domains. In the course of this paper we analysed an autosomal recessive case study. OVAS made effective use of the filtering modules to recapitulate the results of the study by identifying the prescribed compound-heterozygous disease pattern from exome-capture sequence input samples. OVAS is an offline open-source modular-driven analysis environment designed to annotate and extract useful variants from Variant Call Format (VCF) files, and process them under an inheritance context through a top-down filtering schema of swappable modules, run entirely off a live bootable medium and accessed locally through a web-browser.

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

PubMed Central

Pathak, Jyotishman; Bailey, Kent R; Beebe, Calvin E; Bethard, Steven; Carrell, David S; Chen, Pei J; Dligach, Dmitriy; Endle, Cory M; Hart, Lacey A; Haug, Peter J; Huff, Stanley M; Kaggal, Vinod C; Li, Dingcheng; Liu, Hongfang; Marchant, Kyle; Masanz, James; Miller, Timothy; Oniki, Thomas A; Palmer, Martha; Peterson, Kevin J; Rea, Susan; Savova, Guergana K; Stancl, Craig R; Sohn, Sunghwan; Solbrig, Harold R; Suesse, Dale B; Tao, Cui; Taylor, David P; Westberg, Les; Wu, Stephen; Zhuo, Ning; Chute, Christopher G

2013-01-01

Research objective To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction. Materials and methods Software tools and applications were developed to extract information from EHRs. Representative and convenience samples of both structured and unstructured data from two EHR systems—Mayo Clinic and Intermountain Healthcare—were used for development and validation. Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs). These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine. Results Using CEMs and open-source natural language processing and terminology services engines—namely, Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) and Common Terminology Services (CTS2)—we developed a data-normalization platform that ensures data security, end-to-end connectivity, and reliable data flow within and across institutions. We demonstrated the applicability of this platform by executing a QDM-based MU quality measure that determines the percentage of patients between 18 and 75 years with diabetes whose most recent low-density lipoprotein cholesterol test result during the measurement year was <100 mg/dL on a randomly selected cohort of 273 Mayo Clinic patients. The platform identified 21 and 18 patients for the denominator and numerator of the quality measure, respectively. Validation results indicate that all identified patients meet the QDM-based criteria. Conclusions End-to-end automated systems for extracting clinical information from diverse EHR systems require extensive use of standardized vocabularies and terminologies, as well as robust information models for storing, discovering, and processing that information. This study demonstrates the application of modular and open-source resources for enabling secondary use of EHR data through normalization into standards-based, comparable, and consistent format for high-throughput phenotyping to identify patient cohorts. PMID:24190931

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.

Open-source, small-animal magnetic resonance-guided focused ultrasound system.

PubMed

Poorman, Megan E; Chaplin, Vandiver L; Wilkens, Ken; Dockery, Mary D; Giorgio, Todd D; Grissom, William A; Caskey, Charles F

2016-01-01

MR-guided focused ultrasound or high-intensity focused ultrasound (MRgFUS/MRgHIFU) is a non-invasive therapeutic modality with many potential applications in areas such as cancer therapy, drug delivery, and blood-brain barrier opening. However, the large financial costs involved in developing preclinical MRgFUS systems represent a barrier to research groups interested in developing new techniques and applications. We aim to mitigate these challenges by detailing a validated, open-source preclinical MRgFUS system capable of delivering thermal and mechanical FUS in a quantifiable and repeatable manner under real-time MRI guidance. A hardware and software package was developed that includes closed-loop feedback controlled thermometry code and CAD drawings for a therapy table designed for a preclinical MRI scanner. For thermal treatments, the modular software uses a proportional integral derivative controller to maintain a precise focal temperature rise in the target given input from MR phase images obtained concurrently. The software computes the required voltage output and transmits it to a FUS transducer that is embedded in the delivery table within the magnet bore. The delivery table holds the FUS transducer, a small animal and its monitoring equipment, and a transmit/receive RF coil. The transducer is coupled to the animal via a water bath and is translatable in two dimensions from outside the magnet. The transducer is driven by a waveform generator and amplifier controlled by real-time software in Matlab. MR acoustic radiation force imaging is also implemented to confirm the position of the focus for mechanical and thermal treatments. The system was validated in tissue-mimicking phantoms and in vivo during murine tumor hyperthermia treatments. Sonications were successfully controlled over a range of temperatures and thermal doses for up to 20 min with minimal temperature overshoot. MR thermometry was validated with an optical temperature probe, and focus visualization was achieved with acoustic radiation force imaging. We developed an MRgFUS platform for small-animal treatments that robustly delivers accurate, precise, and controllable sonications over extended time periods. This system is an open source and could increase the availability of low-cost small-animal systems to interdisciplinary researchers seeking to develop new MRgFUS applications and technology.

Architecture and Implementation of OpenPET Firmware and Embedded Software

PubMed Central

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; Peng, Qiyu; Choong, Woon-Seng

2016-01-01

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the flexibility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics – a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures and implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration. PMID:27110034

Identifying the Return on Investment for Army Migration to a Modular Open Systems Approach for Future and Legacy Systems

DTIC Science & Technology

2017-04-05

quantitative data on the expected savings. This research attempted to identify and quantify the ROI for transitioning programs to MOSA. Purpose of This...6 Significance of This Research ............................................................................................... 6 Overview...of the Research Methodology ............................................................................... 7 Limitations

Ephus: Multipurpose Data Acquisition Software for Neuroscience Experiments

PubMed Central

Suter, Benjamin A.; O'Connor, Timothy; Iyer, Vijay; Petreanu, Leopoldo T.; Hooks, Bryan M.; Kiritani, Taro; Svoboda, Karel; Shepherd, Gordon M. G.

2010-01-01

Physiological measurements in neuroscience experiments often involve complex stimulus paradigms and multiple data channels. Ephus (http://www.ephus.org) is an open-source software package designed for general-purpose data acquisition and instrument control. Ephus operates as a collection of modular programs, including an ephys program for standard whole-cell recording with single or multiple electrodes in typical electrophysiological experiments, and a mapper program for synaptic circuit mapping experiments involving laser scanning photostimulation based on glutamate uncaging or channelrhodopsin-2 excitation. Custom user functions allow user-extensibility at multiple levels, including on-line analysis and closed-loop experiments, where experimental parameters can be changed based on recently acquired data, such as during in vivo behavioral experiments. Ephus is compatible with a variety of data acquisition and imaging hardware. This paper describes the main features and modules of Ephus and their use in representative experimental applications. PMID:21960959

BurnMan: Towards a multidisciplinary toolkit for reproducible deep Earth science

NASA Astrophysics Data System (ADS)

Myhill, R.; Cottaar, S.; Heister, T.; Rose, I.; Unterborn, C. T.; Dannberg, J.; Martin-Short, R.

2016-12-01

BurnMan (www.burnman.org) is an open-source toolbox to compute thermodynamic and thermoelastic properties as a function of pressure and temperature using published mineral physical parameters and equations-of-state. The framework is user-friendly, written in Python, and modular, allowing the user to implement their own equations of state, endmember and solution model libraries, geotherms, and averaging schemes. Here we introduce various new modules, which can be used to: Fit thermodynamic variables to data from high pressure static and shock wave experiments, Calculate equilibrium assemblages given a bulk composition, pressure and temperature, Calculate chemical potentials and oxygen fugacities for given assemblages Compute 3D synthetic seismic models using output from geodynamic models and compare these results with global seismic tomographic models, Create input files for synthetic seismogram codes. Users can contribute scripts that reproduce the results from peer-reviewed articles and practical demonstrations (e.g. Cottaar et al., 2014).

Pybus -- A Python Software Bus

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

Lavrijsen, Wim T.L.P.

2004-10-14

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

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.

A RESTful Service Oriented Architecture for Science Data Processing

NASA Astrophysics Data System (ADS)

Duggan, B.; Tilmes, C.; Durbin, P.; Masuoka, E.

2012-12-01

The Atmospheric Composition Processing System is an implementation of a RESTful Service Oriented Architecture which handles incoming data from the Ozone Monitoring Instrument and the Ozone Monitoring and Profiler Suite aboard the Aura and NPP spacecrafts respectively. The system has been built entirely from open source components, such as Postgres, Perl, and SQLite and has leveraged the vast resources of the Comprehensive Perl Archive Network (CPAN). The modular design of the system also allows for many of the components to be easily released and integrated into the CPAN ecosystem and reused independently. At minimal expense, the CPAN infrastructure and community provide peer review, feedback and continuous testing in a wide variety of environments and architectures. A well defined set of conventions also facilitates dependency management, packaging, and distribution of code. Test driven development also provides a way to ensure stability despite a continuously changing base of dependencies.

Project Management Software for Distributed Industrial Companies

NASA Astrophysics Data System (ADS)

Dobrojević, M.; Medjo, B.; Rakin, M.; Sedmak, A.

This paper gives an overview of the development of a new software solution for project management, intended mainly to use in industrial environment. The main concern of the proposed solution is application in everyday engineering practice in various, mainly distributed industrial companies. Having this in mind, special care has been devoted to development of appropriate tools for tracking, storing and analysis of the information about the project, and in-time delivering to the right team members or other responsible persons. The proposed solution is Internet-based and uses LAMP/WAMP (Linux or Windows - Apache - MySQL - PHP) platform, because of its stability, versatility, open source technology and simple maintenance. Modular structure of the software makes it easy for customization according to client specific needs, with a very short implementation period. Its main advantages are simple usage, quick implementation, easy system maintenance, short training and only basic computer skills needed for operators.

Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture

PubMed Central

Mandl, Kenneth D; Kohane, Isaac S; McFadden, Douglas; Weber, Griffin M; Natter, Marc; Mandel, Joshua; Schneeweiss, Sebastian; Weiler, Sarah; Klann, Jeffrey G; Bickel, Jonathan; Adams, William G; Ge, Yaorong; Zhou, Xiaobo; Perkins, James; Marsolo, Keith; Bernstam, Elmer; Showalter, John; Quarshie, Alexander; Ofili, Elizabeth; Hripcsak, George; Murphy, Shawn N

2014-01-01

We describe the architecture of the Patient Centered Outcomes Research Institute (PCORI) funded Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS, http://www.SCILHS.org) clinical data research network, which leverages the $48 billion dollar federal investment in health information technology (IT) to enable a queryable semantic data model across 10 health systems covering more than 8 million patients, plugging universally into the point of care, generating evidence and discovery, and thereby enabling clinician and patient participation in research during the patient encounter. Central to the success of SCILHS is development of innovative ‘apps’ to improve PCOR research methods and capacitate point of care functions such as consent, enrollment, randomization, and outreach for patient-reported outcomes. SCILHS adapts and extends an existing national research network formed on an advanced IT infrastructure built with open source, free, modular components. PMID:24821734

Benchmarking heart rate variability toolboxes.

PubMed

Vest, Adriana N; Li, Qiao; Liu, Chengyu; Nemati, Shamim; Shah, Amit; Clifford, Gari D

Heart rate variability (HRV) metrics hold promise as potential indicators for autonomic function, prediction of adverse cardiovascular outcomes, psychophysiological status, and general wellness. Although the investigation of HRV has been prevalent for several decades, the methods used for preprocessing, windowing, and choosing appropriate parameters lack consensus among academic and clinical investigators. A comprehensive and open-source modular program is presented for calculating HRV implemented in Matlab with evidence-based algorithms and output formats. We compare our software with another widely used HRV toolbox written in C and available through PhysioNet.org. Our findings show substantially similar results when using high quality electrocardiograms (ECG) free from arrhythmias. Our software shows equivalent performance alongside an established predecessor and includes validated tools for performing preprocessing, signal quality, and arrhythmia detection to help provide standardization and repeatability in the field, leading to fewer errors in the presence of noise or arrhythmias. Copyright © 2017 Elsevier Inc. All rights reserved.

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

SHARPEN-systematic hierarchical algorithms for rotamers and proteins on an extended network.

PubMed

Loksha, Ilya V; Maiolo, James R; Hong, Cheng W; Ng, Albert; Snow, Christopher D

2009-04-30

Algorithms for discrete optimization of proteins play a central role in recent advances in protein structure prediction and design. We wish to improve the resources available for computational biologists to rapidly prototype such algorithms and to easily scale these algorithms to many processors. To that end, we describe the implementation and use of two new open source resources, citing potential benefits over existing software. We discuss CHOMP, a new object-oriented library for macromolecular optimization, and SHARPEN, a framework for scaling CHOMP scripts to many computers. These tools allow users to develop new algorithms for a variety of applications including protein repacking, protein-protein docking, loop rebuilding, or homology model remediation. Particular care was taken to allow modular energy function design; protein conformations may currently be scored using either the OPLSaa molecular mechanical energy function or an all-atom semiempirical energy function employed by Rosetta. (c) 2009 Wiley Periodicals, Inc.

The conceptual design of a robust, compact, modular tokamak reactor based on high-field superconductors

NASA Astrophysics Data System (ADS)

Whyte, D. G.; Bonoli, P.; Barnard, H.; Haakonsen, C.; Hartwig, Z.; Kasten, C.; Palmer, T.; Sung, C.; Sutherland, D.; Bromberg, L.; Mangiarotti, F.; Goh, J.; Sorbom, B.; Sierchio, J.; Ball, J.; Greenwald, M.; Olynyk, G.; Minervini, J.

2012-10-01

Two of the greatest challenges to tokamak reactors are 1) large single-unit cost of each reactor's construction and 2) their susceptibility to disruptions from operation at or above operational limits. We present an attractive tokamak reactor design that substantially lessens these issues by exploiting recent advancements in superconductor (SC) tapes allowing peak field on SC coil > 20 Tesla. A R˜3.3 m, B˜9.2 T, ˜ 500 MW fusion power tokamak provides high fusion gain while avoiding all disruptive operating boundaries (no-wall beta, kink, and density limits). Robust steady-state core scenarios are obtained by exploiting the synergy of high field, compact size and ideal efficiency current drive using high-field side launch of Lower Hybrid waves. The design features a completely modular replacement of internal solid components enabled by the demountability of the coils/tapes and the use of an immersion liquid blanket. This modularity opens up the possibility of using the device as a nuclear component test facility.

Engineering genetic circuit interactions within and between synthetic minimal cells

NASA Astrophysics Data System (ADS)

Adamala, Katarzyna P.; Martin-Alarcon, Daniel A.; Guthrie-Honea, Katriona R.; Boyden, Edward S.

2017-05-01

Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... STANDARDS (CONTINUED) BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General... this part: (a) “Battery” means a modular electric power source where part or all of the fuel is... and a battery. (b) “Battery manufacturing operations” means all of the specific processes used to...

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... STANDARDS (CONTINUED) BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General... this part: (a) “Battery” means a modular electric power source where part or all of the fuel is... and a battery. (b) “Battery manufacturing operations” means all of the specific processes used to...

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... STANDARDS (CONTINUED) BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General... this part: (a) “Battery” means a modular electric power source where part or all of the fuel is... and a battery. (b) “Battery manufacturing operations” means all of the specific processes used to...

An autonomous sensor module based on a legacy CCTV camera

NASA Astrophysics Data System (ADS)

Kent, P. J.; Faulkner, D. A. A.; Marshall, G. F.

2016-10-01

A UK MoD funded programme into autonomous sensors arrays (SAPIENT) has been developing new, highly capable sensor modules together with a scalable modular architecture for control and communication. As part of this system there is a desire to also utilise existing legacy sensors. The paper reports upon the development of a SAPIENT-compliant sensor module using a legacy Close-Circuit Television (CCTV) pan-tilt-zoom (PTZ) camera. The PTZ camera sensor provides three modes of operation. In the first mode, the camera is automatically slewed to acquire imagery of a specified scene area, e.g. to provide "eyes-on" confirmation for a human operator or for forensic purposes. In the second mode, the camera is directed to monitor an area of interest, with zoom level automatically optimized for human detection at the appropriate range. Open source algorithms (using OpenCV) are used to automatically detect pedestrians; their real world positions are estimated and communicated back to the SAPIENT central fusion system. In the third mode of operation a "follow" mode is implemented where the camera maintains the detected person within the camera field-of-view without requiring an end-user to directly control the camera with a joystick.

Utilizing GPUs to Accelerate Turbomachinery CFD Codes

NASA Technical Reports Server (NTRS)

MacCalla, Weylin; Kulkarni, Sameer

2016-01-01

GPU computing has established itself as a way to accelerate parallel codes in the high performance computing world. This work focuses on speeding up APNASA, a legacy CFD code used at NASA Glenn Research Center, while also drawing conclusions about the nature of GPU computing and the requirements to make GPGPU worthwhile on legacy codes. Rewriting and restructuring of the source code was avoided to limit the introduction of new bugs. The code was profiled and investigated for parallelization potential, then OpenACC directives were used to indicate parallel parts of the code. The use of OpenACC directives was not able to reduce the runtime of APNASA on either the NVIDIA Tesla discrete graphics card, or the AMD accelerated processing unit. Additionally, it was found that in order to justify the use of GPGPU, the amount of parallel work being done within a kernel would have to greatly exceed the work being done by any one portion of the APNASA code. It was determined that in order for an application like APNASA to be accelerated on the GPU, it should not be modular in nature, and the parallel portions of the code must contain a large portion of the code's computation time.

Commander Brand shaves in front of forward middeck lockers

NASA Technical Reports Server (NTRS)

1982-01-01

Commander Brand, wearing shorts, shaves in front of forward middeck lockers using personal hygiene mirror assembly (assy). Open modular locker single tray assy, Field Sequential (FS) crew cabin camera, communications kit assy mini headset (HDST) and HDST interface unit (HIU), personal hygiene kit, and meal tray assemblies appear in view.

Long-range Perspectives in Environmental Education: Producing Practical Problem-solvers.

ERIC Educational Resources Information Center

Barratt, Rod

1997-01-01

Addresses postgraduate environmental education by supported distance learning as offered by the Open University in Great Britain. Refers to techniques for regularly updating material in rapidly developing areas as well as integrating teaching and research. Also refers to the modular course Integrated Safety, Health and Environmental Management.…

Everything is Data - Overview of Modular System of Sensors for Museum Environment

NASA Astrophysics Data System (ADS)

Valach, J.; Juliš, K.; Štefcová, P.; Pech, M.; Wolf, B.; Kotyk, M.; Frankl, J.

2015-08-01

The main aim of project nearing completion was to develop a modular and scalable system of sensors for monitoring of internal environment of museum exhibitions and depositories. The sensors vary according to parameters being monitored and at the same time also according to required energy autonomy, processing capability and bandwidth requirements. Sensors developed can be divided into three groups: environmental sensors, biosensors and sensors of vibrations. Data acquired by the sensors are archived and stored in open format. Metadata stored alongside true numerical data from measurement, represent assurance of future computer readability in data mining application. Long continuous series of data can provide sufficient data for acquisition of dose-response function.

The Community Intercomparison Suite (CIS)

NASA Astrophysics Data System (ADS)

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

2017-04-01

Earth observations (both remote and in-situ) create vast amounts of data providing invaluable constraints for the climate science community. Efficient exploitation of these complex and highly heterogeneous datasets has been limited however by the lack of suitable software tools, particularly for comparison of gridded and ungridded data, thus reducing scientific productivity. CIS (http://cistools.net) is an open-source, command line tool and Python library which allows the straight-forward quantitative analysis, intercomparison and visualisation of remote sensing, in-situ and model data. The CIS can read gridded and ungridded remote sensing, in-situ and model data - and many other data sources 'out-of-the-box', such as ESA Aerosol and Cloud CCI product, MODIS, Cloud CCI, Cloudsat, AERONET. Perhaps most importantly however CIS also employs a modular plugin architecture to allow for the reading of limitless different data types. Users are able to write their own plugins for reading the data sources which they are familiar with, and share them within the community, allowing all to benefit from their expertise. To enable the intercomparison of this data the CIS provides a number of operations including: the aggregation of ungridded and gridded datasets to coarser representations using a number of different built in averaging kernels; the subsetting of data to reduce its extent or dimensionality; the co-location of two distinct datasets onto a single set of co-ordinates; the visualisation of the input or output data through a number of different plots and graphs; the evaluation of arbitrary mathematical expressions against any number of datasets; and a number of other supporting functions such as a statistical comparison of two co-located datasets. These operations can be performed efficiently on local machines or large computing clusters - and is already available on the JASMIN computing facility. A case-study using the GASSP collection of in-situ aerosol observations will demonstrate the power of using CIS to perform model evaluations. The use of an open-source, community developed tool in this way opens up a huge amount of data which would previously have been inaccessible to many users, while also providing replicable, repeatable analysis which scientists and policy-makers alike can trust and understand.

The HYPE Open Source Community

NASA Astrophysics Data System (ADS)

Strömbäck, L.; Pers, C.; Isberg, K.; Nyström, K.; Arheimer, B.

2013-12-01

The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model. It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. HYPE has been successfully used in many hydrological applications at SMHI. For Europe, we currently have three different models; The S-HYPE model for Sweden; The BALT-HYPE model for the Baltic Sea; and the E-HYPE model for the whole Europe. These models simulate hydrological conditions and nutrients for their respective areas and are used for characterization, forecasts, and scenario analyses. Model data can be downloaded from hypeweb.smhi.se. In addition, we provide models for the Arctic region, the Arab (Middle East and Northern Africa) region, India, the Niger River basin, the La Plata Basin. This demonstrates the applicability of the HYPE model for large scale modeling in different regions of the world. An important goal with our work is to make our data and tools available as open data and services. For this aim we created the HYPE Open Source Community (OSC) that makes the source code of HYPE available for anyone interested in further development of HYPE. The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modeling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed and learnt from. New versions of the main code are delivered frequently. HYPE OSC is open to everyone interested in hydrology, hydrological modeling and code development - e.g. scientists, authorities, and consultancies. By joining the HYPE OSC you get access a state-of-the-art operational hydrological model. The HYPE source code is designed to efficiently handle large scale modeling for forecast, hindcast and climate applications. The code is under constant development to improve the hydrological processes, efficiency and readability. In the beginning of 2013 we released a version with new and better modularization based on hydrological processes. This will make the code easier to understand and further develop for a new user. An important challenge in this process is to produce code that is easy for anyone to understand and work with, but still maintain the properties that make the code efficient enough for large scale applications. Input from the HYPE Open Source Community is an important source for future improvements of the HYPE model. Therefore, by joining the community you become an active part of the development, get access to the latest features and can influence future versions of the model.

PD5: a general purpose library for primer design software.

PubMed

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

2013-01-01

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

A New Arduino Datalogger Board for Simple, Low Cost Environmental Monitoring and the EnviroDIY Web Community

NASA Astrophysics Data System (ADS)

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

2015-12-01

Scientists and educators around the world have been building their own dataloggers and devices using a variety of boards based on the Arduino open source electronics platform. While there have been several useful boards on the market in the past few years, they still required significant modification or additional components in order to use them with various sensors or deploy them in remote areas. Here we introduce our new custom datalogger board that makes it very easy to build a rugged environmental monitoring system. These custom boards contain all of the essential features of a solar-powered datalogger with radio telemetry, plus they have a very convenient and modular method for attaching a wide variety of sensors and devices. Various deployment options and installations are shown, as well as the online database that is used for capturing the live streaming data from the loggers and displaying graphs on custom web pages. Following the introduction last year of the EnviroDIY online community (http://enviroDIY.org), it continues to gain new members and share new ideas about open-source hardware and software solutions for observing our environment. EnviroDIY members can showcase their gadgets or describe their projects, ask questions, or follow along with helpful tutorials. Our new datalogger board, together with the EnviroDIY website, will make it easy for anyone to build and deploy their own environmental monitoring stations.

SCHeMA open and modular in situ sensing solution

NASA Astrophysics Data System (ADS)

Tercier-Waeber, Marie Louise; Novellino, Antonio

2017-04-01

Marine environments are highly vulnerable and influenced by a wide diversity of anthropogenic and natural substances and organisms that may have adverse effects on the ecosystem equilibrium, on living resources and, ultimately, on human health. Identification of relevant types of hazards at the appropriate temporal and spatial scale is crucial to detect their sources and origin, to understand the processes governing their magnitude and distribution, and to ultimately evaluate and manage their risks and consequences preventing economic losses. This can be addressed only by the development of innovative, compact, rugged, automated, sensor networks allowing long-term monitoring. Development of such tools is a challenging task as it requires many analytical and technical innovations. The FP7-OCEAN 2013-SCHeMA project aims to contribute to meet this challenge by providing an open and modular sensing solution for autonomous in situ high resolution mapping of a range of anthropogenic and natural chemical compounds (trace metals, nutrients, anthropogenic organic compounds, toxic algae species and toxins, species relevant to the carbon cycle). To achieve this, SCHeMA activities focus on the development of : 1) an array of miniature sensor probes taking advantage of various innovative solutions, namely: (polymer-based) gel-integrated sensors; solid state ion-selective membrane sensors coupled to an on-line desalination module; mid-infrared optical sensors; optochemical multichannel devices; enOcean technology; 2) dedicated hardware, firmware and software components allowing their plug-and-play integration, localization as well as wireless bidirectional communication via advanced OGC-SWE wired/wireless dedicated interfaces; 3) a web-based front-end system compatible with EU standard requirements and principles (INSPIRE, GEO/GEOSS) and configured to insure easy interoperability with national, regional and local marine observation systems. This lecture will present examples of innovative approaches and devices successfully developed and currently explored. Potentiality of the SCHeMA individual probes and integrated system to provide new type of high-resolution environmental data will be illustrated by examples of field application in selected coastal areas. www.schema-ocean.eu

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... STANDARDS BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General definitions. In...) “Battery” means a modular electric power source where part or all of the fuel is contained within the unit... heat cycle engine. In this regulation there is no differentiation between a single cell and a battery...

40 CFR 461.2 - General definitions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... STANDARDS BATTERY MANUFACTURING POINT SOURCE CATEGORY General Provisions § 461.2 General definitions. In...) “Battery” means a modular electric power source where part or all of the fuel is contained within the unit... heat cycle engine. In this regulation there is no differentiation between a single cell and a battery...

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

USGS Publications Warehouse

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

2012-01-01

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

Sensor Open System Architecture (SOSA) evolution for collaborative standards development

NASA Astrophysics Data System (ADS)

Collier, Charles Patrick; Lipkin, Ilya; Davidson, Steven A.; Baldwin, Rusty; Orlovsky, Michael C.; Ibrahim, Tim

2017-04-01

The Sensor Open System Architecture (SOSA) is a C4ISR-focused technical and economic collaborative effort between the Air Force, Navy, Army, the Department of Defense (DoD), Industry, and other Governmental agencies to develop (and incorporate) a technical Open Systems Architecture standard in order to maximize C4ISR sub-system, system, and platform affordability, re-configurability, and hardware/software/firmware re-use. The SOSA effort will effectively create an operational and technical framework for the integration of disparate payloads into C4ISR systems; with a focus on the development of a modular decomposition (defining functions and behaviors) and associated key interfaces (physical and logical) for common multi-purpose architecture for radar, EO/IR, SIGINT, EW, and Communications. SOSA addresses hardware, software, and mechanical/electrical interfaces. The modular decomposition will produce a set of re-useable components, interfaces, and sub-systems that engender reusable capabilities. This, in effect, creates a realistic and affordable ecosystem enabling mission effectiveness through systematic re-use of all available re-composed hardware, software, and electrical/mechanical base components and interfaces. To this end, SOSA will leverage existing standards as much as possible and evolve the SOSA architecture through modification, reuse, and enhancements to achieve C4ISR goals. This paper will present accomplishments over the first year of SOSA initiative.

Open modular architecture controls at GM Powertrain: technology and implementation

NASA Astrophysics Data System (ADS)

Bailo, Clark P.; Yen, C. J.

1997-01-01

General Motors Powertrain Group (GMPTG) has been the leader in implementing open, modular architecture controller (OMAC) technologies in its manufacturing applications since 1986. The interest in OMAC has been greatly expanded for the past two years because of the advancement of personal computer technologies and the publishing of the OMAC whitepaper by the US automotive companies stating the requirements of OMAC technologies in automotive applications. The purpose of this paper is to describe the current OMAC projects and the future direction of implementation at GMPTG. An overview of the OMAC project and the definition of the OMAC concept are described first. The rationale of pursuing open technologies is explained from the perspective of GMPTG in lieu of its agile manufacturing strategy. Examples of existing PC-based control applications are listed to demonstrate the extensive commitment to PC-based technologies that has already been put in place. A migration plan form PC-based to OMAC-based systems with the thorough approach of validation are presented next to convey the direction that GMPTG is taking in implementing OMAC technologies. Leveraged technology development projects are described to illustrate the philosophy and approaches toward the development of OMAC technologies at GMPTG. Finally, certain implementation issues are discussed to emphasize efforts that are still required to have successful implementations of OMAC systems.

Modular radiochemistry synthesis system

DOEpatents

Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, Michael R.; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

2016-11-01

A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

Path to Market for Compact Modular Fusion Power Cores

NASA Astrophysics Data System (ADS)

Woodruff, Simon; Baerny, Jennifer K.; Mattor, Nathan; Stoulil, Don; Miller, Ronald; Marston, Theodore

2012-08-01

The benefits of an energy source whose reactants are plentiful and whose products are benign is hard to measure, but at no time in history has this energy source been more needed. Nuclear fusion continues to promise to be this energy source. However, the path to market for fusion systems is still regularly a matter for long-term (20 + year) plans. This white paper is intended to stimulate discussion of faster commercialization paths, distilling guidance from investors, utilities, and the wider energy research community (including from ARPA-E). There is great interest in a small modular fusion system that can be developed quickly and inexpensively. A simple model shows how compact modular fusion can produce a low cost development path by optimizing traditional systems that burn deuterium and tritium, operating not only at high magnetic field strength, but also by omitting some components that allow for the core to become more compact and easier to maintain. The dominant hurdles to the development of low cost, practical fusion systems are discussed, primarily in terms of the constraints placed on the cost of development stages in the private sector. The main finding presented here is that the bridge from DOE Office of Science to the energy market can come at the Proof of Principle development stage, providing the concept is sufficiently compact and inexpensive that its development allows for a normal technology commercialization path.

Modular radiochemistry synthesis system

DOEpatents

Satyamurthy, Nagichettiar; Barrio, Jorge R.; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark; Shen, Clifton Kwang-Fu

2015-12-15

A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

Modular radiochemistry synthesis system

DOEpatents

Satyamurthy, Nagichettiar; Barrio, Jorge R; Amarasekera, Bernard; Van Dam, R. Michael; Olma, Sebastian; Williams, Dirk; Eddings, Mark A; Shen, Clifton Kwang-Fu

2015-02-10

A modular chemical production system includes multiple modules for performing a chemical reaction, particularly of radiochemical compounds, from a remote location. One embodiment comprises a reaction vessel including a moveable heat source with the position thereof relative to the reaction vessel being controllable from a remote position. Alternatively the heat source may be fixed in location and the reaction vial is moveable into and out of the heat source. The reaction vessel has one or more sealing plugs, the positioning of which in relationship to the reaction vessel is controllable from a remote position. Also the one or more reaction vessel sealing plugs can include one or more conduits there through for delivery of reactants, gases at atmospheric or an elevated pressure, inert gases, drawing a vacuum and removal of reaction end products to and from the reaction vial, the reaction vial with sealing plug in position being operable at elevated pressures. The modular chemical production system is assembled from modules which can each include operating condition sensors and controllers configured for monitoring and controlling the individual modules and the assembled system from a remote position. Other modules include, but are not limited to a Reagent Storage and Delivery Module, a Cartridge Purification Module, a Microwave Reaction Module, an External QC/Analysis/Purification Interface Module, an Aliquotting Module, an F-18 Drying Module, a Concentration Module, a Radiation Counting Module, and a Capillary Reactor Module.

The modular approach enables a fully ab initio simulation of the contacts between 3D and 2D materials.

PubMed

Fediai, Artem; Ryndyk, Dmitry A; Cuniberti, Gianaurelio

2016-10-05

Up to now, the electrical properties of the contacts between 3D metals and 2D materials have never been computed at a fully ab initio level due to the huge number of atomic orbitals involved in a current path from an electrode to a pristine 2D material. As a result, there are still numerous open questions and controversial theories on the electrical properties of systems with 3D/2D interfaces-for example, the current path and the contact length scalability. Our work provides a first-principles solution to this long-standing problem with the use of the modular approach, a method which rigorously combines a Green function formalism with the density functional theory (DFT) for this particular contact type. The modular approach is a general approach valid for any 3D/2D contact. As an example, we apply it to the most investigated among 3D/2D contacts-metal/graphene contacts-and show its abilities and consistency by comparison with existing experimental data. As it is applicable to any 3D/2D interface, the modular approach allows the engineering of 3D/2D contacts with the pre-defined electrical properties.

Development and comparison in uncertainty assessment based Bayesian modularization method in hydrological modeling

NASA Astrophysics Data System (ADS)

Li, Lu; Xu, Chong-Yu; Engeland, Kolbjørn

2013-04-01

SummaryWith respect to model calibration, parameter estimation and analysis of uncertainty sources, various regression and probabilistic approaches are used in hydrological modeling. A family of Bayesian methods, which incorporates different sources of information into a single analysis through Bayes' theorem, is widely used for uncertainty assessment. However, none of these approaches can well treat the impact of high flows in hydrological modeling. This study proposes a Bayesian modularization uncertainty assessment approach in which the highest streamflow observations are treated as suspect information that should not influence the inference of the main bulk of the model parameters. This study includes a comprehensive comparison and evaluation of uncertainty assessments by our new Bayesian modularization method and standard Bayesian methods using the Metropolis-Hastings (MH) algorithm with the daily hydrological model WASMOD. Three likelihood functions were used in combination with standard Bayesian method: the AR(1) plus Normal model independent of time (Model 1), the AR(1) plus Normal model dependent on time (Model 2) and the AR(1) plus Multi-normal model (Model 3). The results reveal that the Bayesian modularization method provides the most accurate streamflow estimates measured by the Nash-Sutcliffe efficiency and provide the best in uncertainty estimates for low, medium and entire flows compared to standard Bayesian methods. The study thus provides a new approach for reducing the impact of high flows on the discharge uncertainty assessment of hydrological models via Bayesian method.

Challenges in atmospheric monitoring of areal emission sources - an Open-path Fourier transform infrared (OP-FTIR) spectroscopic experience report

NASA Astrophysics Data System (ADS)

Schuetze, C.; Sauer, U.; Dietrich, P.

2015-12-01

Reliable detection and assessment of near-surface CO2 emissions from natural or anthropogenic sources require the application of various monitoring tools at different spatial scales. Especially, optical remote sensing tools for atmospheric monitoring have the potential to measure integrally CO2 emissions over larger scales (> 10.000m2). Within the framework of the MONACO project ("Monitoring approach for geological CO2 storage sites using a hierarchical observation concept"), an integrative hierarchical monitoring concept was developed and validated at different field sites with the aim to establish a modular observation strategy including investigations in the shallow subsurface, at ground surface level and the lower atmospheric boundary layer. The main aims of the atmospheric monitoring using optical remote sensing were the observation of the gas dispersion in to the near-surface atmosphere, the determination of maximum concentration values and identification of the main challenges associated with the monitoring of extended emission sources with the proposed methodological set up under typical environmental conditions. The presentation will give an overview about several case studies using the integrative approach of Open-Path Fourier Transform Infrared spectroscopy (OP FTIR) in combination with in situ measurements. As a main result, the method was validated as possible approach for continuous monitoring of the atmospheric composition, in terms of integral determination of GHG concentrations and to identify target areas which are needed to be investigated more in detail. Especially the data interpretation should closely consider the micrometeorological conditions. Technical aspects concerning robust equipment, experimental set up and fast data processing algorithms have to be taken into account for the enhanced automation of atmospheric monitoring.

A new Bayesian Earthquake Analysis Tool (BEAT)

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

SkyNet: A Modular Nuclear Reaction Network Library

NASA Astrophysics Data System (ADS)

Lippuner, Jonas; Roberts, Luke F.

2017-12-01

Almost all of the elements heavier than hydrogen that are present in our solar system were produced by nuclear burning processes either in the early universe or at some point in the life cycle of stars. In all of these environments, there are dozens to thousands of nuclear species that interact with each other to produce successively heavier elements. In this paper, we present SkyNet, a new general-purpose nuclear reaction network that evolves the abundances of nuclear species under the influence of nuclear reactions. SkyNet can be used to compute the nucleosynthesis evolution in all astrophysical scenarios where nucleosynthesis occurs. SkyNet is free and open source, and aims to be easy to use and flexible. Any list of isotopes can be evolved, and SkyNet supports different types of nuclear reactions. SkyNet is modular so that new or existing physics, like nuclear reactions or equations of state, can easily be added or modified. Here, we present in detail the physics implemented in SkyNet with a focus on a self-consistent transition to and from nuclear statistical equilibrium to non-equilibrium nuclear burning, our implementation of electron screening, and coupling of the network to an equation of state. We also present comprehensive code tests and comparisons with existing nuclear reaction networks. We find that SkyNet agrees with published results and other codes to an accuracy of a few percent. Discrepancies, where they exist, can be traced to differences in the physics implementations.

A Modular IoT Platform for Real-Time Indoor Air Quality Monitoring.

PubMed

Benammar, Mohieddine; Abdaoui, Abderrazak; Ahmad, Sabbir H M; Touati, Farid; Kadri, Abdullah

2018-02-14

The impact of air quality on health and on life comfort is well established. In many societies, vulnerable elderly and young populations spend most of their time indoors. Therefore, indoor air quality monitoring (IAQM) is of great importance to human health. Engineers and researchers are increasingly focusing their efforts on the design of real-time IAQM systems using wireless sensor networks. This paper presents an end-to-end IAQM system enabling measurement of CO₂, CO, SO₂, NO₂, O₃, Cl₂, ambient temperature, and relative humidity. In IAQM systems, remote users usually use a local gateway to connect wireless sensor nodes in a given monitoring site to the external world for ubiquitous access of data. In this work, the role of the gateway in processing collected air quality data and its reliable dissemination to end-users through a web-server is emphasized. A mechanism for the backup and the restoration of the collected data in the case of Internet outage is presented. The system is adapted to an open-source Internet-of-Things (IoT) web-server platform, called Emoncms, for live monitoring and long-term storage of the collected IAQM data. A modular IAQM architecture is adopted, which results in a smart scalable system that allows seamless integration of various sensing technologies, wireless sensor networks (WSNs) and smart mobile standards. The paper gives full hardware and software details of the proposed solution. Sample IAQM results collected in various locations are also presented to demonstrate the abilities of the system.

A Modularized Tablet-Based Approach to Preparation for Remedial Mathematics

ERIC Educational Resources Information Center

Parker, K. Andrew

2016-01-01

Basic arithmetic forms the foundation of the math courses that students will face in their undergraduate careers. It is therefore crucial that students have a solid understanding of these fundamental concepts. At an open-access university offering both two-year and four-year degrees, incoming freshmen who were identified as lacking in basic…

Drupal Done Right

ERIC Educational Resources Information Center

Coombs, Karen

2009-01-01

Drupal is a PHP-and MySQL-based system for managing web sites, developed in 2000 and released in 2001 under the open GNU General Public License (GPL). It is modular, extensible, and scalable. In recent years, Drupal has gained a huge following within libraries as a content management system (CMS). Probably the best-known extension of Drupal in the…

Evaporation mitigation by floating modular devices

NASA Astrophysics Data System (ADS)

Hassan, M. M.; Peirson, W. L.

2016-05-01

Prolonged periods of drought and consequent evaporation from open water bodies in arid parts of Australia continue to be a threat to water availability for agricultural production. Over many parts of Australia, the annual average evaporation exceeds the annual precipitation by more than 5 times. Given its significance, it is surprising that no evaporation mitigation technique has gained widespread adoption to date. High capital and maintenance costs of manufactured products are a significant barrier to implementation. The use of directly recycled clean plastic containers as floating modular devices to mitigate evaporation has been investigated for the first time. A six-month trial at an arid zone site in Australia of this potential cost effective solution has been undertaken. The experiment was performed using clean conventional drinking water bottles as floating modules on the open water surface of 240-L tanks with three varying degrees of covering (nil, 34% and 68%). A systematic reduction in evaporation is demonstrated during the whole study period that is approximately linearly proportional to the covered surface. These results provide a potential foundation for robust evaporation mitigation with the prospect of implementing a cost-optimal design.

An Effective Construction Method of Modular Manipulator 3D Virtual Simulation Platform

NASA Astrophysics Data System (ADS)

Li, Xianhua; Lv, Lei; Sheng, Rui; Sun, Qing; Zhang, Leigang

2018-06-01

This work discusses about a fast and efficient method of constructing an open 3D manipulator virtual simulation platform which make it easier for teachers and students to learn about positive and inverse kinematics of a robot manipulator. The method was carried out using MATLAB. In which, the Robotics Toolbox, MATLAB GUI and 3D animation with the help of modelling using SolidWorks, were fully applied to produce a good visualization of the system. The advantages of using quickly build is its powerful function of the input and output and its ability to simulate a 3D manipulator realistically. In this article, a Schunk six DOF modular manipulator was constructed by the author's research group to be used as example. The implementation steps of this method was detailed described, and thereafter, a high-level open and realistic visualization manipulator 3D virtual simulation platform was achieved. With the graphs obtained from simulation, the test results show that the manipulator 3D virtual simulation platform can be constructed quickly with good usability and high maneuverability, and it can meet the needs of scientific research and teaching.

Network Disruption in the Preclinical Stages of Alzheimer's Disease: From Subjective Cognitive Decline to Mild Cognitive Impairment.

PubMed

López-Sanz, David; Garcés, Pilar; Álvarez, Blanca; Delgado-Losada, María Luisa; López-Higes, Ramón; Maestú, Fernando

2017-12-01

Subjective Cognitive Decline (SCD) is a largely unknown state thought to represent a preclinical stage of Alzheimer's Disease (AD) previous to mild cognitive impairment (MCI). However, the course of network disruption in these stages is scarcely characterized. We employed resting state magnetoencephalography in the source space to calculate network smallworldness, clustering, modularity and transitivity. Nodal measures (clustering and node degree) as well as modular partitions were compared between groups. The MCI group exhibited decreased smallworldness, clustering and transitivity and increased modularity in theta and beta bands. SCD showed similar but smaller changes in clustering and transitivity, while exhibiting alterations in the alpha band in opposite direction to those showed by MCI for modularity and transitivity. At the node level, MCI disrupted both clustering and nodal degree while SCD showed minor changes in the latter. Additionally, we observed an increase in modular partition variability in both SCD and MCI in theta and beta bands. SCD elders exhibit a significant network disruption, showing intermediate values between HC and MCI groups in multiple parameters. These results highlight the relevance of cognitive concerns in the clinical setting and suggest that network disorganization in AD could start in the preclinical stages before the onset of cognitive symptoms.

Characterizing the role benthos plays in large coastal seas and estuaries: A modular approach

USGS Publications Warehouse

Tenore, K.R.; Zajac, R.N.; Terwin, J.; Andrade, F.; Blanton, J.; Boynton, W.; Carey, D.; Diaz, R.; Holland, Austin F.; Lopez-Jamar, E.; Montagna, P.; Nichols, F.; Rosenberg, R.; Queiroga, H.; Sprung, M.; Whitlatch, R.B.

2006-01-01

Ecologists studying coastal and estuarine benthic communities have long taken a macroecological view, by relating benthic community patterns to environmental factors across several spatial scales. Although many general ecological patterns have been established, often a significant amount of the spatial and temporal variation in soft-sediment communities within and among systems remains unexplained. Here we propose a framework that may aid in unraveling the complex influence of environmental factors associated with the different components of coastal systems (i.e. the terrestrial and benthic landscapes, and the hydrological seascape) on benthic communities, and use this information to assess the role played by benthos in coastal ecosystems. A primary component of the approach is the recognition of system modules (e.g. marshes, dendritic systems, tidal rivers, enclosed basins, open bays, lagoons). The modules may differentially interact with key forcing functions (e.g. temperature, salinity, currents) that influence system processes and in turn benthic responses and functions. Modules may also constrain benthic characteristics and related processes within certain ecological boundaries and help explain their overall spatio-temporal variation. We present an example of how benthic community characteristics are related to the modular structure of 14 coastal seas and estuaries, and show that benthic functional group composition is significantly related to the modular structure of these systems. We also propose a framework for exploring the role of benthic communities in coastal systems using this modular approach and offer predictions of how benthic communities may vary depending on the modular composition and characteristics of a coastal system. ?? 2006 Elsevier B.V. All rights reserved.

Conceptual design and thermal analysis of a modular cryostat for one single coil of a 10 MW offshore superconducting wind turbine

NASA Astrophysics Data System (ADS)

Sun, Jiuce; Sanz, Santiago; Neumann, Holger

2015-12-01

Superconducting generators show the potential to reduce the head mass of large offshore wind turbines. A 10 MW offshore superconducting wind turbine has been investigated in the SUPRAPOWER project. The superconducting coils based on MgB2 tapes are supposed to work at cryogenic temperature of 20 K. In this paper, a novel modular rotating cryostat was presented for one single coil of the superconducting wind turbine. The modular concept and cryogen-free cooling method were proposed to fulfil the requirements of handling, maintenance, reliability of long term and offshore operations. Two stage Gifford-McMahon cryocoolers were used to provide cooling source. Supporting rods made of titanium alloy were selected as support structures of the cryostat in aim of reducing the heat load. The thermal performance in the modular cryostat was carefully investigated. The heat load applied to the cryocooler second stage was 2.17 W@20 K per coil. The corresponding temperature difference along the superconducting coil was only around 1 K.

FPGA-based firmware model for extended measurement systems with data quality monitoring

NASA Astrophysics Data System (ADS)

Wojenski, A.; Pozniak, K. T.; Mazon, D.; Chernyshova, M.

2017-08-01

Modern physics experiments requires construction of advanced, modular measurement systems for data processing and registration purposes. Components are often designed in one of the common mechanical and electrical standards, e.g. VME or uTCA. The paper is focused on measurement systems using FPGAs as data processing blocks, especially for plasma diagnostics using GEM detectors with data quality monitoring aspects. In the article is proposed standardized model of HDL FPGA firmware implementation, for use in a wide range of different measurement system. The effort was made in term of flexible implementation of data quality monitoring along with source data dynamic selection. In the paper is discussed standard measurement system model followed by detailed model of FPGA firmware for modular measurement systems. Considered are both: functional blocks and data buses. In the summary, necessary blocks and signal lines are described. Implementation of firmware following the presented rules should provide modular design, with ease of change different parts of it. The key benefit is construction of universal, modular HDL design, that can be applied in different measurement system with simple adjustments.

Integrated System Modeling for Nuclear Thermal Propulsion (NTP)

NASA Technical Reports Server (NTRS)

Ryan, Stephen W.; Borowski, Stanley K.

2014-01-01

Nuclear thermal propulsion (NTP) has long been identified as a key enabling technology for space exploration beyond LEO. From Wernher Von Braun's early concepts for crewed missions to the Moon and Mars to the current Mars Design Reference Architecture (DRA) 5.0 and recent lunar and asteroid mission studies, the high thrust and specific impulse of NTP opens up possibilities such as reusability that are just not feasible with competing approaches. Although NTP technology was proven in the Rover / NERVA projects in the early days of the space program, an integrated spacecraft using NTP has never been developed. Such a spacecraft presents a challenging multidisciplinary systems integration problem. The disciplines that must come together include not only nuclear propulsion and power, but also thermal management, power, structures, orbital dynamics, etc. Some of this integration logic was incorporated into a vehicle sizing code developed at NASA's Glenn Research Center (GRC) in the early 1990s called MOMMA, and later into an Excel-based tool called SIZER. Recently, a team at GRC has developed an open source framework for solving Multidisciplinary Design, Analysis and Optimization (MDAO) problems called OpenMDAO. A modeling approach is presented that builds on previous work in NTP vehicle sizing and mission analysis by making use of the OpenMDAO framework to enable modular and reconfigurable representations of various NTP vehicle configurations and mission scenarios. This approach is currently applied to vehicle sizing, but is extensible to optimization of vehicle and mission designs. The key features of the code will be discussed and examples of NTP transfer vehicles and candidate missions will be presented.

Architecture and Implementation of OpenPET Firmware and Embedded Software

DOE PAGES

Abu-Nimeh, Faisal T.; Ito, Jennifer; Moses, William W.; ...

2016-01-11

OpenPET is an open source, modular, extendible, and high-performance platform suitable for multi-channel data acquisition and analysis. Due to the versatility of the hardware, firmware, and software architectures, the platform is capable of interfacing with a wide variety of detector modules not only in medical imaging but also in homeland security applications. Analog signals from radiation detectors share similar characteristics-a pulse whose area is proportional to the deposited energy and whose leading edge is used to extract a timing signal. As a result, a generic design method of the platform is adopted for the hardware, firmware, and software architectures andmore » implementations. The analog front-end is hosted on a module called a Detector Board, where each board can filter, combine, timestamp, and process multiple channels independently. The processed data is formatted and sent through a backplane bus to a module called Support Board, where 1 Support Board can host up to eight Detector Board modules. The data in the Support Board, coming from 8 Detector Board modules, can be aggregated or correlated (if needed) depending on the algorithm implemented or runtime mode selected. It is then sent out to a computer workstation for further processing. The number of channels (detector modules), to be processed, mandates the overall OpenPET System Configuration, which is designed to handle up to 1,024 channels using 16-channel Detector Boards in the Standard System Configuration and 16,384 channels using 32-channel Detector Boards in the Large System Configuration.« less

Fortified Anonymous Communication Protocol for Location Privacy in WSN: A Modular Approach

PubMed Central

Abuzneid, Abdel-Shakour; Sobh, Tarek; Faezipour, Miad; Mahmood, Ausif; James, John

2015-01-01

Wireless sensor network (WSN) consists of many hosts called sensors. These sensors can sense a phenomenon (motion, temperature, humidity, average, max, min, etc.) and represent what they sense in a form of data. There are many applications for WSNs including object tracking and monitoring where in most of the cases these objects need protection. In these applications, data privacy itself might not be as important as the privacy of source location. In addition to the source location privacy, sink location privacy should also be provided. Providing an efficient end-to-end privacy solution would be a challenging task to achieve due to the open nature of the WSN. The key schemes needed for end-to-end location privacy are anonymity, observability, capture likelihood, and safety period. We extend this work to allow for countermeasures against multi-local and global adversaries. We present a network model protected against a sophisticated threat model: passive /active and local/multi-local/global attacks. This work provides a solution for end-to-end anonymity and location privacy as well. We will introduce a framework called fortified anonymous communication (FAC) protocol for WSN. PMID:25763649

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

PubMed

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

2016-01-01

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

SMART-on-FHIR implemented over i2b2

PubMed Central

Mandel, Joshua C; Klann, Jeffery G; Wattanasin, Nich; Mendis, Michael; Chute, Christopher G; Mandl, Kenneth D; Murphy, Shawn N

2017-01-01

We have developed an interface to serve patient data from Informatics for Integrating Biology and the Bedside (i2b2) repositories in the Fast Healthcare Interoperability Resources (FHIR) format, referred to as a SMART-on-FHIR cell. The cell serves FHIR resources on a per-patient basis, and supports the “substitutable” modular third-party applications (SMART) OAuth2 specification for authorization of client applications. It is implemented as an i2b2 server plug-in, consisting of 6 modules: authentication, REST, i2b2-to-FHIR converter, resource enrichment, query engine, and cache. The source code is freely available as open source. We tested the cell by accessing resources from a test i2b2 installation, demonstrating that a SMART app can be launched from the cell that accesses patient data stored in i2b2. We successfully retrieved demographics, medications, labs, and diagnoses for test patients. The SMART-on-FHIR cell will enable i2b2 sites to provide simplified but secure data access in FHIR format, and will spur innovation and interoperability. Further, it transforms i2b2 into an apps platform. PMID:27274012

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

PubMed Central

Filter, Matthias; Falenski, Alexander; Appel, Bernd; Käsbohrer, Annemarie

2016-01-01

FoodChain-Lab is modular open-source software for trace-back and trace-forward analysis in food-borne disease outbreak investigations. Development of FoodChain-Lab has been driven by a need for appropriate software in several food-related outbreaks in Germany since 2011. The software allows integrated data management, data linkage, enrichment and visualization as well as interactive supply chain analyses. Identification of possible outbreak sources or vehicles is facilitated by calculation of tracing scores for food-handling stations (companies or persons) and food products under investigation. The software also supports consideration of station-specific cross-contamination, analysis of geographical relationships, and topological clustering of the tracing network structure. FoodChain-Lab has been applied successfully in previous outbreak investigations, for example during the 2011 EHEC outbreak and the 2013/14 European hepatitis A outbreak. The software is most useful in complex, multi-area outbreak investigations where epidemiological evidence may be insufficient to discriminate between multiple implicated food products. The automated analysis and visualization components would be of greater value if trading information on food ingredients and compound products was more easily available. PMID:26985673

Associating clinical archetypes through UMLS Metathesaurus term clusters.

PubMed

Lezcano, Leonardo; Sánchez-Alonso, Salvador; Sicilia, Miguel-Angel

2012-06-01

Clinical archetypes are modular definitions of clinical data, expressed using standard or open constraint-based data models as the CEN EN13606 and openEHR. There is an increasing archetype specification activity that raises the need for techniques to associate archetypes to support better management and user navigation in archetype repositories. This paper reports on a computational technique to generate tentative archetype associations by mapping them through term clusters obtained from the UMLS Metathesaurus. The terms are used to build a bipartite graph model and graph connectivity measures can be used for deriving associations.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Individual T1-weighted/T2-weighted ratio brain networks: Small-worldness, hubs and modular organization

NASA Astrophysics Data System (ADS)

Wu, Huijun; Wang, Hao; Lü, Linyuan

Applying network science to investigate the complex systems has become a hot topic. In neuroscience, understanding the architectures of complex brain networks was a vital issue. An enormous amount of evidence had supported the brain was cost/efficiency trade-off with small-worldness, hubness and modular organization through the functional MRI and structural MRI investigations. However, the T1-weighted/T2-weighted (T1w/T2w) ratio brain networks were mostly unexplored. Here, we utilized a KL divergence-based method to construct large-scale individual T1w/T2w ratio brain networks and investigated the underlying topological attributes of these networks. Our results supported that the T1w/T2w ratio brain networks were comprised of small-worldness, an exponentially truncated power-law degree distribution, frontal-parietal hubs and modular organization. Besides, there were significant positive correlations between the network metrics and fluid intelligence. Thus, the T1w/T2w ratio brain networks open a new avenue to understand the human brain and are a necessary supplement for future MRI studies.

Method for hierarchical modeling of the command of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Ausfelder, Christian; Castelain, Emmanuel; Gentina, Jean-Claude

1994-04-01

The present paper focuses on the modeling of the command and proposes a hierarchical and modular approach which is oriented on the physical structure of FMS. The requirements issuing from monitoring of FMS are discussed and integrated in the proposed model. Its modularity makes the approach open for extensions concerning as well the production resources as the products. As a modeling tool, we have chosen Object Petri nets. The first part of the paper describes desirable features of an FMS command such as safety, robustness, and adaptability. As it is shown, these features result from the flexibility of the installation. The modeling method presented in the second part of the paper begins with a structural analysis of FMS and defines a natural command hierarchy, where the coordination of the production process, the synchronization of production resources on products, and the internal coordination are treated separately. The method is rigorous and leads to a structured and modular Petri net model which can be used for FMS simulation or translated into the final command code.

Demonstration of a Small Modular BioPower System Using Poultry Litter

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

John P. Reardon; Art Lilley; Jim Wimberly

2002-05-22

The purpose of this project was to assess poultry grower residue, or litter (manure plus absorbent biomass), as a fuel source for Community Power Corporation's small modular biopower system (SMB). A second objective was to assess the poultry industry to identify potential ''on-site'' applications of the SMB system using poultry litter residue as a fuel source, and to adapt CPC's existing SMB to generate electricity and heat from the poultry litter biomass fuel. Bench-scale testing and pilot testing were used to gain design information for the SMB retrofit. System design approach for the Phase II application of the SMB wasmore » the goal of Phase I testing. Cost estimates for an onsite poultry litter SMB were prepared. Finally, a market estimate was prepared for implementation of the on-farm SMB using poultry litter.« less

Modular neuron-based body estimation: maintaining consistency over different limbs, modalities, and frames of reference

PubMed Central

Ehrenfeld, Stephan; Herbort, Oliver; Butz, Martin V.

2013-01-01

This paper addresses the question of how the brain maintains a probabilistic body state estimate over time from a modeling perspective. The neural Modular Modality Frame (nMMF) model simulates such a body state estimation process by continuously integrating redundant, multimodal body state information sources. The body state estimate itself is distributed over separate, but bidirectionally interacting modules. nMMF compares the incoming sensory and present body state information across the interacting modules and fuses the information sources accordingly. At the same time, nMMF enforces body state estimation consistency across the modules. nMMF is able to detect conflicting sensory information and to consequently decrease the influence of implausible sensor sources on the fly. In contrast to the previously published Modular Modality Frame (MMF) model, nMMF offers a biologically plausible neural implementation based on distributed, probabilistic population codes. Besides its neural plausibility, the neural encoding has the advantage of enabling (a) additional probabilistic information flow across the separate body state estimation modules and (b) the representation of arbitrary probability distributions of a body state. The results show that the neural estimates can detect and decrease the impact of false sensory information, can propagate conflicting information across modules, and can improve overall estimation accuracy due to additional module interactions. Even bodily illusions, such as the rubber hand illusion, can be simulated with nMMF. We conclude with an outlook on the potential of modeling human data and of invoking goal-directed behavioral control. PMID:24191151

A Multimodal Dialog System for Language Assessment: Current State and Future Directions. Research Report. ETS RR-17-21

ERIC Educational Resources Information Center

Suendermann-Oeft, David; Ramanarayanan, Vikram; Yu, Zhou; Qian, Yao; Evanini, Keelan; Lange, Patrick; Wang, Xinhao; Zechner, Klaus

2017-01-01

We present work in progress on a multimodal dialog system for English language assessment using a modular cloud-based architecture adhering to open industry standards. Among the modules being developed for the system, multiple modules heavily exploit machine learning techniques, including speech recognition, spoken language proficiency rating,…

WSTIAC Quarterly, Volume 7, Number 2. Naval Ship and Ship Systems Needs for Early 21st Century

DTIC Science & Technology

2007-01-01

Radar Suite Navy Enterprise Warfare System Affordable Future Fleet 2 Intergrated Scalable Modular Open C4I Common Core B/L’s Command & Combatant Ship...discussed. System constraints, which force trade -offs in sensor design and in ultimate performance, are also covered. Time permitting, a projection of

7 CFR Exhibit B to Subpart A of... - Requirements for Modular/Panelized Housing Units

Code of Federal Regulations, 2010 CFR

2010-01-01

..., log wall houses, trussed roof rafters or floor trusses; open panel walls, and other types that can be... windows or crawl space vents with all sizes indicated. 2. Floor Plans of all levels. Show square footage... levels is required to indicate intended occupancy functions of the design. A window and door schedule...

7 CFR Exhibit B to Subpart A of... - Requirements for Modular/Panelized Housing Units

Code of Federal Regulations, 2011 CFR

2011-01-01

..., log wall houses, trussed roof rafters or floor trusses; open panel walls, and other types that can be... windows or crawl space vents with all sizes indicated. 2. Floor Plans of all levels. Show square footage... levels is required to indicate intended occupancy functions of the design. A window and door schedule...

A phase one AR/C system design

NASA Technical Reports Server (NTRS)

Kachmar, Peter M.; Polutchko, Robert J.; Matusky, Martin; Chu, William; Jackson, William; Montez, Moises

1991-01-01

The Phase One AR&C System Design integrates an evolutionary design based on the legacy of previous mission successes, flight tested components from manned Rendezvous and Proximity Operations (RPO) space programs, and additional AR&C components validated using proven methods. The Phase One system has a modular, open architecture with the standardized interfaces proposed for Space Station Freedom system architecture.

A Modular Approach to Video Designation of Manipulation Targets for Manipulators

DTIC Science & Technology

2014-05-12

side view of a ray going through a point cloud of a water bottle sitting on the ground. The bottom left image shows the same point cloud after it has...System (ROS), Point Cloud Library (PCL), and OpenRAVE were used to a great extent to help promote reusability of the code developed during this

Delivering Advanced Methods in Mathematical Programming to Students of All Disciplines Using Abstraction, Modularity and Open-Ended Assignments

ERIC Educational Resources Information Center

Ezra, Elishai; Nahmias, Yaakov

2015-01-01

The advent of integrated multidisciplinary research has given rise to some of the most important breakthroughs of our time, but has also set significant challenges to the current educational paradigm. Current academic education often limits cross-discipline discussion, depends on close-ended problems, and restricts utilization of interdisciplinary…

The Evolutionary Origins of Hierarchy

PubMed Central

Huizinga, Joost; Clune, Jeff

2016-01-01

Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force–the cost of connections–promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics. PMID:27280881

The Evolutionary Origins of Hierarchy.

PubMed

Mengistu, Henok; Huizinga, Joost; Mouret, Jean-Baptiste; Clune, Jeff

2016-06-01

Hierarchical organization-the recursive composition of sub-modules-is ubiquitous in biological networks, including neural, metabolic, ecological, and genetic regulatory networks, and in human-made systems, such as large organizations and the Internet. To date, most research on hierarchy in networks has been limited to quantifying this property. However, an open, important question in evolutionary biology is why hierarchical organization evolves in the first place. It has recently been shown that modularity evolves because of the presence of a cost for network connections. Here we investigate whether such connection costs also tend to cause a hierarchical organization of such modules. In computational simulations, we find that networks without a connection cost do not evolve to be hierarchical, even when the task has a hierarchical structure. However, with a connection cost, networks evolve to be both modular and hierarchical, and these networks exhibit higher overall performance and evolvability (i.e. faster adaptation to new environments). Additional analyses confirm that hierarchy independently improves adaptability after controlling for modularity. Overall, our results suggest that the same force-the cost of connections-promotes the evolution of both hierarchy and modularity, and that these properties are important drivers of network performance and adaptability. In addition to shedding light on the emergence of hierarchy across the many domains in which it appears, these findings will also accelerate future research into evolving more complex, intelligent computational brains in the fields of artificial intelligence and robotics.

The influence of floral traits on specialization and modularity of plant–pollinator networks in a biodiversity hotspot in the Peruvian Andes

PubMed Central

Watts, Stella; Dormann, Carsten F.; Martín González, Ana M.; Ollerton, Jeff

2016-01-01

Background and Aims Modularity is a ubiquitous and important structural property of ecological networks which describes the relative strengths of sets of interacting species and gives insights into the dynamics of ecological communities. However, this has rarely been studied in species-rich, tropical plant–pollinator networks. Working in a biodiversity hotspot in the Peruvian Andes we assessed the structure of quantitative plant–pollinator networks in nine valleys, quantifying modularity among networks, defining the topological roles of species and the influence of floral traits on specialization. Methods A total of 90 transects were surveyed for plants and pollinators at different altitudes and across different life zones. Quantitative modularity (QuanBiMo) was used to detect modularity and six indices were used to quantify specialization. Key Results All networks were highly structured, moderately specialized and significantly modular regardless of size. The strongest hubs were Baccharis plants, Apis mellifera, Bombus funebris and Diptera spp., which were the most ubiquitous and abundant species with the longest phenologies. Species strength showed a strong association with the modular structure of plant–pollinator networks. Hubs and connectors were the most centralized participants in the networks and were ranked highest (high generalization) when quantifying specialization with most indices. However, complementary specialization d' quantified hubs and connectors as moderately specialized. Specialization and topological roles of species were remarkably constant across some sites, but highly variable in others. Networks were dominated by ecologically and functionally generalist plant species with open access flowers which are closely related taxonomically with similar morphology and rewards. Plants associated with hummingbirds had the highest level of complementary specialization and exclusivity in modules (functional specialists) and the longest corollas. Conclusions We have demonstrated that the topology of networks in this tropical montane environment was non-random and highly organized. Our findings underline that specialization indices convey different concepts of specialization and hence quantify different aspects, and that measuring specialization requires careful consideration of what defines a specialist. PMID:27562649

The influence of floral traits on specialization and modularity of plant-pollinator networks in a biodiversity hotspot in the Peruvian Andes.

PubMed

Watts, Stella; Dormann, Carsten F; Martín González, Ana M; Ollerton, Jeff

2016-09-01

Modularity is a ubiquitous and important structural property of ecological networks which describes the relative strengths of sets of interacting species and gives insights into the dynamics of ecological communities. However, this has rarely been studied in species-rich, tropical plant-pollinator networks. Working in a biodiversity hotspot in the Peruvian Andes we assessed the structure of quantitative plant-pollinator networks in nine valleys, quantifying modularity among networks, defining the topological roles of species and the influence of floral traits on specialization. A total of 90 transects were surveyed for plants and pollinators at different altitudes and across different life zones. Quantitative modularity (QuanBiMo) was used to detect modularity and six indices were used to quantify specialization. All networks were highly structured, moderately specialized and significantly modular regardless of size. The strongest hubs were Baccharis plants, Apis mellifera, Bombus funebris and Diptera spp., which were the most ubiquitous and abundant species with the longest phenologies. Species strength showed a strong association with the modular structure of plant-pollinator networks. Hubs and connectors were the most centralized participants in the networks and were ranked highest (high generalization) when quantifying specialization with most indices. However, complementary specialization d' quantified hubs and connectors as moderately specialized. Specialization and topological roles of species were remarkably constant across some sites, but highly variable in others. Networks were dominated by ecologically and functionally generalist plant species with open access flowers which are closely related taxonomically with similar morphology and rewards. Plants associated with hummingbirds had the highest level of complementary specialization and exclusivity in modules (functional specialists) and the longest corollas. We have demonstrated that the topology of networks in this tropical montane environment was non-random and highly organized. Our findings underline that specialization indices convey different concepts of specialization and hence quantify different aspects, and that measuring specialization requires careful consideration of what defines a specialist. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

Donnelly, William; Wong, Gabriel

What is the meaning of entanglement in a theory of extended objects such as strings? To address this question we consider the spatial entanglement between two intervals in the Gross-Taylor model, the string theory dual to two-dimensional Yang-Mills theory at large N. The string diagrams that contribute to the entanglement entropy describe open strings with endpoints anchored to the entangling surface, as first argued by Susskind. We develop a canonical theory of these open strings, and describe how closed strings are divided into open strings at the level of the Hilbert space. Here, we derive the modular Hamiltonian for themore » Hartle-Hawking state and show that the corresponding reduced density matrix describes a thermal ensemble of open strings ending on an object at the entangling surface that we call an entanglement brane, or E-brane.« less

Mining the modular structure of protein interaction networks.

PubMed

Berenstein, Ariel José; Piñero, Janet; Furlong, Laura Inés; Chernomoretz, Ariel

2015-01-01

Cluster-based descriptions of biological networks have received much attention in recent years fostered by accumulated evidence of the existence of meaningful correlations between topological network clusters and biological functional modules. Several well-performing clustering algorithms exist to infer topological network partitions. However, due to respective technical idiosyncrasies they might produce dissimilar modular decompositions of a given network. In this contribution, we aimed to analyze how alternative modular descriptions could condition the outcome of follow-up network biology analysis. We considered a human protein interaction network and two paradigmatic cluster recognition algorithms, namely: the Clauset-Newman-Moore and the infomap procedures. We analyzed to what extent both methodologies yielded different results in terms of granularity and biological congruency. In addition, taking into account Guimera's cartographic role characterization of network nodes, we explored how the adoption of a given clustering methodology impinged on the ability to highlight relevant network meso-scale connectivity patterns. As a case study we considered a set of aging related proteins and showed that only the high-resolution modular description provided by infomap, could unveil statistically significant associations between them and inter/intra modular cartographic features. Besides reporting novel biological insights that could be gained from the discovered associations, our contribution warns against possible technical concerns that might affect the tools used to mine for interaction patterns in network biology studies. In particular our results suggested that sub-optimal partitions from the strict point of view of their modularity levels might still be worth being analyzed when meso-scale features were to be explored in connection with external source of biological knowledge.

SIGNUM: A Matlab, TIN-based landscape evolution model

NASA Astrophysics Data System (ADS)

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

2012-08-01

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

Modular chemiresistive sensor

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

Alam, Maksudul M.; Sampathkumaran, Uma

The present invention relates to a modular chemiresistive sensor. In particular, a modular chemiresistive sensor for hypergolic fuel and oxidizer leak detection, carbon dioxide monitoring and detection of disease biomarkers. The sensor preferably has two gold or platinum electrodes mounted on a silicon substrate where the electrodes are connected to a power source and are separated by a gap of 0.5 to 4.0 .mu.M. A polymer nanowire or carbon nanotube spans the gap between the electrodes and connects the electrodes electrically. The electrodes are further connected to a circuit board having a processor and data storage, where the processor canmore » measure current and voltage values between the electrodes and compare the current and voltage values with current and voltage values stored in the data storage and assigned to particular concentrations of a pre-determined substance such as those listed above or a variety of other substances.« less

The Open Source Snowpack modelling ecosystem

NASA Astrophysics Data System (ADS)

Bavay, Mathias; Fierz, Charles; Egger, Thomas; Lehning, Michael

2016-04-01

As a large number of numerical snow models are available, a few stand out as quite mature and widespread. One such model is SNOWPACK, the Open Source model that is developed at the WSL Institute for Snow and Avalanche Research SLF. Over the years, various tools have been developed around SNOWPACK in order to expand its use or to integrate additional features. Today, the model is part of a whole ecosystem that has evolved to both offer seamless integration and high modularity so each tool can easily be used outside the ecosystem. Many of these Open Source tools experience their own, autonomous development and are successfully used in their own right in other models and applications. There is Alpine3D, the spatially distributed version of SNOWPACK, that forces it with terrain-corrected radiation fields and optionally with blowing and drifting snow. This model can be used on parallel systems (either with OpenMP or MPI) and has been used for applications ranging from climate change to reindeer herding. There is the MeteoIO pre-processing library that offers fully integrated data access, data filtering, data correction, data resampling and spatial interpolations. This library is now used by several other models and applications. There is the SnopViz snow profile visualization library and application that supports both measured and simulated snow profiles (relying on the CAAML standard) as well as time series. This JavaScript application can be used standalone without any internet connection or served on the web together with simulation results. There is the OSPER data platform effort with a data management service (build on the Global Sensor Network (GSN) platform) as well as a data documenting system (metadata management as a wiki). There are several distributed hydrological models for mountainous areas in ongoing development that require very little information about the soil structure based on the assumption that in step terrain, the most relevant information is contained in the Digital Elevation Model (DEM). There is finally a set of tools making up the operational chain to automatically run, monitor and publish SNOWPACK simulations for operational avalanche warning purposes. This tool chain has been developed with the aim of offering very low maintenance operation and very fast deployment and to easily adapt to other avalanche services.

Porting plasma physics simulation codes to modern computing architectures using the libmrc framework

NASA Astrophysics Data System (ADS)

Germaschewski, Kai; Abbott, Stephen

2015-11-01

Available computing power has continued to grow exponentially even after single-core performance satured in the last decade. The increase has since been driven by more parallelism, both using more cores and having more parallelism in each core, e.g. in GPUs and Intel Xeon Phi. Adapting existing plasma physics codes is challenging, in particular as there is no single programming model that covers current and future architectures. We will introduce the open-source libmrc framework that has been used to modularize and port three plasma physics codes: The extended MHD code MRCv3 with implicit time integration and curvilinear grids; the OpenGGCM global magnetosphere model; and the particle-in-cell code PSC. libmrc consolidates basic functionality needed for simulations based on structured grids (I/O, load balancing, time integrators), and also introduces a parallel object model that makes it possible to maintain multiple implementations of computational kernels, on e.g. conventional processors and GPUs. It handles data layout conversions and enables us to port performance-critical parts of a code to a new architecture step-by-step, while the rest of the code can remain unchanged. We will show examples of the performance gains and some physics applications.

Two- and three-dimensional natural and mixed convection simulation using modular zonal models

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

Wurtz, E.; Nataf, J.M.; Winkelmann, F.

We demonstrate the use of the zonal model approach, which is a simplified method for calculating natural and mixed convection in rooms. Zonal models use a coarse grid and use balance equations, state equations, hydrostatic pressure drop equations and power law equations of the form {ital m} = {ital C}{Delta}{sup {ital n}}. The advantage of the zonal approach and its modular implementation are discussed. The zonal model resolution of nonlinear equation systems is demonstrated for three cases: a 2-D room, a 3-D room and a pair of 3-D rooms separated by a partition with an opening. A sensitivity analysis withmore » respect to physical parameters and grid coarseness is presented. Results are compared to computational fluid dynamics (CFD) calculations and experimental data.« less

Network community structure and loop coefficient method

NASA Astrophysics Data System (ADS)

Vragović, I.; Louis, E.

2006-07-01

A modular structure, in which groups of tightly connected nodes could be resolved as separate entities, is a property that can be found in many complex networks. In this paper, we propose a algorithm for identifying communities in networks. It is based on a local measure, so-called loop coefficient that is a generalization of the clustering coefficient. Nodes with a large loop coefficient tend to be core inner community nodes, while other vertices are usually peripheral sites at the borders of communities. Our method gives satisfactory results for both artificial and real-world graphs, if they have a relatively pronounced modular structure. This type of algorithm could open a way of interpreting the role of nodes in communities in terms of the local loop coefficient, and could be used as a complement to other methods.

Discovering perturbation of modular structure in HIV progression by integrating multiple data sources through non-negative matrix factorization.

PubMed

Ray, Sumanta; Maulik, Ujjwal

2016-12-20

Detecting perturbation in modular structure during HIV-1 disease progression is an important step to understand stage specific infection pattern of HIV-1 virus in human cell. In this article, we proposed a novel methodology on integration of multiple biological information to identify such disruption in human gene module during different stages of HIV-1 infection. We integrate three different biological information: gene expression information, protein-protein interaction information and gene ontology information in single gene meta-module, through non negative matrix factorization (NMF). As the identified metamodules inherit those information so, detecting perturbation of these, reflects the changes in expression pattern, in PPI structure and in functional similarity of genes during the infection progression. To integrate modules of different data sources into strong meta-modules, NMF based clustering is utilized here. Perturbation in meta-modular structure is identified by investigating the topological and intramodular properties and putting rank to those meta-modules using a rank aggregation algorithm. We have also analyzed the preservation structure of significant GO terms in which the human proteins of the meta-modules participate. Moreover, we have performed an analysis to show the change of coregulation pattern of identified transcription factors (TFs) over the HIV progression stages.

Modular Approaches to Earth Science Scientific Computing: 3D Electromagnetic Induction Modeling as an Example

NASA Astrophysics Data System (ADS)

Tandon, K.; Egbert, G.; Siripunvaraporn, W.

2003-12-01

We are developing a modular system for three-dimensional inversion of electromagnetic (EM) induction data, using an object oriented programming approach. This approach allows us to modify the individual components of the inversion scheme proposed, and also reuse the components for variety of problems in earth science computing howsoever diverse they might be. In particular, the modularity allows us to (a) change modeling codes independently of inversion algorithm details; (b) experiment with new inversion algorithms; and (c) modify the way prior information is imposed in the inversion to test competing hypothesis and techniques required to solve an earth science problem. Our initial code development is for EM induction equations on a staggered grid, using iterative solution techniques in 3D. An example illustrated here is an experiment with the sensitivity of 3D magnetotelluric inversion to uncertainties in the boundary conditions required for regional induction problems. These boundary conditions should reflect the large-scale geoelectric structure of the study area, which is usually poorly constrained. In general for inversion of MT data, one fixes boundary conditions at the edge of the model domain, and adjusts the earth?s conductivity structure within the modeling domain. Allowing for errors in specification of the open boundary values is simple in principle, but no existing inversion codes that we are aware of have this feature. Adding a feature such as this is straightforward within the context of the modular approach. More generally, a modular approach provides an efficient methodology for setting up earth science computing problems to test various ideas. As a concrete illustration relevant to EM induction problems, we investigate the sensitivity of MT data near San Andreas Fault at Parkfield (California) to uncertainties in the regional geoelectric structure.

Distance education course on spatial multi-hazard risk assessment, using Open Source software

NASA Astrophysics Data System (ADS)

van Westen, C. J.; Frigerio, S.

2009-04-01

As part of the capacity building activities of the United Nations University - ITC School on Disaster Geo-Information Management (UNU-ITC DGIM) the International Institute for Geoinformation Science and Earth Observation (ITC) has developed a distance education course on the application of Geographic Information Systems for multi-hazard risk assessment. This course is designed for academic staff, as well as for professionals working in (non-) governmental organizations where knowledge of disaster risk management is essential. The course guides the participants through the entire process of risk assessment, on the basis of a case study of a city exposed to multiple hazards, in a developing country. The courses consists of eight modules, each with a guide book explaining the theoretical background, and guiding the participants through spatial data requirements for risk assessment, hazard assessment procedures, generation of elements at risk databases, vulnerability assessment, qualitative and quantitative risk assessment methods, risk evaluation and risk reduction. Linked to the theory is a large set of exercises, with exercise descriptions, answer sheets, demos and GIS data. The exercises deal with four different types of hazards: earthquakes, flooding, technological hazards, and landslides. One important consideration in designing the course is that people from developing countries should not be restricted in using it due to financial burdens for software acquisition. Therefore the aim was to use Open Source software as a basis. The GIS exercises are written for the ILWIS software. All exercises have also been integrated into a WebGIS, using the Open source software CartoWeb (based on GNU License). It is modular and customizable thanks to its object-oriented architecture and based on a hierarchical structure (to manage and organize every package of information of every step required in risk assessment). Different switches for every component of the risk assessment course have been defined and through various menus the user can define the options for every exercise. For every layer of information tools for querying, printing, searching and surface analysis are implemented, allowing the option to compare maps at different scale and for on-line interpretations.

Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): architecture.

PubMed

Mandl, Kenneth D; Kohane, Isaac S; McFadden, Douglas; Weber, Griffin M; Natter, Marc; Mandel, Joshua; Schneeweiss, Sebastian; Weiler, Sarah; Klann, Jeffrey G; Bickel, Jonathan; Adams, William G; Ge, Yaorong; Zhou, Xiaobo; Perkins, James; Marsolo, Keith; Bernstam, Elmer; Showalter, John; Quarshie, Alexander; Ofili, Elizabeth; Hripcsak, George; Murphy, Shawn N

2014-01-01

We describe the architecture of the Patient Centered Outcomes Research Institute (PCORI) funded Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS, http://www.SCILHS.org) clinical data research network, which leverages the $48 billion dollar federal investment in health information technology (IT) to enable a queryable semantic data model across 10 health systems covering more than 8 million patients, plugging universally into the point of care, generating evidence and discovery, and thereby enabling clinician and patient participation in research during the patient encounter. Central to the success of SCILHS is development of innovative 'apps' to improve PCOR research methods and capacitate point of care functions such as consent, enrollment, randomization, and outreach for patient-reported outcomes. SCILHS adapts and extends an existing national research network formed on an advanced IT infrastructure built with open source, free, modular components. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

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

NASA Astrophysics Data System (ADS)

Gerard-Marchant, P. G.

2008-12-01

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

JDFTx: Software for joint density-functional theory

DOE PAGES

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.; ...

2017-11-14

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

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

PubMed Central

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

2017-01-01

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

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

PubMed

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

2017-01-01

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

Experimental research control software system

NASA Astrophysics Data System (ADS)

Cohn, I. A.; Kovalenko, A. G.; Vystavkin, A. N.

2014-05-01

A software system, intended for automation of a small scale research, has been developed. The software allows one to control equipment, acquire and process data by means of simple scripts. The main purpose of that development is to increase experiment automation easiness, thus significantly reducing experimental setup automation efforts. In particular, minimal programming skills are required and supervisors have no reviewing troubles. Interactions between scripts and equipment are managed automatically, thus allowing to run multiple scripts simultaneously. Unlike well-known data acquisition commercial software systems, the control is performed by an imperative scripting language. This approach eases complex control and data acquisition algorithms implementation. A modular interface library performs interaction with external interfaces. While most widely used interfaces are already implemented, a simple framework is developed for fast implementations of new software and hardware interfaces. While the software is in continuous development with new features being implemented, it is already used in our laboratory for automation of a helium-3 cryostat control and data acquisition. The software is open source and distributed under Gnu Public License.

JDFTx: Software for joint density-functional theory

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

Sundararaman, Ravishankar; Letchworth-Weaver, Kendra; Schwarz, Kathleen A.

Density-functional theory (DFT) has revolutionized computational prediction of atomic-scale properties from first principles in physics, chemistry and materials science. Continuing development of new methods is necessary for accurate predictions of new classes of materials and properties, and for connecting to nano- and mesoscale properties using coarse-grained theories. JDFTx is a fully-featured open-source electronic DFT software designed specifically to facilitate rapid development of new theories, models and algorithms. Using an algebraic formulation as an abstraction layer, compact C++11 code automatically performs well on diverse hardware including GPUs (Graphics Processing Units). This code hosts the development of joint density-functional theory (JDFT) thatmore » combines electronic DFT with classical DFT and continuum models of liquids for first-principles calculations of solvated and electrochemical systems. In addition, the modular nature of the code makes it easy to extend and interface with, facilitating the development of multi-scale toolkits that connect to ab initio calculations, e.g. photo-excited carrier dynamics combining electron and phonon calculations with electromagnetic simulations.« less

Science yield modeling with the Exoplanet Open-Source Imaging Mission Simulator (EXOSIMS)

NASA Astrophysics Data System (ADS)

Delacroix, Christian; Savransky, Dmitry; Garrett, Daniel; Lowrance, Patrick; Morgan, Rhonda

2016-08-01

We report on our ongoing development of EXOSIMS and mission simulation results for WFIRST. We present the interface control and the modular structure of the software, along with corresponding prototypes and class definitions for some of the software modules. More specifically, we focus on describing the main steps of our high-fidelity mission simulator EXOSIMS, i.e., the completeness, optical system and zodiacal light modules definition, the target list module filtering, and the creation of a planet population within our simulated universe module. For the latter, we introduce the integration of a recent mass-radius model from the FORECASTER software. We also provide custom modules dedicated to WFIRST using both the Hybrid Lyot Coronagraph (HLC) and the Shaped Pupil Coronagraph (SPC) for detection and characterization, respectively. In that context, we show and discuss the results of some preliminary WFIRST simulations, focusing on comparing different methods of integration time calculation, through ensembles (large numbers) of survey simulations.

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

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

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

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

Designing and Implementing a Computational Methods Course for Upper-level Undergraduates and Postgraduates in Atmospheric and Oceanic Sciences

NASA Astrophysics Data System (ADS)

Nelson, E.; L'Ecuyer, T. S.; Douglas, A.; Hansen, Z.

2017-12-01

In the modern computing age, scientists must utilize a wide variety of skills to carry out scientific research. Programming, including a focus on collaborative development, has become more prevalent in both academic and professional career paths. Faculty in the Department of Atmospheric and Oceanic Sciences at the University of Wisconsin—Madison recognized this need and recently approved a new course offering for undergraduates and postgraduates in computational methods that was first held in Spring 2017. Three programming languages were covered in the inaugural course semester and development themes such as modularization, data wrangling, and conceptual code models were woven into all of the sections. In this presentation, we will share successes and challenges in developing a research project-focused computational course that leverages hands-on computer laboratory learning and open-sourced course content. Improvements and changes in future iterations of the course based on the first offering will also be discussed.

PLUMED 2: New feathers for an old bird

NASA Astrophysics Data System (ADS)

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

2014-02-01

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

3D-Lab: a collaborative web-based platform for molecular modeling.

PubMed

Grebner, Christoph; Norrby, Magnus; Enström, Jonatan; Nilsson, Ingemar; Hogner, Anders; Henriksson, Jonas; Westin, Johan; Faramarzi, Farzad; Werner, Philip; Boström, Jonas

2016-09-01

The use of 3D information has shown impact in numerous applications in drug design. However, it is often under-utilized and traditionally limited to specialists. We want to change that, and present an approach making 3D information and molecular modeling accessible and easy-to-use 'for the people'. A user-friendly and collaborative web-based platform (3D-Lab) for 3D modeling, including a blazingly fast virtual screening capability, was developed. 3D-Lab provides an interface to automatic molecular modeling, like conformer generation, ligand alignments, molecular dockings and simple quantum chemistry protocols. 3D-Lab is designed to be modular, and to facilitate sharing of 3D-information to promote interactions between drug designers. Recent enhancements to our open-source virtual reality tool Molecular Rift are described. The integrated drug-design platform allows drug designers to instantaneously access 3D information and readily apply advanced and automated 3D molecular modeling tasks, with the aim to improve decision-making in drug design projects.

Inselect: Automating the Digitization of Natural History Collections

PubMed Central

Hudson, Lawrence N.; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W.; van der Walt, Stéfan; Smith, Vincent S.

2015-01-01

The world’s natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect—a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization. PMID:26599208

Inselect: Automating the Digitization of Natural History Collections.

PubMed

Hudson, Lawrence N; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W; van der Walt, Stéfan; Smith, Vincent S

2015-01-01

The world's natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect-a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization.

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

DOE PAGES

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

2017-12-01

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

The development of a learning management system for dental radiology education: A technical report.

PubMed

Chang, Hee-Jin; Symkhampha, Khanthaly; Huh, Kyung-Hoe; Yi, Won-Jin; Heo, Min-Suk; Lee, Sam-Sun; Choi, Soon-Chul

2017-03-01

This study was conducted to suggest the development of a learning management system for dental radiology education using the Modular Object-Oriented Dynamic Learning Environment (Moodle). Moodle is a well-known and verified open-source software-learning management system (OSS-LMS). The Moodle software was installed on a server computer and customized for dental radiology education. The system was implemented for teaching undergraduate students to diagnose dental caries in panoramic images. Questions were chosen that could assess students' diagnosis ability. Students were given several questions corre-sponding to each of 100 panoramic images. The installation and customization of Moodle was feasible, cost-effective, and time-saving. By having students answer questions repeatedly, it was possible to train them to examine panoramic images sequentially and thoroughly. Based on its educational efficiency and efficacy, the adaptation of an OSS-LMS in dental school may be highly recommended. The system could be extended to continuing education for dentists. Further studies on the objective evaluation of knowledge acquisition and retention are needed.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

A Modular IoT Platform for Real-Time Indoor Air Quality Monitoring

PubMed Central

Abdaoui, Abderrazak; Ahmad, Sabbir H.M.; Touati, Farid; Kadri, Abdullah

2018-01-01

The impact of air quality on health and on life comfort is well established. In many societies, vulnerable elderly and young populations spend most of their time indoors. Therefore, indoor air quality monitoring (IAQM) is of great importance to human health. Engineers and researchers are increasingly focusing their efforts on the design of real-time IAQM systems using wireless sensor networks. This paper presents an end-to-end IAQM system enabling measurement of CO2, CO, SO2, NO2, O3, Cl2, ambient temperature, and relative humidity. In IAQM systems, remote users usually use a local gateway to connect wireless sensor nodes in a given monitoring site to the external world for ubiquitous access of data. In this work, the role of the gateway in processing collected air quality data and its reliable dissemination to end-users through a web-server is emphasized. A mechanism for the backup and the restoration of the collected data in the case of Internet outage is presented. The system is adapted to an open-source Internet-of-Things (IoT) web-server platform, called Emoncms, for live monitoring and long-term storage of the collected IAQM data. A modular IAQM architecture is adopted, which results in a smart scalable system that allows seamless integration of various sensing technologies, wireless sensor networks (WSNs) and smart mobile standards. The paper gives full hardware and software details of the proposed solution. Sample IAQM results collected in various locations are also presented to demonstrate the abilities of the system. PMID:29443893

The Dichotomy in Degree Correlation of Biological Networks

PubMed Central

Hao, Dapeng; Li, Chuanxing

2011-01-01

Most complex networks from different areas such as biology, sociology or technology, show a correlation on node degree where the possibility of a link between two nodes depends on their connectivity. It is widely believed that complex networks are either disassortative (links between hubs are systematically suppressed) or assortative (links between hubs are enhanced). In this paper, we analyze a variety of biological networks and find that they generally show a dichotomous degree correlation. We find that many properties of biological networks can be explained by this dichotomy in degree correlation, including the neighborhood connectivity, the sickle-shaped clustering coefficient distribution and the modularity structure. This dichotomy distinguishes biological networks from real disassortative networks or assortative networks such as the Internet and social networks. We suggest that the modular structure of networks accounts for the dichotomy in degree correlation and vice versa, shedding light on the source of modularity in biological networks. We further show that a robust and well connected network necessitates the dichotomy of degree correlation, suggestive of an evolutionary motivation for its existence. Finally, we suggest that a dichotomous degree correlation favors a centrally connected modular network, by which the integrity of network and specificity of modules might be reconciled. PMID:22164269

Virtual Labs (Science Gateways) as platforms for Free and Open Source Science

NASA Astrophysics Data System (ADS)

Lescinsky, David; Car, Nicholas; Fraser, Ryan; Friedrich, Carsten; Kemp, Carina; Squire, Geoffrey

2016-04-01

The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the NCI National Environmental Research Data Interoperability Platform), or by uploading data directly from user supplied addresses or files. Similarly, scientific software is accessed through registries pointing to software repositories (e.g., GitHub). Runs are configured by using or modifying default templates designed by subject matter experts. After the appropriate computational resources are identified by the user, Virtual Machines (VMs) are spun up and jobs are submitted to service providers (currently the NeCTAR public cloud or Amazon Web Services). Following completion of the jobs the results can be reviewed and downloaded if desired. By providing a unified platform for science, the VL infrastructure enables sophisticated provenance capture and management. The source of input data (including both collection and queries), user information, software information (version and configuration details) and output information are all captured and managed as a VL resource which can be linked to output data sets. This provenance resource provides a mechanism for publication and citation for Free and Open Source Science.

Simulating Operation of a Large Turbofan Engine

NASA Technical Reports Server (NTRS)

Litt, Jonathan S.; Frederick, Dean K.; DeCastro, Jonathan

2008-01-01

The Commercial Modular Aero- Propulsion System Simulation (C-MAPSS) is a computer program for simulating transient operation of a commercial turbofan engine that can generate as much as 90,000 lb (.0.4 MN) of thrust. It includes a power-management system that enables simulation of open- or closed-loop engine operation over a wide range of thrust levels throughout the full range of flight conditions. C-MAPSS provides the user with a set of tools for performing open- and closed-loop transient simulations and comparison of linear and non-linear models throughout its operating envelope, in an easy-to-use graphical environment.

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

Sankaran, R.; Jacob, R. L.; Beckman, P. H.; Catlett, C. E.; Keahey, K.

2014-12-01

Advances in sensor-driven computation and computationally steered sensing will greatly enable future research in fields including environmental and atmospheric sciences. We will present "Waggle," an open-source hardware and software infrastructure developed with two goals: (1) reducing the separation and latency between sensing and computing and (2) improving the reliability and longevity of sensing-actuation platforms in challenging and costly deployments. Inspired by "deep-space probe" systems, the Waggle platform design includes features that can support longitudinal studies, deployments with varying communication links, and remote management capabilities. Waggle lowers the barrier for scientists to incorporate real-time data from their sensors into their computations and to manipulate the sensors or provide feedback through actuators. A standardized software and hardware design allows quick addition of new sensors/actuators and associated software in the nodes and enables them to be coupled with computational codes both insitu and on external compute infrastructure. The Waggle framework currently drives the deployment of two observational systems - a portable and self-sufficient weather platform for study of small-scale effects in Chicago's urban core and an open-ended distributed instrument in Chicago that aims to support several research pursuits across a broad range of disciplines including urban planning, microbiology and computer science. Built around open-source software, hardware, and Linux OS, the Waggle system comprises two components - the Waggle field-node and Waggle cloud-computing infrastructure. Waggle field-node affords a modular, scalable, fault-tolerant, secure, and extensible platform for hosting sensors and actuators in the field. It supports insitu computation and data storage, and integration with cloud-computing infrastructure. The Waggle cloud infrastructure is designed with the goal of scaling to several hundreds of thousands of Waggle nodes. It supports aggregating data from sensors hosted by the nodes, staging computation, relaying feedback to the nodes and serving data to end-users. We will discuss the Waggle design principles and their applicability to various observational research pursuits, and demonstrate its capabilities.

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

NASA Astrophysics Data System (ADS)

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

2014-12-01

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

MODULAR MANIPULATOR FOR ROBOTICS APPLICATIONS

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

Joseph W. Geisinger, Ph.D.

ARM Automation, Inc. is developing a framework of modular actuators that can address the DOE's wide range of robotics needs. The objective of this effort is to demonstrate the effectiveness of this technology by constructing a manipulator from these actuators within a glovebox for Automated Plutonium Processing (APP). At the end of the project, the system of actuators was used to construct several different manipulator configurations, which accommodate common glovebox tasks such as repackaging. The modular nature and quickconnects of this system simplify installation into ''hot'' boxes and any potential modifications or repair therein. This work focused on the developmentmore » of self-contained robotic actuator modules including the embedded electronic controls for the purpose of building a manipulator system. Both of the actuators developed under this project contain the control electronics, sensors, motor, gear train, wiring, system communications and mechanical interfaces of a complete robotics servo device. Test actuators and accompanying DISC{trademark}s underwent validation testing at The University of Texas at Austin and ARM Automation, Inc. following final design and fabrication. The system also included custom links, an umbilical cord, an open architecture PC-based system controller, and operational software that permitted integration into a completely functional robotic manipulator system. The open architecture on which this system is based avoids proprietary interfaces and communication protocols which only serve to limit the capabilities and flexibility of automation equipment. The system was integrated and tested in the contractor's facility for intended performance and operations. The manipulator was tested using the full-scale equipment and process mock-ups. The project produced a practical and operational system including a quantitative evaluation of its performance and cost.« less

Exploratory Application of Augmented Reality/Mixed Reality Devices for Acute Care Procedure Training.

PubMed

Kobayashi, Leo; Zhang, Xiao Chi; Collins, Scott A; Karim, Naz; Merck, Derek L

2018-01-01

Augmented reality (AR), mixed reality (MR), and virtual reality devices are enabling technologies that may facilitate effective communication in healthcare between those with information and knowledge (clinician/specialist; expert; educator) and those seeking understanding and insight (patient/family; non-expert; learner). Investigators initiated an exploratory program to enable the study of AR/MR use-cases in acute care clinical and instructional settings. Academic clinician educators, computer scientists, and diagnostic imaging specialists conducted a proof-of-concept project to 1) implement a core holoimaging pipeline infrastructure and open-access repository at the study institution, and 2) use novel AR/MR techniques on off-the-shelf devices with holoimages generated by the infrastructure to demonstrate their potential role in the instructive communication of complex medical information. The study team successfully developed a medical holoimaging infrastructure methodology to identify, retrieve, and manipulate real patients' de-identified computed tomography and magnetic resonance imagesets for rendering, packaging, transfer, and display of modular holoimages onto AR/MR headset devices and connected displays. Holoimages containing key segmentations of cervical and thoracic anatomic structures and pathology were overlaid and registered onto physical task trainers for simulation-based "blind insertion" invasive procedural training. During the session, learners experienced and used task-relevant anatomic holoimages for central venous catheter and tube thoracostomy insertion training with enhanced visual cues and haptic feedback. Direct instructor access into the learner's AR/MR headset view of the task trainer was achieved for visual-axis interactive instructional guidance. Investigators implemented a core holoimaging pipeline infrastructure and modular open-access repository to generate and enable access to modular holoimages during exploratory pilot stage applications for invasive procedure training that featured innovative AR/MR techniques on off-the-shelf headset devices.

Exploratory Application of Augmented Reality/Mixed Reality Devices for Acute Care Procedure Training

PubMed Central

Kobayashi, Leo; Zhang, Xiao Chi; Collins, Scott A.; Karim, Naz; Merck, Derek L.

2018-01-01

Introduction Augmented reality (AR), mixed reality (MR), and virtual reality devices are enabling technologies that may facilitate effective communication in healthcare between those with information and knowledge (clinician/specialist; expert; educator) and those seeking understanding and insight (patient/family; non-expert; learner). Investigators initiated an exploratory program to enable the study of AR/MR use-cases in acute care clinical and instructional settings. Methods Academic clinician educators, computer scientists, and diagnostic imaging specialists conducted a proof-of-concept project to 1) implement a core holoimaging pipeline infrastructure and open-access repository at the study institution, and 2) use novel AR/MR techniques on off-the-shelf devices with holoimages generated by the infrastructure to demonstrate their potential role in the instructive communication of complex medical information. Results The study team successfully developed a medical holoimaging infrastructure methodology to identify, retrieve, and manipulate real patients’ de-identified computed tomography and magnetic resonance imagesets for rendering, packaging, transfer, and display of modular holoimages onto AR/MR headset devices and connected displays. Holoimages containing key segmentations of cervical and thoracic anatomic structures and pathology were overlaid and registered onto physical task trainers for simulation-based “blind insertion” invasive procedural training. During the session, learners experienced and used task-relevant anatomic holoimages for central venous catheter and tube thoracostomy insertion training with enhanced visual cues and haptic feedback. Direct instructor access into the learner’s AR/MR headset view of the task trainer was achieved for visual-axis interactive instructional guidance. Conclusion Investigators implemented a core holoimaging pipeline infrastructure and modular open-access repository to generate and enable access to modular holoimages during exploratory pilot stage applications for invasive procedure training that featured innovative AR/MR techniques on off-the-shelf headset devices. PMID:29383074

Modularity and evolutionary constraints in a baculovirus gene regulatory network

PubMed Central

2013-01-01

Background The structure of regulatory networks remains an open question in our understanding of complex biological systems. Interactions during complete viral life cycles present unique opportunities to understand how host-parasite network take shape and behave. The Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is a large double-stranded DNA virus, whose genome may encode for 152 open reading frames (ORFs). Here we present the analysis of the ordered cascade of the AgMNPV gene expression. Results We observed an earlier onset of the expression than previously reported for other baculoviruses, especially for genes involved in DNA replication. Most ORFs were expressed at higher levels in a more permissive host cell line. Genes with more than one copy in the genome had distinct expression profiles, which could indicate the acquisition of new functionalities. The transcription gene regulatory network (GRN) for 149 ORFs had a modular topology comprising five communities of highly interconnected nodes that separated key genes that are functionally related on different communities, possibly maximizing redundancy and GRN robustness by compartmentalization of important functions. Core conserved functions showed expression synchronicity, distinct GRN features and significantly less genetic diversity, consistent with evolutionary constraints imposed in key elements of biological systems. This reduced genetic diversity also had a positive correlation with the importance of the gene in our estimated GRN, supporting a relationship between phylogenetic data of baculovirus genes and network features inferred from expression data. We also observed that gene arrangement in overlapping transcripts was conserved among related baculoviruses, suggesting a principle of genome organization. Conclusions Albeit with a reduced number of nodes (149), the AgMNPV GRN had a topology and key characteristics similar to those observed in complex cellular organisms, which indicates that modularity may be a general feature of biological gene regulatory networks. PMID:24006890

Configuration of electro-optic fire source detection system

NASA Astrophysics Data System (ADS)

Fabian, Ram Z.; Steiner, Zeev; Hofman, Nir

2007-04-01

The recent fighting activities in various parts of the world have highlighted the need for accurate fire source detection on one hand and fast "sensor to shooter cycle" capabilities on the other. Both needs can be met by the SPOTLITE system which dramatically enhances the capability to rapidly engage hostile fire source with a minimum of casualties to friendly force and to innocent bystanders. Modular system design enable to meet each customer specific requirements and enable excellent future growth and upgrade potential. The design and built of a fire source detection system is governed by sets of requirements issued by the operators. This can be translated into the following design criteria: I) Long range, fast and accurate fire source detection capability. II) Different threat detection and classification capability. III) Threat investigation capability. IV) Fire source data distribution capability (Location, direction, video image, voice). V) Men portability. ) In order to meet these design criteria, an optimized concept was presented and exercised for the SPOTLITE system. Three major modular components were defined: I) Electro Optical Unit -Including FLIR camera, CCD camera, Laser Range Finder and Marker II) Electronic Unit -including system computer and electronic. III) Controller Station Unit - Including the HMI of the system. This article discusses the system's components definition and optimization processes, and also show how SPOTLITE designers successfully managed to introduce excellent solutions for other system parameters.

Entanglement branes in a two-dimensional string theory

DOE PAGES

Donnelly, William; Wong, Gabriel

2017-09-20

What is the meaning of entanglement in a theory of extended objects such as strings? To address this question we consider the spatial entanglement between two intervals in the Gross-Taylor model, the string theory dual to two-dimensional Yang-Mills theory at large N. The string diagrams that contribute to the entanglement entropy describe open strings with endpoints anchored to the entangling surface, as first argued by Susskind. We develop a canonical theory of these open strings, and describe how closed strings are divided into open strings at the level of the Hilbert space. Here, we derive the modular Hamiltonian for themore » Hartle-Hawking state and show that the corresponding reduced density matrix describes a thermal ensemble of open strings ending on an object at the entangling surface that we call an entanglement brane, or E-brane.« less

The iFlow modelling framework v2.4: a modular idealized process-based model for flow and transport in estuaries

NASA Astrophysics Data System (ADS)

Dijkstra, Yoeri M.; Brouwer, Ronald L.; Schuttelaars, Henk M.; Schramkowski, George P.

2017-07-01

The iFlow modelling framework is a width-averaged model for the systematic analysis of the water motion and sediment transport processes in estuaries and tidal rivers. The distinctive solution method, a mathematical perturbation method, used in the model allows for identification of the effect of individual physical processes on the water motion and sediment transport and study of the sensitivity of these processes to model parameters. This distinction between processes provides a unique tool for interpreting and explaining hydrodynamic interactions and sediment trapping. iFlow also includes a large number of options to configure the model geometry and multiple choices of turbulence and salinity models. Additionally, the model contains auxiliary components, including one that facilitates easy and fast sensitivity studies. iFlow has a modular structure, which makes it easy to include, exclude or change individual model components, called modules. Depending on the required functionality for the application at hand, modules can be selected to construct anything from very simple quasi-linear models to rather complex models involving multiple non-linear interactions. This way, the model complexity can be adjusted to the application. Once the modules containing the required functionality are selected, the underlying model structure automatically ensures modules are called in the correct order. The model inserts iteration loops over groups of modules that are mutually dependent. iFlow also ensures a smooth coupling of modules using analytical and numerical solution methods. This way the model combines the speed and accuracy of analytical solutions with the versatility of numerical solution methods. In this paper we present the modular structure, solution method and two examples of the use of iFlow. In the examples we present two case studies, of the Yangtze and Scheldt rivers, demonstrating how iFlow facilitates the analysis of model results, the understanding of the underlying physics and the testing of parameter sensitivity. A comparison of the model results to measurements shows a good qualitative agreement. iFlow is written in Python and is available as open source code under the LGPL license.

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

PubMed

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

2010-09-01

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

In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

PubMed Central

Zagrijchuk, Elizaveta A.; Sabirov, Marat A.; Holloway, David M.; Spirov, Alexander V.

2014-01-01

Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes. PMID:24712536

Quantification of complex modular architecture in plants.

PubMed

Reeb, Catherine; Kaandorp, Jaap; Jansson, Fredrik; Puillandre, Nicolas; Dubuisson, Jean-Yves; Cornette, Raphaël; Jabbour, Florian; Coudert, Yoan; Patiño, Jairo; Flot, Jean-François; Vanderpoorten, Alain

2018-04-01

Morphometrics, the assignment of quantities to biological shapes, is a powerful tool to address taxonomic, evolutionary, functional and developmental questions. We propose a novel method for shape quantification of complex modular architecture in thalloid plants, whose extremely reduced morphologies, combined with the lack of a formal framework for thallus description, have long rendered taxonomic and evolutionary studies extremely challenging. Using graph theory, thalli are described as hierarchical series of nodes and edges, allowing for accurate, homologous and repeatable measurements of widths, lengths and angles. The computer program MorphoSnake was developed to extract the skeleton and contours of a thallus and automatically acquire, at each level of organization, width, length, angle and sinuosity measurements. Through the quantification of leaf architecture in Hymenophyllum ferns (Polypodiopsida) and a fully worked example of integrative taxonomy in the taxonomically challenging thalloid liverwort genus Riccardia, we show that MorphoSnake is applicable to all ramified plants. This new possibility of acquiring large numbers of quantitative traits in plants with complex modular architectures opens new perspectives of applications, from the development of rapid species identification tools to evolutionary analyses of adaptive plasticity. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Parallel heuristics for scalable community detection

DOE PAGES

Lu, Hao; Halappanavar, Mahantesh; Kalyanaraman, Ananth

2015-08-14

Community detection has become a fundamental operation in numerous graph-theoretic applications. Despite its potential for application, there is only limited support for community detection on large-scale parallel computers, largely owing to the irregular and inherently sequential nature of the underlying heuristics. In this paper, we present parallelization heuristics for fast community detection using the Louvain method as the serial template. The Louvain method is an iterative heuristic for modularity optimization. Originally developed in 2008, the method has become increasingly popular owing to its ability to detect high modularity community partitions in a fast and memory-efficient manner. However, the method ismore » also inherently sequential, thereby limiting its scalability. Here, we observe certain key properties of this method that present challenges for its parallelization, and consequently propose heuristics that are designed to break the sequential barrier. For evaluation purposes, we implemented our heuristics using OpenMP multithreading, and tested them over real world graphs derived from multiple application domains. Compared to the serial Louvain implementation, our parallel implementation is able to produce community outputs with a higher modularity for most of the inputs tested, in comparable number or fewer iterations, while providing real speedups of up to 16x using 32 threads.« less

Coating graphene paper with 2D-assembly of electrocatalytic nanoparticles: a modular approach toward high-performance flexible electrodes.

PubMed

Xiao, Fei; Song, Jibin; Gao, Hongcai; Zan, Xiaoli; Xu, Rong; Duan, Hongwei

2012-01-24

The development of flexible electrodes is of considerable current interest because of the increasing demand for modern electronics, portable medical products, and compact energy devices. We report a modular approach to fabricating high-performance flexible electrodes by structurally integrating 2D-assemblies of nanoparticles with freestanding graphene paper. We have shown that the 2D array of gold nanoparticles at oil-water interfaces can be transferred on freestanding graphene oxide paper, leading to a monolayer of densely packed gold nanoparticles of uniform sizes loaded on graphene oxide paper. One major finding is that the postassembly electrochemical reduction of graphene oxide paper restores the ordered structure and electron-transport properties of graphene, and gives rise to robust and biocompatible freestanding electrodes with outstanding electrocatalytic activities, which have been manifested by the sensitive and selective detection of two model analytes: glucose and hydrogen peroxide (H(2)O(2)) secreted by live cells. The modular nature of this approach coupled with recent progress in nanocrystal synthesis and surface engineering opens new possibilities to systematically study the dependence of catalytic performance on the structural parameters and chemical compositions of the nanocrystals. © 2011 American Chemical Society

Different micromanipulation applications based on common modular control architecture

NASA Astrophysics Data System (ADS)

Sipola, Risto; Vallius, Tero; Pudas, Marko; Röning, Juha

2010-01-01

This paper validates a previously introduced scalable modular control architecture and shows how it can be used to implement research equipment. The validation is conducted by presenting different kinds of micromanipulation applications that use the architecture. Conditions of the micro-world are very different from those of the macro-world. Adhesive forces are significant compared to gravitational forces when micro-scale objects are manipulated. Manipulation is mainly conducted by automatic control relying on haptic feedback provided by force sensors. The validated architecture is a hierarchical layered hybrid architecture, including a reactive layer and a planner layer. The implementation of the architecture is modular, and the architecture has a lot in common with open architectures. Further, the architecture is extensible, scalable, portable and it enables reuse of modules. These are the qualities that we validate in this paper. To demonstrate the claimed features, we present different applications that require special control in micrometer, millimeter and centimeter scales. These applications include a device that measures cell adhesion, a device that examines properties of thin films, a device that measures adhesion of micro fibers and a device that examines properties of submerged gel produced by bacteria. Finally, we analyze how the architecture is used in these applications.

Modular data acquisition system and its use in gas-filled detector readout at ESRF

NASA Astrophysics Data System (ADS)

Sever, F.; Epaud, F.; Poncet, F.; Grave, M.; Rey-Bakaikoa, V.

1996-09-01

Since 1992, 18 ESRF beamlines are open to users. Although the data acquisition requirements vary a lot from one beamline to another, we are trying to implement a modular data acquisition system architecture that would fit with the maximum number of acquisition projects at ESRF. Common to all of these systems are large acquisition memories and the requirement to visualize the data during an acquisition run and to transfer them quickly after the run to safe storage. We developed a general memory API handling the acquisition memory and its organization and another library that provides calls for transferring the data over TCP/IP sockets. Interesting utility programs using these libraries are the `online display' program and the `data transfer' program. The data transfer program as well as an acquisition control program rely on our well-established `device server model', which was originally designed for the machine control system and then successfully reused in beamline control systems. In the second half of this paper, the acquisition system for a 2D gas-filled detector is presented, which is one of the first concrete examples using the proposed modular data acquisition architecture.

Development of Modular Outdoor Furniture Product Using Lightweight Concrete for Public Parks in Surabaya

NASA Astrophysics Data System (ADS)

Mulyono, Grace; Thamrin, Diana; Antoni

2017-09-01

The development of public parks into green city facilities in Surabaya has triggered the need of outdoor furniture designs that can resist the tropical wet and dry weather conditions while also having a certain mobility to support flexible park arrangement. However, present furniture designs made of concrete material are generally heavy and immovable. Flexible designs are needed for various activities that can take place at the same time such as sitting and playing, and to support changes in arrangement to keep the green open spaces attractive from time to time. This research develops the idea of a modular outdoor furniture design using cellular lightweight concrete (CLC) as the main material as a result from observing its resistance towards weather change and its relative light weight. It starts with analysis of problems, formulation of design concept, creation of design alternatives, selection of design, calculation of mouldings, adaptation of design to the mouldings and production of a scaled mock-up using CLC. Findings of this research reveal that the modular design along with the CLC material used not only support the flexibility of change in function and arrangement but also make these furniture resistant to the hot and humid weather of Surabaya.

A modular computational framework for automated peak extraction from ion mobility spectra

PubMed Central

2014-01-01

Background An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological and medical applications. Each peak in an MCC/IM measurement represents a certain compound, which may be known or unknown. For clustering and classification of measurements, the raw data matrix must be reduced to a set of peaks. Each peak is described by its coordinates (retention time in the MCC and reduced inverse ion mobility) and shape (signal intensity, further shape parameters). This fundamental step is referred to as peak extraction. It is the basis for identifying discriminating peaks, and hence putative biomarkers, between two classes of measurements, such as a healthy control group and a group of patients with a confirmed disease. Current state-of-the-art peak extraction methods require human interaction, such as hand-picking approximate peak locations, assisted by a visualization of the data matrix. In a high-throughput context, however, it is preferable to have robust methods for fully automated peak extraction. Results We introduce PEAX, a modular framework for automated peak extraction. The framework consists of several steps in a pipeline architecture. Each step performs a specific sub-task and can be instantiated by different methods implemented as modules. We provide open-source software for the framework and several modules for each step. Additionally, an interface that allows easy extension by a new module is provided. Combining the modules in all reasonable ways leads to a large number of peak extraction methods. We evaluate all combinations using intrinsic error measures and by comparing the resulting peak sets with an expert-picked one. Conclusions Our software PEAX is able to automatically extract peaks from MCC/IM measurements within a few seconds. The automatically obtained results keep up with the results provided by current state-of-the-art peak extraction methods. This opens a high-throughput context for the MCC/IM application field. Our software is available at http://www.rahmannlab.de/research/ims. PMID:24450533

A modular computational framework for automated peak extraction from ion mobility spectra.

PubMed

D'Addario, Marianna; Kopczynski, Dominik; Baumbach, Jörg Ingo; Rahmann, Sven

2014-01-22

An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological and medical applications. Each peak in an MCC/IM measurement represents a certain compound, which may be known or unknown. For clustering and classification of measurements, the raw data matrix must be reduced to a set of peaks. Each peak is described by its coordinates (retention time in the MCC and reduced inverse ion mobility) and shape (signal intensity, further shape parameters). This fundamental step is referred to as peak extraction. It is the basis for identifying discriminating peaks, and hence putative biomarkers, between two classes of measurements, such as a healthy control group and a group of patients with a confirmed disease. Current state-of-the-art peak extraction methods require human interaction, such as hand-picking approximate peak locations, assisted by a visualization of the data matrix. In a high-throughput context, however, it is preferable to have robust methods for fully automated peak extraction. We introduce PEAX, a modular framework for automated peak extraction. The framework consists of several steps in a pipeline architecture. Each step performs a specific sub-task and can be instantiated by different methods implemented as modules. We provide open-source software for the framework and several modules for each step. Additionally, an interface that allows easy extension by a new module is provided. Combining the modules in all reasonable ways leads to a large number of peak extraction methods. We evaluate all combinations using intrinsic error measures and by comparing the resulting peak sets with an expert-picked one. Our software PEAX is able to automatically extract peaks from MCC/IM measurements within a few seconds. The automatically obtained results keep up with the results provided by current state-of-the-art peak extraction methods. This opens a high-throughput context for the MCC/IM application field. Our software is available at http://www.rahmannlab.de/research/ims.

Modular, security enclosure and method of assembly

DOEpatents

Linker, Kevin L.; Moyer, John W.

1995-01-01

A transportable, reusable rapidly assembled and disassembled, resizable modular, security enclosure utilizes a stepped panel construction. Each panel has an inner portion and an outer portion which form joints. A plurality of channels can be affixed to selected joints of the panels. Panels can be affixed to a base member and then affixed to one another by the use of elongated pins extending through the channel joints. Alternatively, the base member can be omitted and the panels themselves can be used as the floor of the enclosure. The pins will extend generally parallel to the joint in which they are located. These elongated pins are readily inserted into and removable from the channels in a predetermined sequence to allow assembly and disassembly of the enclosure. A door constructed from panels is used to close the opening to the enclosure.

EASEE: an open architecture approach for modeling battlespace signal and sensor phenomenology

NASA Astrophysics Data System (ADS)

Waldrop, Lauren E.; Wilson, D. Keith; Ekegren, Michael T.; Borden, Christian T.

2017-04-01

Open architecture in the context of defense applications encourages collaboration across government agencies and academia. This paper describes a success story in the implementation of an open architecture framework that fosters transparency and modularity in the context of Environmental Awareness for Sensor and Emitter Employment (EASEE), a complex physics-based software package for modeling the effects of terrain and atmospheric conditions on signal propagation and sensor performance. Among the highlighted features in this paper are: (1) a code refactorization to separate sensitive parts of EASEE, thus allowing collaborators the opportunity to view and interact with non-sensitive parts of the EASEE framework with the end goal of supporting collaborative innovation, (2) a data exchange and validation effort to enable the dynamic addition of signatures within EASEE thus supporting a modular notion that components can be easily added or removed to the software without requiring recompilation by developers, and (3) a flexible and extensible XML interface, which aids in decoupling graphical user interfaces from EASEE's calculation engine, and thus encourages adaptability to many different defense applications. In addition to the outlined points above, this paper also addresses EASEE's ability to interface with both proprietary systems such as ArcGIS. A specific use case regarding the implementation of an ArcGIS toolbar that leverages EASEE's XML interface and enables users to set up an EASEE-compliant configuration for probability of detection or optimal sensor placement calculations in various modalities is discussed as well.

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

DTIC Science & Technology

1999-08-01

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

An Open-Book Modular Watershed Modeling Framework for Rapid Prototyping of GPM- based Flood Forecasting in International River Basins

NASA Astrophysics Data System (ADS)

Katiyar, N.; Hossain, F.

2006-05-01

Floods have always been disastrous for human life. It accounts for about 15 % of the total death related to natural disasters. There are around 263 transboundary river basins listed by UNESCO, wherein at least 30 countries have more than 95% of their territory locked in one or more such transboundary basins. For flood forecasting in the lower riparian nations of these International River Basins (IRBs), real-time rainfall data from upstream nations is naturally the most critical factor governing the forecasting effectiveness. However, many upstream nations fail to provide data to the lower riparian nations due to a lack of in-situ rainfall measurement infrastructure or a lack of a treaty for real-time sharing of rainfall data. A potential solution is therefore to use satellites that inherently measure rainfall across political boundaries. NASA's proposed Global Precipitation Measurement (GPM) mission appears very promising in providing this vital rainfall information under the data- limited scenario that will continue to prevail in most IRBs. However, satellite rainfall is associated with uncertainty and hence, proper characterization of the satellite rainfall error propagation in hydrologic models for flood forecasting is a critical priority that should be resolved in the coming years in anticipation of GPM. In this study, we assess an open book modular watershed modeling approach for estimating the expected error in flood forecasting related to GPM rainfall data. Our motivation stems from the critical challenge in identifying the specific IRBs that would benefit from a pre-programmed satellite-based forecasting system in anticipation of GPM. As the number of flood-prone IRBs is large, conventional data-intensive implementation of existing physically-based distributed hydrologic models on case-by-case IRBs is considered time-consuming for completing such a global assessment. A more parsimonious approach is justified at the expense of a tolerable loss of detail and accuracy. Through assessment of our proposed modular modeling framework, we present our initial understanding in resolving the fundamental question - Can a parsimonious open-book watershed modeling framework be a physically consistent proxy for rapid and global identification of IRBs in greater need of a GPM-based flood forecasting system?

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

PubMed

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

2018-06-01

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

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.

A modular Human Exposure Model (HEM) framework to ...

EPA Pesticide Factsheets

Life Cycle Impact Analysis (LCIA) has proven to be a valuable tool for systematically comparing processes and products, and has been proposed for use in Chemical Alternatives Analysis (CAA). The exposure assessment portion of the human health impact scores of LCIA has historically focused on far-field sources (environmentally mediated exposures) while research has shown that use related exposures, (near-field exposures) typically dominate population exposure. Characterizing the human health impacts of chemicals in consumer products over the life cycle of these products requires an evaluation of both near-field as well far-field sources. Assessing the impacts of the near-field exposures requires bridging the scientific and technical gaps that currently prevent the harmonious use of the best available methods and tools from the fields of LCIA and human health exposure and risk assessment. The U.S. EPA’s Chemical Safety and Sustainability LC-HEM project is developing the Human Exposure Model (HEM) to assess near-field exposures to chemicals that occur to various populations over the life cycle of a commercial product. The HEM will be a publically available, web-based, modular system which will allow for the evaluation of chemical/product impacts in a LCIA framework to support CAA. We present here an overview of the framework for the modular HEM system. The framework includes a data flow diagram of in-progress and future planned modules, the definition of each mod

mRM - multiscale Routing Model for Land Surface and Hydrologic Models

NASA Astrophysics Data System (ADS)

Cuntz, M.; Thober, S.; Mai, J.; Samaniego, L. E.; Gochis, D. J.; Kumar, R.

2015-12-01

Routing streamflow through a river network is a basic step within any distributed hydrologic model. It integrates the generated runoff and allows comparison with observed discharge at the outlet of a catchment. The Muskingum routing is a textbook river routing scheme that has been implemented in Earth System Models (e.g., WRF-HYDRO), stand-alone routing schemes (e.g., RAPID), and hydrologic models (e.g., the mesoscale Hydrologic Model). Most implementations suffer from a high computational demand because the spatial routing resolution is fixed to that of the elevation model irrespective of the hydrologic modeling resolution. This is because the model parameters are scale-dependent and cannot be used at other resolutions without re-estimation. Here, we present the multiscale Routing Model (mRM) that allows for a flexible choice of the routing resolution. mRM exploits the Multiscale Parameter Regionalization (MPR) included in the open-source mesoscale Hydrologic Model (mHM, www.ufz.de/mhm) that relates model parameters to physiographic properties and allows to estimate scale-independent model parameters. mRM is currently coupled to mHM and is presented here as stand-alone Free and Open Source Software (FOSS). The mRM source code is highly modular and provides a subroutine for internal re-use in any land surface scheme. mRM is coupled in this work to the state-of-the-art land surface model Noah-MP. Simulation results using mRM are compared with those available in WRF-HYDRO for the Red River during the period 1990-2000. mRM allows to increase the routing resolution from 100m to more than 10km without deteriorating the model performance. Therefore, it speeds up model calculation by reducing the contribution of routing to total runtime from over 80% to less than 5% in the case of WRF-HYDRO. mRM thus makes discharge data available to land surface modeling with only little extra calculations.

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.

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

Shin, Yong-Hoon, E-mail: chaotics@snu.ac.kr; Park, Sangrok; Kim, Byong Sup

Since the first nuclear power was engaged in Korean electricity grid in 1978, intensive research and development has been focused on localization and standardization of large pressurized water reactors (PWRs) aiming at providing Korean peninsula and beyond with economical and safe power source. With increased priority placed on the safety since Chernobyl accident, Korean nuclear power R and D activity has been diversified into advanced PWR, small modular PWR and generation IV reactors. After the outbreak of Fukushima accident, inherently safe small modular reactor (SMR) receives growing interest in Korea and Europe. In this paper, we will describe recent statusmore » of evolving designs of SMR, their advantages and challenges. In particular, the conceptual design of lead-bismuth cooled SMR in Korea, URANUS with 40∼70 MWe is examined in detail. This paper will cover a framework of the program and a strategy for the successful deployment of small modular reactor how the goals would entail and the approach to collaboration with other entities.« less

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

PubMed

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

2016-01-01

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

Towards a new generation of agricultural system data, models and knowledge products: Information and communication technology.

PubMed

Janssen, Sander J C; Porter, Cheryl H; Moore, Andrew D; Athanasiadis, Ioannis N; Foster, Ian; Jones, James W; Antle, John M

2017-07-01

Agricultural modeling has long suffered from fragmentation in model implementation. Many models are developed, there is much redundancy, models are often poorly coupled, model component re-use is rare, and it is frequently difficult to apply models to generate real solutions for the agricultural sector. To improve this situation, we argue that an open, self-sustained, and committed community is required to co-develop agricultural models and associated data and tools as a common resource. Such a community can benefit from recent developments in information and communications technology (ICT). We examine how such developments can be leveraged to design and implement the next generation of data, models, and decision support tools for agricultural production systems. Our objective is to assess relevant technologies for their maturity, expected development, and potential to benefit the agricultural modeling community. The technologies considered encompass methods for collaborative development and for involving stakeholders and users in development in a transdisciplinary manner. Our qualitative evaluation suggests that as an overall research challenge, the interoperability of data sources, modular granular open models, reference data sets for applications and specific user requirements analysis methodologies need to be addressed to allow agricultural modeling to enter in the big data era. This will enable much higher analytical capacities and the integrated use of new data sources. Overall agricultural systems modeling needs to rapidly adopt and absorb state-of-the-art data and ICT technologies with a focus on the needs of beneficiaries and on facilitating those who develop applications of their models. This adoption requires the widespread uptake of a set of best practices as standard operating procedures.

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

PubMed Central

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

2016-01-01

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

Modular multiple sensors information management for computer-integrated surgery.

PubMed

Vaccarella, Alberto; Enquobahrie, Andinet; Ferrigno, Giancarlo; Momi, Elena De

2012-09-01

In the past 20 years, technological advancements have modified the concept of modern operating rooms (ORs) with the introduction of computer-integrated surgery (CIS) systems, which promise to enhance the outcomes, safety and standardization of surgical procedures. With CIS, different types of sensor (mainly position-sensing devices, force sensors and intra-operative imaging devices) are widely used. Recently, the need for a combined use of different sensors raised issues related to synchronization and spatial consistency of data from different sources of information. In this study, we propose a centralized, multi-sensor management software architecture for a distributed CIS system, which addresses sensor information consistency in both space and time. The software was developed as a data server module in a client-server architecture, using two open-source software libraries: Image-Guided Surgery Toolkit (IGSTK) and OpenCV. The ROBOCAST project (FP7 ICT 215190), which aims at integrating robotic and navigation devices and technologies in order to improve the outcome of the surgical intervention, was used as the benchmark. An experimental protocol was designed in order to prove the feasibility of a centralized module for data acquisition and to test the application latency when dealing with optical and electromagnetic tracking systems and ultrasound (US) imaging devices. Our results show that a centralized approach is suitable for minimizing synchronization errors; latency in the client-server communication was estimated to be 2 ms (median value) for tracking systems and 40 ms (median value) for US images. The proposed centralized approach proved to be adequate for neurosurgery requirements. Latency introduced by the proposed architecture does not affect tracking system performance in terms of frame rate and limits US images frame rate at 25 fps, which is acceptable for providing visual feedback to the surgeon in the OR. Copyright © 2012 John Wiley & Sons, Ltd.

An i2b2-based, generalizable, open source, self-scaling chronic disease registry

PubMed Central

Quan, Justin; Ortiz, David M; Bousvaros, Athos; Ilowite, Norman T; Inman, Christi J; Marsolo, Keith; McMurry, Andrew J; Sandborg, Christy I; Schanberg, Laura E; Wallace, Carol A; Warren, Robert W; Weber, Griffin M; Mandl, Kenneth D

2013-01-01

Objective Registries are a well-established mechanism for obtaining high quality, disease-specific data, but are often highly project-specific in their design, implementation, and policies for data use. In contrast to the conventional model of centralized data contribution, warehousing, and control, we design a self-scaling registry technology for collaborative data sharing, based upon the widely adopted Integrating Biology & the Bedside (i2b2) data warehousing framework and the Shared Health Research Information Network (SHRINE) peer-to-peer networking software. Materials and methods Focusing our design around creation of a scalable solution for collaboration within multi-site disease registries, we leverage the i2b2 and SHRINE open source software to create a modular, ontology-based, federated infrastructure that provides research investigators full ownership and access to their contributed data while supporting permissioned yet robust data sharing. We accomplish these objectives via web services supporting peer-group overlays, group-aware data aggregation, and administrative functions. Results The 56-site Childhood Arthritis & Rheumatology Research Alliance (CARRA) Registry and 3-site Harvard Inflammatory Bowel Diseases Longitudinal Data Repository now utilize i2b2 self-scaling registry technology (i2b2-SSR). This platform, extensible to federation of multiple projects within and between research networks, encompasses >6000 subjects at sites throughout the USA. Discussion We utilize the i2b2-SSR platform to minimize technical barriers to collaboration while enabling fine-grained control over data sharing. Conclusions The implementation of i2b2-SSR for the multi-site, multi-stakeholder CARRA Registry has established a digital infrastructure for community-driven research data sharing in pediatric rheumatology in the USA. We envision i2b2-SSR as a scalable, reusable solution facilitating interdisciplinary research across diseases. PMID:22733975

Python-Assisted MODFLOW Application and Code Development

NASA Astrophysics Data System (ADS)

Langevin, C.

2013-12-01

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

An i2b2-based, generalizable, open source, self-scaling chronic disease registry.

PubMed

Natter, Marc D; Quan, Justin; Ortiz, David M; Bousvaros, Athos; Ilowite, Norman T; Inman, Christi J; Marsolo, Keith; McMurry, Andrew J; Sandborg, Christy I; Schanberg, Laura E; Wallace, Carol A; Warren, Robert W; Weber, Griffin M; Mandl, Kenneth D

2013-01-01

Registries are a well-established mechanism for obtaining high quality, disease-specific data, but are often highly project-specific in their design, implementation, and policies for data use. In contrast to the conventional model of centralized data contribution, warehousing, and control, we design a self-scaling registry technology for collaborative data sharing, based upon the widely adopted Integrating Biology & the Bedside (i2b2) data warehousing framework and the Shared Health Research Information Network (SHRINE) peer-to-peer networking software. Focusing our design around creation of a scalable solution for collaboration within multi-site disease registries, we leverage the i2b2 and SHRINE open source software to create a modular, ontology-based, federated infrastructure that provides research investigators full ownership and access to their contributed data while supporting permissioned yet robust data sharing. We accomplish these objectives via web services supporting peer-group overlays, group-aware data aggregation, and administrative functions. The 56-site Childhood Arthritis & Rheumatology Research Alliance (CARRA) Registry and 3-site Harvard Inflammatory Bowel Diseases Longitudinal Data Repository now utilize i2b2 self-scaling registry technology (i2b2-SSR). This platform, extensible to federation of multiple projects within and between research networks, encompasses >6000 subjects at sites throughout the USA. We utilize the i2b2-SSR platform to minimize technical barriers to collaboration while enabling fine-grained control over data sharing. The implementation of i2b2-SSR for the multi-site, multi-stakeholder CARRA Registry has established a digital infrastructure for community-driven research data sharing in pediatric rheumatology in the USA. We envision i2b2-SSR as a scalable, reusable solution facilitating interdisciplinary research across diseases.

SOFIA: a flexible source finder for 3D spectral line data

NASA Astrophysics Data System (ADS)

Serra, Paolo; Westmeier, Tobias; Giese, Nadine; Jurek, Russell; Flöer, Lars; Popping, Attila; Winkel, Benjamin; van der Hulst, Thijs; Meyer, Martin; Koribalski, Bärbel S.; Staveley-Smith, Lister; Courtois, Hélène

2015-04-01

We introduce SOFIA, a flexible software application for the detection and parametrization of sources in 3D spectral line data sets. SOFIA combines for the first time in a single piece of software a set of new source-finding and parametrization algorithms developed on the way to future H I surveys with ASKAP (WALLABY, DINGO) and APERTIF. It is designed to enable the general use of these new algorithms by the community on a broad range of data sets. The key advantages of SOFIA are the ability to: search for line emission on multiple scales to detect 3D sources in a complete and reliable way, taking into account noise level variations and the presence of artefacts in a data cube; estimate the reliability of individual detections; look for signal in arbitrarily large data cubes using a catalogue of 3D coordinates as a prior; provide a wide range of source parameters and output products which facilitate further analysis by the user. We highlight the modularity of SOFIA, which makes it a flexible package allowing users to select and apply only the algorithms useful for their data and science questions. This modularity makes it also possible to easily expand SOFIA in order to include additional methods as they become available. The full SOFIA distribution, including a dedicated graphical user interface, is publicly available for download.

Human-like characteristics for high degree of freedom robotic door-opening end-effector

NASA Astrophysics Data System (ADS)

Gray, Jeremy P.; Campagna, Frank

2011-05-01

In the field of military Unmanned Ground Vehicles (UGV's), military units are forced to sweep largely populated cities and towns in search of hostile enemies. These urban types of operations are referred to as MOUT (Military Operations on Urban Terrain). During urban operations, these UGV's encounter difficulties when opening doors. Current manipulator end effectors have these difficulties, because they are not designed to mimic human hand operations. This paper explains the mechanical nature of the Modular Universal Door Opening End-effector (MUDOE). MUDOE is a result of our development research to improve robotic manipulators ability to negotiate closed doors. The presented solution has the ability to mimic human hand characteristics when opening doors. The end-effector possesses an ability to maintain a high Degree of Freedom (DoF), and grasp the doorknob by applying equally distributed forces to all points of contact.

[Development of opened instrument for generating and measuring physiological signal].

PubMed

Chen, Longcong; Hu, Guohu; Gao, Bin

2004-12-01

An opened instrument with liquid crystal display (LCD) for generating and measuring physiological signal is introduced in this paper. Based on a single-chip microcomputer. the instrument uses the technique of LCD screen to display signal wave and information, and it realizes man-machine interaction by keyboard. This instrument can produce not only defined signal in common use by utilizing important saved data and relevant arithmetic, but also user-defined signal. Therefore, it is open to produce signal. In addition, this instrument has strong extension because of its modularized design as computer, which has much function such as displaying, measuring and saving physiological signal, and many features such as low power consumption, small volume, low cost and portability. Hence this instrument is convenient for experiment teaching, clinic examining, maintaining of medical instrument.

D GIS for Flood Modelling in River Valleys

NASA Astrophysics Data System (ADS)

Tymkow, P.; Karpina, M.; Borkowski, A.

2016-06-01

The objective of this study is implementation of system architecture for collecting and analysing data as well as visualizing results for hydrodynamic modelling of flood flows in river valleys using remote sensing methods, tree-dimensional geometry of spatial objects and GPU multithread processing. The proposed solution includes: spatial data acquisition segment, data processing and transformation, mathematical modelling of flow phenomena and results visualization. Data acquisition segment was based on aerial laser scanning supplemented by images in visible range. Vector data creation was based on automatic and semiautomatic algorithms of DTM and 3D spatial features modelling. Algorithms for buildings and vegetation geometry modelling were proposed or adopted from literature. The implementation of the framework was designed as modular software using open specifications and partially reusing open source projects. The database structure for gathering and sharing vector data, including flood modelling results, was created using PostgreSQL. For the internal structure of feature classes of spatial objects in a database, the CityGML standard was used. For the hydrodynamic modelling the solutions of Navier-Stokes equations in two-dimensional version was implemented. Visualization of geospatial data and flow model results was transferred to the client side application. This gave the independence from server hardware platform. A real-world case in Poland, which is a part of Widawa River valley near Wroclaw city, was selected to demonstrate the applicability of proposed system.

Integration of an open interface PC scene generator using COTS DVI converter hardware

NASA Astrophysics Data System (ADS)

Nordland, Todd; Lyles, Patrick; Schultz, Bret

2006-05-01

Commercial-Off-The-Shelf (COTS) personal computer (PC) hardware is increasingly capable of computing high dynamic range (HDR) scenes for military sensor testing at high frame rates. New electro-optical and infrared (EO/IR) scene projectors feature electrical interfaces that can accept the DVI output of these PC systems. However, military Hardware-in-the-loop (HWIL) facilities such as those at the US Army Aviation and Missile Research Development and Engineering Center (AMRDEC) utilize a sizeable inventory of existing projection systems that were designed to use the Silicon Graphics Incorporated (SGI) digital video port (DVP, also known as DVP2 or DD02) interface. To mate the new DVI-based scene generation systems to these legacy projection systems, CG2 Inc., a Quantum3D Company (CG2), has developed a DVI-to-DVP converter called Delta DVP. This device takes progressive scan DVI input, converts it to digital parallel data, and combines and routes color components to derive a 16-bit wide luminance channel replicated on a DVP output interface. The HWIL Functional Area of AMRDEC has developed a suite of modular software to perform deterministic real-time, wave band-specific rendering of sensor scenes, leveraging the features of commodity graphics hardware and open source software. Together, these technologies enable sensor simulation and test facilities to integrate scene generation and projection components with diverse pedigrees.

PSRPOPPy: an open-source package for pulsar population simulations

NASA Astrophysics Data System (ADS)

Bates, S. D.; Lorimer, D. R.; Rane, A.; Swiggum, J.

2014-04-01

We have produced a new software package for the simulation of pulsar populations, PSRPOPPY, based on the PSRPOP package. The codebase has been re-written in Python (save for some external libraries, which remain in their native Fortran), utilizing the object-oriented features of the language, and improving the modularity of the code. Pre-written scripts are provided for running the simulations in `standard' modes of operation, but the code is flexible enough to support the writing of personalised scripts. The modular structure also makes the addition of experimental features (such as new models for period or luminosity distributions) more straightforward than with the previous code. We also discuss potential additions to the modelling capabilities of the software. Finally, we demonstrate some potential applications of the code; first, using results of surveys at different observing frequencies, we find pulsar spectral indices are best fitted by a normal distribution with mean -1.4 and standard deviation 1.0. Secondly, we model pulsar spin evolution to calculate the best fit for a relationship between a pulsar's luminosity and spin parameters. We used the code to replicate the analysis of Faucher-Giguère & Kaspi, and have subsequently optimized their power-law dependence of radio luminosity, L, with period, P, and period derivative, Ṗ. We find that the underlying population is best described by L ∝ P-1.39±0.09 Ṗ0.48±0.04 and is very similar to that found for γ-ray pulsars by Perera et al. Using this relationship, we generate a model population and examine the age-luminosity relation for the entire pulsar population, which may be measurable after future large-scale surveys with the Square Kilometre Array.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines

PubMed Central

2011-01-01

Background Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. Results To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). Conclusions PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples. PMID:21352538

Medical Data Architecture Capabilities and Design

NASA Technical Reports Server (NTRS)

Middour, C.; Krihak, M.; Lindsey, A.; Marker, N.; Wolfe, S.; Winther, S.; Ronzano, K.; Bolles, D.; Toscano, W.; Shaw, T.

2017-01-01

Mission constraints will challenge the delivery of medical care on a long-term, deep space explorationmission. This type of mission will be restricted in the availability of medical knowledge, skills, procedures and resourcesto prevent, diagnose, and treat in-flight medical events. Challenges to providing medical care are anticipated, includingresource and resupply constraints, delayed communications and no ability for medical evacuation. The Medical DataArchitecture (MDA) project will enable medical care capability in this constrained environment.The first version of thesystem, called Test Bed 1, includes capabilities for automated data collection, data storage and data retrieval to provideinformation to the Crew Medical Officer (CMO). Test Bed 1 seeks to establish a data architecture foundation and developa scalable data management system through modular design and standardized interfaces. In addition, it will demonstrateto stakeholders the potential for an improved, automated, flow of data to and from the medical system over the currentmethods employed on the International Space Station (ISS). It integrates a set of external devices, software andprocesses, and a Subjective, Objective, Assessment, and Plan (SOAP) note commonly used by clinicians. Medical datalike electrocardiogram plots, heart rate, skin temperature, respiration rate, medications taken, and more are collectedfrom devices and stored in the Electronic Medical Records (EMR) system, and reported to crew and clinician. Devicesintegrated include the Astroskin biosensor vest and IMED CARDIAX electrocardiogram (ECG) device with INEED MDECG Glove, and the NASA-developed Medical Dose Tracker application.The system is designed to be operated as astandalone system, and can be deployed in a variety of environments, from a laptop to a data center. The system isprimarily composed of open-source software tools, and is designed to be modular, so new capabilities can be added. Thesoftware components and integration methods will be discussed.

A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines.

PubMed

Cieślik, Marcin; Mura, Cameron

2011-02-25

Bioinformatic analyses typically proceed as chains of data-processing tasks. A pipeline, or 'workflow', is a well-defined protocol, with a specific structure defined by the topology of data-flow interdependencies, and a particular functionality arising from the data transformations applied at each step. In computer science, the dataflow programming (DFP) paradigm defines software systems constructed in this manner, as networks of message-passing components. Thus, bioinformatic workflows can be naturally mapped onto DFP concepts. To enable the flexible creation and execution of bioinformatics dataflows, we have written a modular framework for parallel pipelines in Python ('PaPy'). A PaPy workflow is created from re-usable components connected by data-pipes into a directed acyclic graph, which together define nested higher-order map functions. The successive functional transformations of input data are evaluated on flexibly pooled compute resources, either local or remote. Input items are processed in batches of adjustable size, all flowing one to tune the trade-off between parallelism and lazy-evaluation (memory consumption). An add-on module ('NuBio') facilitates the creation of bioinformatics workflows by providing domain specific data-containers (e.g., for biomolecular sequences, alignments, structures) and functionality (e.g., to parse/write standard file formats). PaPy offers a modular framework for the creation and deployment of parallel and distributed data-processing workflows. Pipelines derive their functionality from user-written, data-coupled components, so PaPy also can be viewed as a lightweight toolkit for extensible, flow-based bioinformatics data-processing. The simplicity and flexibility of distributed PaPy pipelines may help users bridge the gap between traditional desktop/workstation and grid computing. PaPy is freely distributed as open-source Python code at http://muralab.org/PaPy, and includes extensive documentation and annotated usage examples.

Mod3DMT and EMTF: Free Software for MT Data Processing and Inversion

NASA Astrophysics Data System (ADS)

Egbert, G. D.; Kelbert, A.; Meqbel, N. M.

2017-12-01

"ModEM" was developed at Oregon State University as a modular system for inversion of electromagnetic (EM) geophysical data (Egbert and Kelbert, 2012; Kelbert et al., 2014). Although designed for more general (frequency domain) EM applications, and originally intended as a testbed for exploring inversion search and regularization strategies, our own initial uses of ModEM were for 3-D imaging of the deep crust and upper mantle at large scales. Since 2013 we have offered a version of the source code suitable for 3D magnetotelluric (MT) inversion on an "as is, user beware" basis for free for non-commercial applications. This version, which we refer to as Mod3DMT, has since been widely used by the international MT community. Over 250 users have registered to download the source code, and at least 50 MT studies in the refereed literature, covering locations around the globe at a range of spatial scales, cite use of ModEM for 3D inversion. For over 30 years I have also made MT processing software available for free use. In this presentation, I will discuss my experience with these freely available (but perhaps not truly open-source) computer codes. Although users are allowed to make modifications to the codes (on conditions that they provide a copy of the modified version) only a handful of users have tried to make any modification, and only rarely are modifications even reported, much less provided back to the developers.

Transitioning to Integrated Modular Avionics with a Mission Management System

DTIC Science & Technology

2000-10-01

software structure, which is based on the use of a of interchangeable processing modules of a limited COTS Real - Time Operating System . number of...open standardised interfaces system hardware or the Real - Time Operating System directly supports the use of COTS components, which implementation, to...System RTOS Real - Time Operating System SMBP System Management Blueprint Interface SMOS System Management to Operating System Interface Figure 2: The ASAAC

Defense Acquisition Review Journal. Volume 14, Number 1, February 2007

DTIC Science & Technology

2007-02-01

price, delivery schedules, or policies, such as the Berry Amendment Specialty Metals Clause,3 Critical Safety Items (CSI),4 and Business System Status...management, quality assurance, client care and subcontractor management. Ms. Shaw holds a BS in Business from University of Baltimore and a masters in...William Kleiner Matthew Popham A Business Model for Defense Acquisition under the Modular Open Systems Approach Eugene Gholz Decision Support for Best

Coupling Spatial Segregation with Synthetic Circuits to Control Bacterial Survival (Open Access)

DTIC Science & Technology

2016-02-29

Subject Categories Synthetic Biology & Biotechnology; Quantitative Biology & Dynamical Systems DOI 10.15252/msb.20156567 | Received 9 September 2015...survival. Experimentally , we program collective survival using three different gene circuits, which allow us to evaluate the modularity of the...QS-CAT circuit depends on QS regulation. The QS-BlaM circuit depends on both QS regulation and enzyme release (by lysis and export). G–I Experimental

(NTF) National Transonic Facility Test 213-SFW Flow Control II,

NASA Image and Video Library

2012-11-19

(NTF) National Transonic Facility Test 213-SFW Flow Control II, Fast-MAC Model: The fundamental Aerodynamics Subsonic Transonic-Modular Active Control (Fast-MAC) Model was tested for the 2nd time in the NTF. The objectives were to document the effects of Reynolds numbers on circulation control aerodynamics and to develop and open data set for CFD code validation. Image taken in building 1236, National Transonic Facility

Modular control of endothelial sheet migration

PubMed Central

Vitorino, Philip; Meyer, Tobias

2008-01-01

Growth factor-induced migration of endothelial cell monolayers enables embryonic development, wound healing, and angiogenesis. Although collective migration is widespread and therapeutically relevant, the underlying mechanism by which cell monolayers respond to growth factor, sense directional signals, induce motility, and coordinate individual cell movements is only partially understood. Here we used RNAi to identify 100 regulatory proteins that enhance or suppress endothelial sheet migration into cell-free space. We measured multiple live-cell migration parameters for all siRNA perturbations and found that each targeted protein primarily regulates one of four functional outputs: cell motility, directed migration, cell–cell coordination, or cell density. We demonstrate that cell motility regulators drive random, growth factor-independent motility in the presence or absence of open space. In contrast, directed migration regulators selectively transduce growth factor signals to direct cells along the monolayer boundary toward open space. Lastly, we found that regulators of cell–cell coordination are growth factor-independent and reorient randomly migrating cells inside the sheet when boundary cells begin to migrate. Thus, cells transition from random to collective migration through a modular control system, whereby growth factor signals convert boundary cells into pioneers, while cells inside the monolayer reorient and follow pioneers through growth factor-independent migration and cell–cell coordination. PMID:19056882

Minicourses in Astrophysics, Modular Approach, Vol. II.

ERIC Educational Resources Information Center

Illinois Univ., Chicago.

This is the second of a two-volume minicourse in astrophysics. It contains chapters on the following topics: stellar nuclear energy sources and nucleosynthesis; stellar evolution; stellar structure and its determination; and pulsars. Each chapter gives much technical discussion, mathematical treatment, diagrams, and examples. References are…

Modular uncooled video engines based on a DSP processor

NASA Astrophysics Data System (ADS)

Schapiro, F.; Milstain, Y.; Aharon, A.; Neboshchik, A.; Ben-Simon, Y.; Kogan, I.; Lerman, I.; Mizrahi, U.; Maayani, S.; Amsterdam, A.; Vaserman, I.; Duman, O.; Gazit, R.

2011-06-01

The market demand for low SWaP (Size, Weight and Power) uncooled engines keeps growing. Low SWaP is especially critical in battery-operated applications such as goggles and Thermal Weapon Sights. A new approach for the design of the engines was implemented by SCD to optimize size and power consumption at system level. The new approach described in the paper, consists of: 1. A modular hardware design that allows the user to define the exact level of integration needed for his system 2. An "open architecture" based on the OMAPTM530 DSP that allows the integrator to take advantage of unused hardware (FPGA) and software (DSP) resources, for implementation of additional algorithms or functionality. The approach was successfully implemented on the first generation of 25μm pitch BIRD detectors, and more recently on the new, 640 x480, 17 μm pitch detector.

Modular "plug-and-play" capsules for multi-capsule environment in the gastrointestinal tract.

PubMed

Phee, S J; Ting, E K; Lin, L; Huynh, V A; Kencana, A P; Wong, K J; Tan, S L

2009-01-01

The invention of wireless capsule endoscopy has opened new ways of diagnosing and treating diseases in the gastrointestinal tract. Current wireless capsules can perform simple operations such as imaging and data collection (like temperature, pressure, and pH) in the gastrointestinal tract. Researchers are now focusing on adding more sophisticated functions such as drug delivery, surgical clips/tags deployment, and tissue samples collection. The finite on-board power on these capsules is one of the factors that limits the functionalities of these wireless capsules. Thus multiple application-specific capsules would be needed to complete an endoscopic operation. This would give rise to a multi-capsule environment. Having a modular "plug-and-play" capsule design would facilitate doctors in configuring multiple application-specific capsules, e.g. tagging capsule, for use in the gastrointestinal tract. This multi-capsule environment also has the advantage of reducing power consumption through asymmetric multi-hop communication.

Final Report, University Research Program in Robotics (URPR), Nuclear Facilities Clean-up

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

Tesar, Delbert; Kapoor, Chetan; Pryor, Mitch

This final report describes the research activity at the University of Texas at Austin with application to EM needs at DOE. This research activity is divided in to two major thrusts and contributes to the overall University Research Program in Robotics (URPR) thrust by providing mechanically oriented robotic solutions based on modularity and generalized software. These thrusts are also the core strengths of the UTA program that has a 40-year history in machine development, 30 years specifically devoted to robotics. Since 1975, much of this effort has been to establish the general analytical and design infrastructure for an open (modular)more » architecture of systems with many degrees of freedom that are able to satisfy a broad range of applications for future production machines. This work has coalesced from two principal areas: standardized actuators and generalized software.« less

Evolutionary Telemetry and Command Processor (TCP) architecture

NASA Technical Reports Server (NTRS)

Schneider, John R.

1992-01-01

A low cost, modular, high performance, and compact Telemetry and Command Processor (TCP) is being built as the foundation of command and data handling subsystems for the next generation of satellites. The TCP product line will support command and telemetry requirements for small to large spacecraft and from low to high rate data transmission. It is compatible with the latest TDRSS, STDN and SGLS transponders and provides CCSDS protocol communications in addition to standard TDM formats. Its high performance computer provides computing resources for hosted flight software. Layered and modular software provides common services using standardized interfaces to applications thereby enhancing software re-use, transportability, and interoperability. The TCP architecture is based on existing standards, distributed networking, distributed and open system computing, and packet technology. The first TCP application is planned for the 94 SDIO SPAS 3 mission. The architecture enhances rapid tailoring of functions thereby reducing costs and schedules developed for individual spacecraft missions.

The topological requirements for robust perfect adaptation in networks of any size.

PubMed

Araujo, Robyn P; Liotta, Lance A

2018-05-01

Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.

Sensor Networks, Dataloggers, and Other Handy Gadgets Using Open-Source Electronics for the Christina River Basin CZO

NASA Astrophysics Data System (ADS)

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

2011-12-01

The search for biogeochemical "hot spots" and "hot moments" that control ecosystem-level processes requires a rethinking of how we observe the environment. Extensive multi-sensor/measurement arrays are required to realize 2D, 3D, or 4D maps of environmental properties with sufficient spatial and temporal resolution to find and understand hot spots and hot moments. To date, the cost of the data logging and communication infrastructure has been a major limitation to large-scale sensor deployment, especially for near-real-time (NRT) wireless networks. A low-cost, user-friendly alternative is needed so that resources can be prioritized toward sensor hardware rather than data acquisition and communication hardware. A flexible development platform would also allow for easy creation of other useful devices in addition to the already apparent need for economical dataloggers. The recent proliferation of open-source electronics platforms offers an opportunity for environmental observatories to deploy sensors at large scales by reducing data logging and communications costs by more than an order of magnitude. Leading the open-source electronics revolution is the Arduino project, designed to make the process of using electronics in multidisciplinary projects more accessible to hobbyists and professionals alike. A large user community has developed and shared hundreds of practical applications for projects that interface with a variety of sensors and use embedded logic to control external hardware. Likewise, dozens of companies and individuals sell low-cost Arduino-compatible boards that can connect together in a modular framework, allowing the user to quickly create devices for a wide range of applications. Based on these open-source technologies and products, we are designing and building a variety of circuit devices for use in our research watersheds. One Arduino-based device is a multi-channel datalogger that can be used with a variety of analog and digital sensors, such as pressure transducers, conductivity sensors, soil moisture and temperature probes, and redox probes. Radio modules can be added to the loggers to create a self-meshing wireless network for streaming live sensor data. A variation of the logger circuit is a smaller handheld unit with a text display that can be used when testing sensors in the field. Another useful custom device is a remote streamwater sampling system, made up of an Arduino circuit and a prepaid cell phone, allowing a user to remotely control multiple pumps by following interactive voice menus and hearing live sensor value readouts. In the lab, an Arduino circuit is used in a multi-chamber CO2 respiration experiment where it is controlling dozens of solenoid valves and logging the data from the analytical instruments. One of the biggest benefits of open source hardware is the low cost of the components. Each of the devices we have built costs less than $100 and can be assembled in a few hours. These circuits could easily be adapted to other applications or interfaced with other sensors in a variety of configurations, making the Arduino platform an incredibly useful tool for researchers.

Demagnetization Analysis in Excel (DAIE) - An open source workbook in Excel for viewing and analyzing demagnetization data from paleomagnetic discrete samples and u-channels

NASA Astrophysics Data System (ADS)

Sagnotti, Leonardo

2013-04-01

Modern rock magnetometers and stepwise demagnetization procedures result in the production of large datasets, which need a versatile and fast software for their display and analysis. Various software packages for paleomagnetic analyses have been recently developed to overcome the problems linked to the limited capability and the loss of operability of early codes written in obsolete computer languages and/or platforms, not compatible with modern 64 bit processors. The Demagnetization Analysis in Excel (DAIE) workbook is a new software that has been designed to make the analysis of demagnetization data easy and accessible on an application (Microsoft Excel) widely diffused and available on both the Microsoft Windows and Mac OS X operating systems. The widespread diffusion of Excel should guarantee a long term working life, since compatibility and functionality of current Excel files should be most likely maintained during the development of new processors and operating systems. DAIE is designed for viewing and analyzing stepwise demagnetization data of both discrete and u-channel samples. DAIE consists of a single file and has an open modular structure organized in 10 distinct worksheets. The standard demagnetization diagrams and various parameters of common use are shown on the same worksheet including selectable parameters and user's choices. The remanence characteristic components may be computed by principal component analysis (PCA) on a selected interval of demagnetization steps. Saving of the PCA data can be done both sample by sample, or in automatic by applying the selected choices to all the samples included in the file. The DAIE open structure allows easy personalization, development and improvement. The workbook has the following features which may be valuable for various users: - Operability in nearly all the computers and platforms; - Easy inputs of demagnetization data by "copy and paste" from ASCII files; - Easy export of computed parameters and demagnetization plots; - Complete control of the whole workflow and possibility of implementation of the workbook by any user; - Modular structure in distinct worksheets for each type of analyses and plots, in order to make implementation and personalization easier; - Opportunity to use the workbook for educational purposes, since all the computations and analyses are easily traceable and accessible; - Automatic and fast analysis of a large batch of demagnetization data, such as those measured on u-channel samples. The DAIE workbook and the "User manual" are available for download on a dedicated web site (http://roma2.rm.ingv.it/en/facilities/software/49/daie).

Modular forms, Schwarzian conditions, and symmetries of differential equations in physics

NASA Astrophysics Data System (ADS)

Abdelaziz, Y.; Maillard, J.-M.

2017-05-01

We give examples of infinite order rational transformations that leave linear differential equations covariant. These examples are non-trivial yet simple enough illustrations of exact representations of the renormalization group. We first illustrate covariance properties on order-two linear differential operators associated with identities relating the same {}_2F1 hypergeometric function with different rational pullbacks. These rational transformations are solutions of a differentially algebraic equation that already emerged in a paper by Casale on the Galoisian envelopes. We provide two new and more general results of the previous covariance by rational functions: a new Heun function example and a higher genus {}_2F1 hypergeometric function example. We then focus on identities relating the same {}_2F1 hypergeometric function with two different algebraic pullback transformations: such remarkable identities correspond to modular forms, the algebraic transformations being solution of another differentially algebraic Schwarzian equation that also emerged in Casale’s paper. Further, we show that the first differentially algebraic equation can be seen as a subcase of the last Schwarzian differential condition, the restriction corresponding to a factorization condition of some associated order-two linear differential operator. Finally, we also explore generalizations of these results, for instance, to {}_3F2 , hypergeometric functions, and show that one just reduces to the previous {}_2F1 cases through a Clausen identity. The question of the reduction of these Schwarzian conditions to modular correspondences remains an open question. In a _2F1 hypergeometric framework the Schwarzian condition encapsulates all the modular forms and modular equations of the theory of elliptic curves, but these two conditions are actually richer than elliptic curves or {}_2F1 hypergeometric functions, as can be seen on the Heun and higher genus example. This work is a strong incentive to develop more differentially algebraic symmetry analysis in physics.

A Design of a Modular GPHS-Stirling Power System for a Lunar Habitation Module

NASA Technical Reports Server (NTRS)

Schmitz, Paul C.; Penswick, L. Barry; Shaltens, Richard K.

2005-01-01

Lunar habitation modules need electricity and potentially heat to operate. Because of the low amounts of radiation emitted by General Purpose Heat Source (GPHS) modules, power plants incorporating these as heat sources could be placed in close proximity to habitation modules. A design concept is discussed for a high efficiency power plant based on a GPHS assembly integrated with a Stirling convertor. This system could provide both electrical power and heat, if required, for a lunar habitation module. The conceptual GPHS/Stirling system is modular in nature and made up of a basic 5.5 KWe Stirling convertor/GPHS module assembly, convertor controller/PMAD electronics, waste heat radiators, and associated thermal insulation. For the specific lunar application under investigation eight modules are employed to deliver 40 KWe to the habitation module. This design looks at three levels of Stirling convertor technology and addresses the issues of integrating the Stirling convertors with the GPHS heat sources assembly using proven technology whenever possible. In addition, issues related to the high-temperature heat transport system, power management, convertor control, vibration isolation, and potential system packaging configurations to ensure safe operation during all phases of deployment will be discussed.

The HYPE Open Source Community

NASA Astrophysics Data System (ADS)

Strömbäck, Lena; Arheimer, Berit; Pers, Charlotta; Isberg, Kristina

2013-04-01

The Hydrological Predictions for the Environment (HYPE) model is a dynamic, semi-distributed, process-based, integrated catchment model (Lindström et al., 2010). It uses well-known hydrological and nutrient transport concepts and can be applied for both small and large scale assessments of water resources and status. In the model, the landscape is divided into classes according to soil type, vegetation and altitude. The soil representation is stratified and can be divided in up to three layers. Water and substances are routed through the same flow paths and storages (snow, soil, groundwater, streams, rivers, lakes) considering turn-over and transformation on the way towards the sea. In Sweden, the model is used by water authorities to fulfil the Water Framework Directive and the Marine Strategy Framework Directive. It is used for characterization, forecasts, and scenario analyses. Model data can be downloaded for free from three different HYPE applications: Europe (www.smhi.se/e-hype), Baltic Sea basin (www.smhi.se/balt-hype), and Sweden (vattenweb.smhi.se) The HYPE OSC (hype.sourceforge.net) is an open source initiative under the Lesser GNU Public License taken by SMHI to strengthen international collaboration in hydrological modelling and hydrological data production. The hypothesis is that more brains and more testing will result in better models and better code. The code is transparent and can be changed and learnt from. New versions of the main code will be delivered frequently. The main objective of the HYPE OSC is to provide public access to a state-of-the-art operational hydrological model and to encourage hydrologic expertise from different parts of the world to contribute to model improvement. HYPE OSC is open to everyone interested in hydrology, hydrological modelling and code development - e.g. scientists, authorities, and consultancies. The HYPE Open Source Community was initiated in November 2011 by a kick-off and workshop with 50 eager participants from twelve different countries. In beginning of 2013 we will release a new version of the code featuring new and better modularization, corresponding to hydrological processes which will make the code easier to understand and further develop. During 2013 we also plan a new workshop and HYPE course for everyone interested in the community. Lindström, G., Pers, C.P., Rosberg, R., Strömqvist, J., Arheimer, B. 2010. Development and test of the HYPE (Hydrological Predictions for the Environment) model - A water quality model for different spatial scales. Hydrology Research 41.3-4:295-319

deepTools: a flexible platform for exploring deep-sequencing data.

PubMed

Ramírez, Fidel; Dündar, Friederike; Diehl, Sarah; Grüning, Björn A; Manke, Thomas

2014-07-01

We present a Galaxy based web server for processing and visualizing deeply sequenced data. The web server's core functionality consists of a suite of newly developed tools, called deepTools, that enable users with little bioinformatic background to explore the results of their sequencing experiments in a standardized setting. Users can upload pre-processed files with continuous data in standard formats and generate heatmaps and summary plots in a straight-forward, yet highly customizable manner. In addition, we offer several tools for the analysis of files containing aligned reads and enable efficient and reproducible generation of normalized coverage files. As a modular and open-source platform, deepTools can easily be expanded and customized to future demands and developments. The deepTools webserver is freely available at http://deeptools.ie-freiburg.mpg.de and is accompanied by extensive documentation and tutorials aimed at conveying the principles of deep-sequencing data analysis. The web server can be used without registration. deepTools can be installed locally either stand-alone or as part of Galaxy. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications

PubMed Central

Kalinin, Alexandr A.; Palanimalai, Selvam; Dinov, Ivo D.

2018-01-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis. PMID:29630069

SOCRAT Platform Design: A Web Architecture for Interactive Visual Analytics Applications.

PubMed

Kalinin, Alexandr A; Palanimalai, Selvam; Dinov, Ivo D

2017-04-01

The modern web is a successful platform for large scale interactive web applications, including visualizations. However, there are no established design principles for building complex visual analytics (VA) web applications that could efficiently integrate visualizations with data management, computational transformation, hypothesis testing, and knowledge discovery. This imposes a time-consuming design and development process on many researchers and developers. To address these challenges, we consider the design requirements for the development of a module-based VA system architecture, adopting existing practices of large scale web application development. We present the preliminary design and implementation of an open-source platform for Statistics Online Computational Resource Analytical Toolbox (SOCRAT). This platform defines: (1) a specification for an architecture for building VA applications with multi-level modularity, and (2) methods for optimizing module interaction, re-usage, and extension. To demonstrate how this platform can be used to integrate a number of data management, interactive visualization, and analysis tools, we implement an example application for simple VA tasks including raw data input and representation, interactive visualization and analysis.

SeeStar: an open-source, low-cost imaging system for subsea observations

NASA Astrophysics Data System (ADS)

Cazenave, F.; Kecy, C. D.; Haddock, S.

2016-02-01

Scientists and engineers at the Monterey Bay Aquarium Research Institute (MBARI) have collaborated to develop SeeStar, a modular, light weight, self-contained, low-cost subsea imaging system for short- to long-term monitoring of marine ecosystems. SeeStar is composed of separate camera, battery, and LED lighting modules. Two versions of the system exist: one rated to 300 meters depth, the other rated to 1500 meters. Users can download plans and instructions from an online repository and build the system using low-cost off-the-shelf components. The system utilizes an easily programmable Arduino based controller, and the widely distributed GoPro camera. The system can be deployed in a variety of scenarios taking still images and video and can be operated either autonomously or tethered on a range of platforms, including ROVs, AUVs, landers, piers, and moorings. Several Seestar systems have been built and used for scientific studies and engineering tests. The long-term goal of this project is to have a widely distributed marine imaging network across thousands of locations, to develop baselines of biological information.