WorldWideScience

Sample records for modeling toolbox nft

  1. Towards a binaural modelling toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Culling, John F.; Dau, Torsten

    2011-01-01

    The Auditory Modelling Toolbox (AMToolbox) is a new Matlab / Octave toolbox for developing and applying auditory perceptual models and in particular binaural models. The philosophy behind the project is that the models should be implemented in a consistent manner, well documented and user......-friendly in order to allow students and researchers to actively work with current models and further develop existing ones. In addition to providing the models, it is a goal of the project to collect published human data and denitions of model experiments. This will simplify the verication of models by running...

  2. Towards a binaural modelling toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Culling, John F.; Dau, Torsten

    2011-01-01

    The Auditory Modelling Toolbox (AMToolbox) is a new Matlab / Octave toolbox for developing and applying auditory perceptual models and in particular binaural models. The philosophy behind the project is that the models should be implemented in a consistent manner, well documented and user......-friendly in order to allow students and researchers to actively work with current models and further develop existing ones. In addition to providing the models, it is a goal of the project to collect published human data and denitions of model experiments. This will simplify the verication of models by running...... the model experiments and comparing the predictions to human data. The software is released under the GNU Public License (GPL) version 3, and can be downloaded from http://amtoolbox.sourceforge.net....

  3. A MATLAB toolbox for structural kinetic modeling.

    Science.gov (United States)

    Girbig, Dorothee; Selbig, Joachim; Grimbs, Sergio

    2012-10-01

    Structural kinetic modeling (SKM) enables the analysis of dynamical properties of metabolic networks solely based on topological information and experimental data. Current SKM-based experiments are hampered by the time-intensive process of assigning model parameters and choosing appropriate sampling intervals for Monte-Carlo experiments. We introduce a toolbox for the automatic and efficient construction and evaluation of structural kinetic models (SK models). Quantitative and qualitative analyses of network stability properties are performed in an automated manner. We illustrate the model building and analysis process in detailed example scripts that provide toolbox implementations of previously published literature models. The source code is freely available for download at http://bioinformatics.uni-potsdam.de/projects/skm. girbig@mpimp-golm.mpg.de.

  4. The Toolbox for Conditional Zebrafish Cancer Models.

    Science.gov (United States)

    Mayrhofer, Marie; Mione, Marina

    2016-01-01

    Here we describe the conditional zebrafish cancer toolbox, which allows for fine control of the expression of oncogenes or downregulation of tumor suppressors at the spatial and temporal level. Methods such as the Gal4/UAS or the Cre/lox systems paved the way to the development of elegant tumor models, which are now being used to study cancer cell biology, clonal evolution, identification of cancer stem cells and anti-cancer drug screening. Combination of these tools, as well as novel developments such as the promising genome editing system through CRISPR/Cas9 and clever application of light reactive proteins will enable the development of even more sophisticated zebrafish cancer models. Here, we introduce this growing toolbox of conditional transgenic approaches, discuss its current application in zebrafish cancer models and provide an outlook on future perspectives.

  5. TMS modeling toolbox for realistic simulation.

    Science.gov (United States)

    Cho, Young Sun; Suh, Hyun Sang; Lee, Won Hee; Kim, Tae-Seong

    2010-01-01

    Transcranial magnetic stimulation (TMS) is a technique for brain stimulation using rapidly changing magnetic fields generated by coils. It has been established as an effective stimulation technique to treat patients suffering from damaged brain functions. Although TMS is known to be painless and noninvasive, it can also be harmful to the brain by incorrect focusing and excessive stimulation which might result in seizure. Therefore there is ongoing research effort to elucidate and better understand the effect and mechanism of TMS. Lately Boundary element method (BEM) and Finite element method (FEM) have been used to simulate the electromagnetic phenomenon of TMS. However, there is a lack of general tools to generate the models of TMS due to some difficulties in realistic modeling of the human head and TMS coils. In this study, we have developed a toolbox through which one can generate high-resolution FE TMS models. The toolbox allows creating FE models of the head with isotropic and anisotropic electrical conductivities in five different tissues of the head and the coils in 3D. The generated TMS model is importable to FE software packages such as ANSYS for further and efficient electromagnetic analysis. We present a set of demonstrative results of realistic simulation of TMS with our toolbox.

  6. Object Oriented Toolbox for Modelling and Simulation of Dynamic Systems

    DEFF Research Database (Denmark)

    Thomsen, Per Grove; Poulsen, Mikael Zebbelin; Wagner, Falko Jens

    1999-01-01

    Design and Implementation of a simulation toolbox based on Object Oriented modelling Techniques.Experimental implementation in C++ using the Godess ODE-solution platform.......Design and Implementation of a simulation toolbox based on Object Oriented modelling Techniques.Experimental implementation in C++ using the Godess ODE-solution platform....

  7. Object Oriented Toolbox for Modelling and Simulation of Dynamical Systems

    DEFF Research Database (Denmark)

    Poulsen, Mikael Zebbelin; Wagner, Falko Jens; Thomsen, Per Grove

    1998-01-01

    This paper presents the results of an ongoing project, dealing with design and implementation of a simulation toolbox based on object oriented modelling techniques. The paper describes an experimental implementation of parts of such a toolbox in C++, and discusses the experiences drawn from...

  8. APPLICATION OF FUZZY LOGIC TOOLBOX FOR MODELLING FUZZY LOGIC CONTROLLERS

    OpenAIRE

    Olesiak, Krzysztof

    2017-01-01

    Computer technology, which has been developing very fast in the recent years, can be also fruitfully applied in teaching. For example, the software package Matlab is highly useful in teaching students at Bachelor Programs of Electrical Engineering and Automatics and Robotics. Fuzzy Logic Toolbox of the Matlab package can be used for designing and modelling controllers. Thanks to a large number of pre-defined elements available in the libraries, it is possible to create even highly complicated...

  9. Model Updating Nonlinear System Identification Toolbox Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology (ZONA) proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology that utilizes flight data with...

  10. Model Updating Nonlinear System Identification Toolbox Project

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology by adopting the flight data with state-of-the-art...

  11. A Module for Graphical Display of Model Results with the CBP Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2015-04-21

    This report describes work performed by the Savannah River National Laboratory (SRNL) in fiscal year 2014 to add enhanced graphical capabilities to display model results in the Cementitious Barriers Project (CBP) Toolbox. Because Version 2.0 of the CBP Toolbox has just been released, the graphing enhancements described in this report have not yet been integrated into a new version of the Toolbox. Instead they have been tested using a standalone GoldSim model and, while they are substantially complete, may undergo further refinement before full implementation. Nevertheless, this report is issued to document the FY14 development efforts which will provide a basis for further development of the CBP Toolbox.

  12. Reinforcement Toolbox, a Parametric Reinforcement Modelling Tool for Curved Surface Structures

    NARCIS (Netherlands)

    Lauppe, J.; Rolvink, A.; Coenders, J.L.

    2013-01-01

    This paper presents a computational strategy and parametric modelling toolbox which aim at enhancing the design- and production process of reinforcement in freeform curved surface structures. The computational strategy encompasses the necessary steps of raising an architectural curved surface model

  13. mpdcm: A toolbox for massively parallel dynamic causal modeling.

    Science.gov (United States)

    Aponte, Eduardo A; Raman, Sudhir; Sengupta, Biswa; Penny, Will D; Stephan, Klaas E; Heinzle, Jakob

    2016-01-15

    Dynamic causal modeling (DCM) for fMRI is an established method for Bayesian system identification and inference on effective brain connectivity. DCM relies on a biophysical model that links hidden neuronal activity to measurable BOLD signals. Currently, biophysical simulations from DCM constitute a serious computational hindrance. Here, we present Massively Parallel Dynamic Causal Modeling (mpdcm), a toolbox designed to address this bottleneck. mpdcm delegates the generation of simulations from DCM's biophysical model to graphical processing units (GPUs). Simulations are generated in parallel by implementing a low storage explicit Runge-Kutta's scheme on a GPU architecture. mpdcm is publicly available under the GPLv3 license. We found that mpdcm efficiently generates large number of simulations without compromising their accuracy. As applications of mpdcm, we suggest two computationally expensive sampling algorithms: thermodynamic integration and parallel tempering. mpdcm is up to two orders of magnitude more efficient than the standard implementation in the software package SPM. Parallel tempering increases the mixing properties of the traditional Metropolis-Hastings algorithm at low computational cost given efficient, parallel simulations of a model. Future applications of DCM will likely require increasingly large computational resources, for example, when the likelihood landscape of a model is multimodal, or when implementing sampling methods for multi-subject analysis. Due to the wide availability of GPUs, algorithmic advances can be readily available in the absence of access to large computer grids, or when there is a lack of expertise to implement algorithms in such grids. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. A Statistical Toolbox For Mining And Modeling Spatial Data

    Directory of Open Access Journals (Sweden)

    D’Aubigny Gérard

    2016-12-01

    Full Text Available Most data mining projects in spatial economics start with an evaluation of a set of attribute variables on a sample of spatial entities, looking for the existence and strength of spatial autocorrelation, based on the Moran’s and the Geary’s coefficients, the adequacy of which is rarely challenged, despite the fact that when reporting on their properties, many users seem likely to make mistakes and to foster confusion. My paper begins by a critical appraisal of the classical definition and rational of these indices. I argue that while intuitively founded, they are plagued by an inconsistency in their conception. Then, I propose a principled small change leading to corrected spatial autocorrelation coefficients, which strongly simplifies their relationship, and opens the way to an augmented toolbox of statistical methods of dimension reduction and data visualization, also useful for modeling purposes. A second section presents a formal framework, adapted from recent work in statistical learning, which gives theoretical support to our definition of corrected spatial autocorrelation coefficients. More specifically, the multivariate data mining methods presented here, are easily implementable on the existing (free software, yield methods useful to exploit the proposed corrections in spatial data analysis practice, and, from a mathematical point of view, whose asymptotic behavior, already studied in a series of papers by Belkin & Niyogi, suggests that they own qualities of robustness and a limited sensitivity to the Modifiable Areal Unit Problem (MAUP, valuable in exploratory spatial data analysis.

  15. Nutrient Film Technique (NFT Hydroponic Monitoring System

    Directory of Open Access Journals (Sweden)

    Helmy Helmy

    2016-10-01

    Full Text Available Plant cultivation using hydroponic is very popular today. Nutrient Film Technique (NFT hydroponic system is commonly used by people. It can be applied indoor or outdoor. Plants in this systemneed nutrient solution to grow well. pH, TDS and temperature of the nutrient solution must be check to ensure plant gets sufficient nutrients. This research aims todevelop monitoring system of NFT hydroponic. Farmer will be able to monitor pH, TDS and temperature online. It will ease farmer to decide which plant is suitable to be cultivated and time to boost growth.Delay of the system will be measured to know system performance. Result shows that pH is directly proportional with TDS. Temperature value has no correlation with pH and TDS. System has highest delay during daylight and afternoon but it will decline in the night and morning. Average of delay in the morning is 11 s, 28.5 s in daylight, 32 s in the afternoon and 17.5 s in the night.

  16. Testing adaptive toolbox models: a Bayesian hierarchical approach

    NARCIS (Netherlands)

    Scheibehenne, B.; Rieskamp, J.; Wagenmakers, E.-J.

    2013-01-01

    Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often

  17. The PhysIO Toolbox for Modeling Physiological Noise in fMRI Data.

    Science.gov (United States)

    Kasper, Lars; Bollmann, Steffen; Diaconescu, Andreea O; Hutton, Chloe; Heinzle, Jakob; Iglesias, Sandra; Hauser, Tobias U; Sebold, Miriam; Manjaly, Zina-Mary; Pruessmann, Klaas P; Stephan, Klaas E

    2017-01-30

    Physiological noise is one of the major confounds for fMRI. A common class of correction methods model noise from peripheral measures, such as ECGs or pneumatic belts. However, physiological noise correction has not emerged as a standard preprocessing step for fMRI data yet due to: (1) the varying data quality of physiological recordings, (2) non-standardized peripheral data formats and (3) the lack of full automatization of processing and modeling physiology, required for large-cohort studies. We introduce the PhysIO Toolbox for preprocessing of physiological recordings and model-based noise correction. It implements a variety of noise models, such as RETROICOR, respiratory volume per time and heart rate variability responses (RVT/HRV). The toolbox covers all intermediate steps - from flexible read-in of data formats to GLM regressor/contrast creation - without any manual intervention. We demonstrate the workflow of the toolbox and its functionality for datasets from different vendors, recording devices, field strengths and subject populations. Automatization of physiological noise correction and performance evaluation are reported in a group study (N=35). The PhysIO Toolbox reproduces physiological noise patterns and correction efficacy of previously implemented noise models. It increases modeling robustness by outperforming vendor-provided peak detection methods for physiological cycles. Finally, the toolbox offers an integrated framework with full automatization, including performance monitoring, and flexibility with respect to the input data. Through its platform-independent Matlab implementation, open-source distribution, and modular structure, the PhysIO Toolbox renders physiological noise correction an accessible preprocessing step for fMRI data. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

  18. DACE - A Matlab Kriging Toolbox

    DEFF Research Database (Denmark)

    2002-01-01

    DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models.......DACE, Design and Analysis of Computer Experiments, is a Matlab toolbox for working with kriging approximations to computer models....

  19. The SSI TOOLBOX Source Term Model SOSIM - Screening for important radionuclides and parameter sensitivity analysis

    International Nuclear Information System (INIS)

    Avila Moreno, R.; Barrdahl, R.; Haegg, C.

    1995-05-01

    The main objective of the present study was to carry out a screening and a sensitivity analysis of the SSI TOOLBOX source term model SOSIM. This model is a part of the SSI TOOLBOX for radiological impact assessment of the Swedish disposal concept for high-level waste KBS-3. The outputs of interest for this purpose were: the total released fraction, the time of total release, the time and value of maximum release rate, the dose rates after direct releases of the biosphere. The source term equations were derived and simple equations and methods were proposed for calculation of these. A literature survey has been performed in order to determine a characteristic variation range and a nominal value for each model parameter. In order to reduce the model uncertainties the authors recommend a change in the initial boundary condition for solution of the diffusion equation for highly soluble nuclides. 13 refs

  20. ALTWAVE: Toolbox for use of satellite L2P altimeter data for wave model validation

    Science.gov (United States)

    Appendini, Christian M.; Camacho-Magaña, Víctor; Breña-Naranjo, José Agustín

    2016-03-01

    To characterize some of the world's ocean physical processes such as its wave height, wind speed and sea surface elevation is a major need for coastal and marine infrastructure planning and design, tourism activities, wave power and storm surge risk assessment, among others. Over the last decades, satellite remote sensing tools have provided quasi-global measurements of ocean altimetry by merging data from different satellite missions. While there is a widely use of altimeter data for model validation, practical tools for model validation remain scarce. Our purpose is to fill this gap by introducing ALTWAVE, a MATLAB user-oriented toolbox for oceanographers and coastal engineers developed to validate wave model results based on visual features and statistical estimates against satellite derived altimetry. Our toolbox uses altimetry information from the GlobWave initiative, and provides a sample application to validate a one year wave hindcast for the Gulf of Mexico. ALTWAVE also offers an effective toolbox to validate wave model results using altimeter data, as well as a guidance for non-experienced satellite data users. This article is intended for wave modelers with no experience using altimeter data to validate their results.

  1. Tolerance of continuous NFT spectrum to the optical fiber channel impairments

    DEFF Research Database (Denmark)

    Gaiarin, Simone; Da Ros, Francesco; Sørensen, Mads Peter

    2016-01-01

    The impact of launch power, additive white Gaussian noise and fiber loss on the nonlinear Fourier transform (NFT) continuous spectrum is investigated. NFT is shown to undergo lower spectral distortion than the discrete Fourier transform.......The impact of launch power, additive white Gaussian noise and fiber loss on the nonlinear Fourier transform (NFT) continuous spectrum is investigated. NFT is shown to undergo lower spectral distortion than the discrete Fourier transform....

  2. Model Updating Nonlinear System Identification Toolbox, Phase II

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology (ZONA) proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology that utilizes flight data with...

  3. MOtoNMS: A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation.

    Science.gov (United States)

    Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

    2015-01-01

    Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust tools for the pre-processing of experimental movement data for their use in neuromusculoskeletal modeling software. This paper presents MOtoNMS (matlab MOtion data elaboration TOolbox for NeuroMusculoSkeletal applications), a toolbox freely available to the community, that aims to fill this lack. MOtoNMS processes experimental data from different motion analysis devices and generates input data for neuromusculoskeletal modeling and simulation software, such as OpenSim and CEINMS (Calibrated EMG-Informed NMS Modelling Toolbox). MOtoNMS implements commonly required processing steps and its generic architecture simplifies the integration of new user-defined processing components. MOtoNMS allows users to setup their laboratory configurations and processing procedures through user-friendly graphical interfaces, without requiring advanced computer skills. Finally, configuration choices can be stored enabling the full reproduction of the processing steps. MOtoNMS is released under GNU General Public License and it is available at the SimTK website and from the GitHub repository. Motion data collected at four institutions demonstrate that, despite differences in laboratory instrumentation and procedures, MOtoNMS succeeds in processing data and producing consistent inputs for OpenSim and CEINMS. MOtoNMS fills the gap between motion analysis and neuromusculoskeletal modeling and simulation. Its support to several devices, a complete implementation of the pre-processing procedures, its simple extensibility, the available user interfaces, and its free availability can boost the translation of neuromusculoskeletal methods in daily and clinical practice.

  4. Model Updating Nonlinear System Identification Toolbox, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — ZONA Technology proposes to develop an enhanced model updating nonlinear system identification (MUNSID) methodology by adopting the flight data with state-of-the-art...

  5. The Visible Signature Modelling and Evaluation ToolBox

    Science.gov (United States)

    2008-12-01

    Rhinoceros . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 2.5.2 MODTRAN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33...HYDROLIGHT. The commercial support software has a number of dif- ferent functionalities. Rhinoceros provides the wireframe models required as input...Greyscale texture synthesis takes a greyscale input image and a uniform white -noise texture. The white -noise texture is modified to reproduce certain

  6. Model Identification and Validation for a Heating System using MATLAB System Identification Toolbox

    International Nuclear Information System (INIS)

    Rabbani, Muhammad Junaid; Hussain, Kashan; Khan, Asim-ur-Rehman; Ali, Abdullah

    2013-01-01

    This paper proposed a systematic approach to select a mathematical model for an industrial heating system by adopting system identification techniques with the aim of fulfilling the design requirement for the controller. The model identification process will begin by collecting real measurement data samples with the aid of MATLAB system identification toolbox. The criteria for selecting the model that could validate model output with actual data will based upon: parametric identification technique, picking the best model structure with low order among ARX, ARMAX and BJ, and then applying model estimation and validation tests. Simulated results have shown that the BJ model has been best in providing good estimation and validation based upon performance criteria such as: final prediction error, loss function, best percentage of model fit, and co-relation analysis of residual for output

  7. Cantera Integration with the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Lavelle, Thomas M.; Chapman, Jeffryes W.; May, Ryan D.; Litt, Jonathan S.; Guo, Ten-Huei

    2014-01-01

    NASA Glenn Research Center (GRC) has recently developed a software package for modeling generic thermodynamic systems called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a library of building blocks that can be assembled to represent any thermodynamic system in the Simulink (The MathWorks, Inc.) environment. These elements, along with a Newton Raphson solver (also provided as part of the T-MATS package), enable users to create models of a wide variety of systems. The current version of T-MATS (v1.0.1) uses tabular data for providing information about a specific mixture of air, water (humidity), and hydrocarbon fuel in calculations of thermodynamic properties. The capabilities of T-MATS can be expanded by integrating it with the Cantera thermodynamic package. Cantera is an object-oriented analysis package that calculates thermodynamic solutions for any mixture defined by the user. Integration of Cantera with T-MATS extends the range of systems that may be modeled using the toolbox. In addition, the library of elements released with Cantera were developed using MATLAB native M-files, allowing for quicker prototyping of elements. This paper discusses how the new Cantera-based elements are created and provides examples for using T-MATS integrated with Cantera.

  8. Improved saliency toolbox/Itti model for region of interest extraction

    Science.gov (United States)

    He, Dong-Jian; Liu, Shang-Wang; Liang, Xin-Hong; Cai, Cheng

    2011-09-01

    The saliency toolbox (STB)/Itti model is an outstanding computational selective visual attention model. In this paper, we propose an improved STB/Itti model to overcome the drawback of STB/Itti--its output ``saliency map'' is not large enough for region of interest (ROI) extraction. First, we employ a simplified pulse coupled neural network (PCNN) with a special input image, and more importantly, the PCNN does not require iterations. Subsequently, the PCNN takes the place of the winner-take-all network in STB/Itti. Experimental results show that the improved STB/Itti model works well for ROI extraction, with the mean area under the curve value of 0.8306 and robustness against noise and geometric attacks. The proposed model can greatly enhance the performances of both STB/Itti and PCNN model in image processing.

  9. AN OPEN SOURCE GEOVISUAL ANALYTICS TOOLBOX FOR MULTIVARIATE SPATIO-TEMPORAL DATA IN ENVIRONMENTAL CHANGE MODELLING

    Directory of Open Access Journals (Sweden)

    M. Bernasocchi

    2012-07-01

    Full Text Available In environmental change studies, often multiple variables are measured or modelled, and temporal information is essential for the task. These multivariate geographic time-series datasets are often big and difficult to analyse. While many established methods such as PCP (parallel coordinate plots, STC (space-time cubes, scatter-plots and multiple (linked visualisations help provide more information, we observe that most of the common geovisual analytics suits do not include three-dimensional (3D visualisations. However, in many environmental studies, we hypothesize that the addition of 3D terrain visualisations along with appropriate data plots and two-dimensional views can help improve the analysts’ ability to interpret the spatial relevance better. To test our ideas, we conceptualize, develop, implement and evaluate a geovisual analytics toolbox in a user-centred manner. The conceptualization of the tool is based on concrete user needs that have been identified and collected during informal brainstorming sessions and in a structured focus group session prior to the development. The design process, therefore, is based on a combination of user-centred design with a requirement analysis and agile development. Based on the findings from this phase, the toolbox was designed to have a modular structure and was built on open source geographic information systems (GIS program Quantum GIS (QGIS, thus benefiting from existing GIS functionality. The modules include a globe view for 3D terrain visualisation (OSGEarth, a scattergram, a time vs. value plot, and a 3D helix visualisation as well as the possibility to view the raw data. The visualisation frame allows real-time linking of these representations. After the design and development stage, a case study was created featuring data from Zermatt valley and the toolbox was evaluated based on expert interviews. Analysts performed multiple spatial and temporal tasks with the case study using the toolbox

  10. CADLIVE toolbox for MATLAB: automatic dynamic modeling of biochemical networks with comprehensive system analysis.

    Science.gov (United States)

    Inoue, Kentaro; Maeda, Kazuhiro; Miyabe, Takaaki; Matsuoka, Yu; Kurata, Hiroyuki

    2014-09-01

    Mathematical modeling has become a standard technique to understand the dynamics of complex biochemical systems. To promote the modeling, we had developed the CADLIVE dynamic simulator that automatically converted a biochemical map into its associated mathematical model, simulated its dynamic behaviors and analyzed its robustness. To enhance the feasibility by CADLIVE and extend its functions, we propose the CADLIVE toolbox available for MATLAB, which implements not only the existing functions of the CADLIVE dynamic simulator, but also the latest tools including global parameter search methods with robustness analysis. The seamless, bottom-up processes consisting of biochemical network construction, automatic construction of its dynamic model, simulation, optimization, and S-system analysis greatly facilitate dynamic modeling, contributing to the research of systems biology and synthetic biology. This application can be freely downloaded from http://www.cadlive.jp/CADLIVE_MATLAB/ together with an instruction.

  11. An Emulator Toolbox to Approximate Radiative Transfer Models with Statistical Learning

    Directory of Open Access Journals (Sweden)

    Juan Pablo Rivera

    2015-07-01

    Full Text Available Physically-based radiative transfer models (RTMs help in understanding the processes occurring on the Earth’s surface and their interactions with vegetation and atmosphere. When it comes to studying vegetation properties, RTMs allows us to study light interception by plant canopies and are used in the retrieval of biophysical variables through model inversion. However, advanced RTMs can take a long computational time, which makes them unfeasible in many real applications. To overcome this problem, it has been proposed to substitute RTMs through so-called emulators. Emulators are statistical models that approximate the functioning of RTMs. Emulators are advantageous in real practice because of the computational efficiency and excellent accuracy and flexibility for extrapolation. We hereby present an “Emulator toolbox” that enables analysing multi-output machine learning regression algorithms (MO-MLRAs on their ability to approximate an RTM. The toolbox is included in the free-access ARTMO’s MATLAB suite for parameter retrieval and model inversion and currently contains both linear and non-linear MO-MLRAs, namely partial least squares regression (PLSR, kernel ridge regression (KRR and neural networks (NN. These MO-MLRAs have been evaluated on their precision and speed to approximate the soil vegetation atmosphere transfer model SCOPE (Soil Canopy Observation, Photochemistry and Energy balance. SCOPE generates, amongst others, sun-induced chlorophyll fluorescence as the output signal. KRR and NN were evaluated as capable of reconstructing fluorescence spectra with great precision. Relative errors fell below 0.5% when trained with 500 or more samples using cross-validation and principal component analysis to alleviate the underdetermination problem. Moreover, NN reconstructed fluorescence spectra about 50-times faster and KRR about 800-times faster than SCOPE. The Emulator toolbox is foreseen to open new opportunities in the use of advanced

  12. DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

    Science.gov (United States)

    Sherfey, Jason S; Soplata, Austin E; Ardid, Salva; Roberts, Erik A; Stanley, David A; Pittman-Polletta, Benjamin R; Kopell, Nancy J

    2018-01-01

    DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

  13. SimTB, a simulation toolbox for fMRI data under a model of spatiotemporal separability.

    Science.gov (United States)

    Erhardt, Erik B; Allen, Elena A; Wei, Yonghua; Eichele, Tom; Calhoun, Vince D

    2012-02-15

    We introduce SimTB, a MATLAB toolbox designed to simulate functional magnetic resonance imaging (fMRI) datasets under a model of spatiotemporal separability. The toolbox meets the increasing need of the fMRI community to more comprehensively understand the effects of complex processing strategies by providing a ground truth that estimation methods may be compared against. SimTB captures the fundamental structure of real data, but data generation is fully parameterized and fully controlled by the user, allowing for accurate and precise comparisons. The toolbox offers a wealth of options regarding the number and configuration of spatial sources, implementation of experimental paradigms, inclusion of tissue-specific properties, addition of noise and head movement, and much more. A straightforward data generation method and short computation time (3-10 seconds for each dataset) allow a practitioner to simulate and analyze many datasets to potentially understand a problem from many angles. Beginning MATLAB users can use the SimTB graphical user interface (GUI) to design and execute simulations while experienced users can write batch scripts to automate and customize this process. The toolbox is freely available at http://mialab.mrn.org/software together with sample scripts and tutorials. Copyright © 2011 Elsevier Inc. All rights reserved.

  14. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    Directory of Open Access Journals (Sweden)

    Jensen Paul A

    2011-09-01

    Full Text Available Abstract Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data.

  15. Production of calla lily grown in an NFT system

    Directory of Open Access Journals (Sweden)

    Paulo Roberto Correa Landgraf

    2017-12-01

    Full Text Available The objective of this study was to evaluate the production of calla lily in an NFT system. The experiment was carried out in a greenhouse, using a 2 x 2 factorial scheme in a completely randomized design (CRD, with fifteen replications. The treatments were a combination of two hydroponic profiles (100 and 150 mm of height and two nutrient solutions. Calla lily plantlets obtained from rhizome buds in trays containing nutrient solution, were transferred to a laminar flow of nutrients, and the experiment lasted 12 months. The height of stems and inflorescences were evaluated, as well as the length and diameter of the inflorescence, the number of flowers per plant and number of flowers per m2 . Growing calla lily plants in an NFT system is feasible. The nutrient solution with the highest concentration of nutrients, particularly N and K, and the profile of 150 mm, are the most suitable for the production of calla lily as a cut flower in a laminar flow of nutrients.

  16. MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models

    Science.gov (United States)

    Aurich, Maike K.; Fleming, Ronan M. T.; Thiele, Ines

    2016-01-01

    Metabolomic data sets provide a direct read-out of cellular phenotypes and are increasingly generated to study biological questions. Previous work, by us and others, revealed the potential of analyzing extracellular metabolomic data in the context of the metabolic model using constraint-based modeling. With the MetaboTools, we make our methods available to the broader scientific community. The MetaboTools consist of a protocol, a toolbox, and tutorials of two use cases. The protocol describes, in a step-wise manner, the workflow of data integration, and computational analysis. The MetaboTools comprise the Matlab code required to complete the workflow described in the protocol. Tutorials explain the computational steps for integration of two different data sets and demonstrate a comprehensive set of methods for the computational analysis of metabolic models and stratification thereof into different phenotypes. The presented workflow supports integrative analysis of multiple omics data sets. Importantly, all analysis tools can be applied to metabolic models without performing the entire workflow. Taken together, the MetaboTools constitute a comprehensive guide to the intra-model analysis of extracellular metabolomic data from microbial, plant, or human cells. This computational modeling resource offers a broad set of computational analysis tools for a wide biomedical and non-biomedical research community. PMID:27536246

  17. DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation

    Directory of Open Access Journals (Sweden)

    Jason S. Sherfey

    2018-03-01

    Full Text Available DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML, simulators (e.g., NEURON, Brian, NEST, and web-based applications (e.g., Geppetto outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community.

  18. Sediment and pollutant load modelling using an integrated urban drainage modelling toolbox: an application of City Drain.

    Science.gov (United States)

    Rodríguez, J P; Achleitner, S; Möderl, M; Rauch, W; Maksimović, C; McIntyre, N; Díaz-Granados, M A; Rodríguez, M S

    2010-01-01

    Numerical and computational modelling of flow and pollutant dynamics in urban drainage systems is becoming more and more integral to planning and design. The main aim of integrated flow and pollutant models is to quantify the efficiency of different measures at reducing the amount of pollutants discharged into receiving water bodies and minimise the consequent negative water quality impact. The open source toolbox CITY DRAIN developed in the Matlab/Simulink environment, which was designed for integrated modelling of urban drainage systems, is used in this work. The goal in this study was to implement and test computational routines for representing sediment and pollutant loads in order to evaluate catchment surface pollution. Tested models estimate the accumulation, erosion and transport of pollutants--aggregately--on urban surfaces and in sewers. The toolbox now includes mathematical formulations for accumulation of pollutants during dry weather period and their wash-off during rainfall events. The experimental data acquired in a previous research project carried out by the Environmental Engineering Research Centre (CIIA) at the Universidad de los Andes in Bogotá (Colombia) was used for the calibration of the models. Different numerical approaches were tested for their ability to calibrate to the sediment transport conditions. Initial results indicate, when there is more than one peak during the rainfall event duration, wash-off processes probably can be better represented using a model based on the flow instead of the rainfall intensity. Additionally, it was observed that using more detailed models (compared with an instantaneous approach) for representing pollutant accumulation do not necessarily lead to better results.

  19. Building the Nanoplasmonics Toolbox Through Shape Modeling and Single Particle Optical Studies

    Science.gov (United States)

    Ringe, Emilie

    Interest in nanotechnology is driven by unprecedented properties tailorability, achievable by controlling particle structure and composition. Unlike bulk components, minute changes in size and shape affect the optical and electronic properties of nanoparticles. Characterization of such structure-function relationships and better understanding of structure control mechanisms is crucial to the development of applications such as plasmonic sensors and devices. The objective of the current research is thus twofold: to theoretically predict and understand how shape is controlled by synthesis conditions, and to experimentally unravel, through single particle studies, how shape, composition, size, and surrounding environment affect plasmonic properties in noble metal particles. Quantitative, predictive rules and fundamental knowledge obtained from this research contributes to the "nanoplasmonics toolbox", a library designed to provide scientists and engineers the tools to create and optimize novel nanotechnology applications. In this dissertation, single particle approaches are developed and used to unravel the effects of size, shape, substrate, aggregation state and surrounding environment on the optical response of metallic nanoparticles. Ag and Au nanocubes on different substrates are first presented, followed by the discussion of the concept of plasmon length, a universal parameter to describe plasmon energy for a variety of particle shapes and plasmon modes. Plasmonic sensing (both refractive index sensing and surface-enhanced Raman spectroscopy) and polarization effects are then studied at the single particle level. In the last two Chapters, analytical shape models based on the Wulff construction provide unique modeling tools for alloy and kinetically grown nanoparticles. The former reveals a size-dependence of the shape of small alloy particles (such as those used in catalysis) because of surface segregation, while the latter uniquely models the shape of many

  20. Convis: A Toolbox to Fit and Simulate Filter-Based Models of Early Visual Processing.

    Science.gov (United States)

    Huth, Jacob; Masquelier, Timothée; Arleo, Angelo

    2018-01-01

    We developed Convis , a Python simulation toolbox for large scale neural populations which offers arbitrary receptive fields by 3D convolutions executed on a graphics card. The resulting software proves to be flexible and easily extensible in Python, while building on the PyTorch library (The Pytorch Project, 2017), which was previously used successfully in deep learning applications, for just-in-time optimization and compilation of the model onto CPU or GPU architectures. An alternative implementation based on Theano (Theano Development Team, 2016) is also available, although not fully supported. Through automatic differentiation, any parameter of a specified model can be optimized to approach a desired output which is a significant improvement over e.g., Monte Carlo or particle optimizations without gradients. We show that a number of models including even complex non-linearities such as contrast gain control and spiking mechanisms can be implemented easily. We show in this paper that we can in particular recreate the simulation results of a popular retina simulation software VirtualRetina (Wohrer and Kornprobst, 2009), with the added benefit of providing (1) arbitrary linear filters instead of the product of Gaussian and exponential filters and (2) optimization routines utilizing the gradients of the model. We demonstrate the utility of 3d convolution filters with a simple direction selective filter. Also we show that it is possible to optimize the input for a certain goal, rather than the parameters, which can aid the design of experiments as well as closed-loop online stimulus generation. Yet, Convis is more than a retina simulator. For instance it can also predict the response of V1 orientation selective cells. Convis is open source under the GPL-3.0 license and available from https://github.com/jahuth/convis/ with documentation at https://jahuth.github.io/convis/.

  1. Advances in porcine genomics and proteomics - a toolbox for developing the pig as a model organism for molecular biomedical research

    DEFF Research Database (Denmark)

    Bendixen, Emøke; Danielsen, Marianne; Larsen, Knud

    2010-01-01

    Our current knowledge of human biology is often based on studying a wide range of animal species. In particular, for understanding human diseases, the development of adequate animal models is of immediate importance. Although genetic strains and transgenic animal model organisms like fruit fly...... the pig into a novel model organism for biomedical research. This toolbox includes the near completion of the pig genome, catalogues of genes and genetic variation in pigs, extensive characterization of pig proteomes and transcriptomes, as well as the development of transgenic disease models. The aim...

  2. A Data Analysis Toolbox for Modeling the Global Food-Energy-Water Nexus

    Science.gov (United States)

    AghaKouchak, A.; Sadegh, M.; Mallakpour, I.

    2017-12-01

    Water, Food and energy systems are highly interconnected. More than seventy percent of global water resource is used for food production. Water withdrawal, purification, and transfer systems are energy intensive. Furthermore, energy generation strongly depends on water availability. Therefore, considering the interactions in the nexus of water, food and energy is crucial for sustainable management of available resources. In this presentation, we introduce a user-friendly data analysis toolbox that mines the available global data on food, energy and water, and analyzes their interactions. This toolbox provides estimates of water footprint for a wide range of food types in different countries and also approximates the required energy and water resources. The toolbox also provides estimates of the corresponding emissions and biofuel production of different crops. In summary, this toolbox allows evaluating dependencies of the food, energy, and water systems at the country scale. We present global analysis of the interactions between water, food and energy from different perspectives including efficiency and diversity of resources use.

  3. Virtual toolbox

    Science.gov (United States)

    Jacobus, Charles J.; Jacobus, Heidi N.; Mitchell, Brian T.; Riggs, A. J.; Taylor, Mark J.

    1993-04-01

    At least three of the five senses must be fully addressed in a successful virtual reality (VR) system. Sight, sound, and touch are the most critical elements for the creation of the illusion of presence. Since humans depend so much on sight to collect information about their environment, this area has been the focus of much of the prior art in virtual reality, however, it is also crucial that we provide facilities for force, torque, and touch reflection, and sound replay and 3-D localization. In this paper we present a sampling of hardware and software in the virtual environment maker's `toolbox' which can support rapidly building up of customized VR systems. We provide demonstrative examples of how some of the tools work and we speculate about VR applications and future technology needs.

  4. a Matlab Toolbox for Basin Scale Fluid Flow Modeling Applied to Hydrology and Geothermal Energy

    Science.gov (United States)

    Alcanie, M.; Lupi, M.; Carrier, A.

    2017-12-01

    Recent boosts in the development of geothermal energy were fostered by the latest oil crises and by the need of reducing CO2 emissions generated by the combustion of fossil fuels. Various numerical codes (e.g. FEHM, CSMP++, HYDROTHERM, TOUGH) have thus been implemented for the simulation and quantification of fluid flow in the upper crust. One possible limitation of such codes is the limited accessibility and the complex structure of the simulators. For this reason, we began to develop a Hydrothermal Fluid Flow Matlab library as part of MRST (Matlab Reservoir Simulation Toolbox). MRST is designed for the simulation of oil and gas problems including carbon capture storage. However, a geothermal module is still missing. We selected the Geneva Basin as a natural laboratory because of the large amount of data available in the region. The Geneva Basin has been intensely investigated in the past with exploration wells, active seismic and gravity surveys. In addition, the energy strategy of Switzerland promotes the development of geothermal energy that lead to recent geophysical prospections. Previous and ongoing projects have shown the geothermal potential of the Geneva Basin but a consistent fluid flow model assessing the deep circulation in the region is yet to be defined. The first step of the study was to create the basin-scale static model. We integrated available active seismic, gravity inversions and borehole data to describe the principal geologic and tectonic features of the Geneva Basin. Petrophysical parameters were obtained from available and widespread well logs. This required adapting MRST to standard text format file imports and outline a new methodology for quick static model creation in an open source environment. We implemented several basin-scale fluid flow models to test the effects of petrophysical properties on the circulation dynamics of deep fluids in the Geneva Basin. Preliminary results allow the identification of preferential fluid flow

  5. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

    Directory of Open Access Journals (Sweden)

    Rasmus Agren

    Full Text Available We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production.

  6. The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum.

    Science.gov (United States)

    Agren, Rasmus; Liu, Liming; Shoaie, Saeed; Vongsangnak, Wanwipa; Nookaew, Intawat; Nielsen, Jens

    2013-01-01

    We present the RAVEN (Reconstruction, Analysis and Visualization of Metabolic Networks) Toolbox: a software suite that allows for semi-automated reconstruction of genome-scale models. It makes use of published models and/or the KEGG database, coupled with extensive gap-filling and quality control features. The software suite also contains methods for visualizing simulation results and omics data, as well as a range of methods for performing simulations and analyzing the results. The software is a useful tool for system-wide data analysis in a metabolic context and for streamlined reconstruction of metabolic networks based on protein homology. The RAVEN Toolbox workflow was applied in order to reconstruct a genome-scale metabolic model for the important microbial cell factory Penicillium chrysogenum Wisconsin54-1255. The model was validated in a bibliomic study of in total 440 references, and it comprises 1471 unique biochemical reactions and 1006 ORFs. It was then used to study the roles of ATP and NADPH in the biosynthesis of penicillin, and to identify potential metabolic engineering targets for maximization of penicillin production.

  7. ESA Atmospheric Toolbox

    Science.gov (United States)

    Niemeijer, Sander

    2017-04-01

    The ESA Atmospheric Toolbox (BEAT) is one of the ESA Sentinel Toolboxes. It consists of a set of software components to read, analyze, and visualize a wide range of atmospheric data products. In addition to the upcoming Sentinel-5P mission it supports a wide range of other atmospheric data products, including those of previous ESA missions, ESA Third Party missions, Copernicus Atmosphere Monitoring Service (CAMS), ground based data, etc. The toolbox consists of three main components that are called CODA, HARP and VISAN. CODA provides interfaces for direct reading of data from earth observation data files. These interfaces consist of command line applications, libraries, direct interfaces to scientific applications (IDL and MATLAB), and direct interfaces to programming languages (C, Fortran, Python, and Java). CODA provides a single interface to access data in a wide variety of data formats, including ASCII, binary, XML, netCDF, HDF4, HDF5, CDF, GRIB, RINEX, and SP3. HARP is a toolkit for reading, processing and inter-comparing satellite remote sensing data, model data, in-situ data, and ground based remote sensing data. The main goal of HARP is to assist in the inter-comparison of datasets. By appropriately chaining calls to HARP command line tools one can pre-process datasets such that two datasets that need to be compared end up having the same temporal/spatial grid, same data format/structure, and same physical unit. The toolkit comes with its own data format conventions, the HARP format, which is based on netcdf/HDF. Ingestion routines (based on CODA) allow conversion from a wide variety of atmospheric data products to this common format. In addition, the toolbox provides a wide range of operations to perform conversions on the data such as unit conversions, quantity conversions (e.g. number density to volume mixing ratios), regridding, vertical smoothing using averaging kernels, collocation of two datasets, etc. VISAN is a cross-platform visualization and

  8. Orbit Determination Toolbox

    Science.gov (United States)

    Carpenter, James R.; Berry, Kevin; Gregpru. Late; Speckman, Keith; Hur-Diaz, Sun; Surka, Derek; Gaylor, Dave

    2010-01-01

    The Orbit Determination Toolbox is an orbit determination (OD) analysis tool based on MATLAB and Java that provides a flexible way to do early mission analysis. The toolbox is primarily intended for advanced mission analysis such as might be performed in concept exploration, proposal, early design phase, or rapid design center environments. The emphasis is on flexibility, but it has enough fidelity to produce credible results. Insight into all flight dynamics source code is provided. MATLAB is the primary user interface and is used for piecing together measurement and dynamic models. The Java Astrodynamics Toolbox is used as an engine for things that might be slow or inefficient in MATLAB, such as high-fidelity trajectory propagation, lunar and planetary ephemeris look-ups, precession, nutation, polar motion calculations, ephemeris file parsing, and the like. The primary analysis functions are sequential filter/smoother and batch least-squares commands that incorporate Monte-Carlo data simulation, linear covariance analysis, measurement processing, and plotting capabilities at the generic level. These functions have a user interface that is based on that of the MATLAB ODE suite. To perform a specific analysis, users write MATLAB functions that implement truth and design system models. The user provides his or her models as inputs to the filter commands. The software provides a capability to publish and subscribe to a software bus that is compliant with the NASA Goddard Mission Services Evolution Center (GMSEC) standards, to exchange data with other flight dynamics tools to simplify the flight dynamics design cycle. Using the publish and subscribe approach allows for analysts in a rapid design center environment to seamlessly incorporate changes in spacecraft and mission design into navigation analysis and vice versa.

  9. GOCE user toolbox and tutorial

    DEFF Research Database (Denmark)

    Knudsen, Per; Benveniste, Jerome

    2011-01-01

    consists of a series of advanced computer routines that carry out the required computations. It may be used on Windows PCs, UNIX/Linux Workstations, and Mac. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. A set of a-priori data and models are made...

  10. The Life Cycle Analysis Toolbox

    International Nuclear Information System (INIS)

    Bishop, L.; Tonn, B.E.; Williams, K.A.; Yerace, P.; Yuracko, K.L.

    1999-01-01

    The life cycle analysis toolbox is a valuable integration of decision-making tools and supporting materials developed by Oak Ridge National Laboratory (ORNL) to help Department of Energy managers improve environmental quality, reduce costs, and minimize risk. The toolbox provides decision-makers access to a wide variety of proven tools for pollution prevention (P2) and waste minimization (WMin), as well as ORNL expertise to select from this toolbox exactly the right tool to solve any given P2/WMin problem. The central element of the toolbox is a multiple criteria approach to life cycle analysis developed specifically to aid P2/WMin decision-making. ORNL has developed numerous tools that support this life cycle analysis approach. Tools are available to help model P2/WMin processes, estimate human health risks, estimate costs, and represent and manipulate uncertainties. Tools are available to help document P2/WMin decision-making and implement programs. Tools are also available to help track potential future environmental regulations that could impact P2/WMin programs and current regulations that must be followed. An Internet-site will provide broad access to the tools

  11. Induced Norm Control Toolbox

    DEFF Research Database (Denmark)

    Beran, Eric Bengt

    1996-01-01

    This paper describes the basic nature of the InducedNorm Control Toolbox (INCT). The toolbox is a set of Matlab-filesusing LMITOOL and the Semidefinite Programming package(SP). Thetoolbox is public domain. The INCT provides a series of analysisand synthesis tools for continuous time...

  12. Air Sensor Toolbox

    Science.gov (United States)

    Air Sensor Toolbox provides information to citizen scientists, researchers and developers interested in learning more about new lower-cost compact air sensor technologies and tools for measuring air quality.

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

    Science.gov (United States)

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

  14. Overview and application of the Model Optimization, Uncertainty, and SEnsitivity Analysis (MOUSE) toolbox

    Science.gov (United States)

    For several decades, optimization and sensitivity/uncertainty analysis of environmental models has been the subject of extensive research. Although much progress has been made and sophisticated methods developed, the growing complexity of environmental models to represent real-world systems makes it...

  15. A Simulation Platform To Model, Optimize And Design Wind Turbines. The Matlab/Simulink Toolbox

    Directory of Open Access Journals (Sweden)

    Anca Daniela HANSEN

    2002-12-01

    Full Text Available In the last years Matlab / Simulink® has become the most used software for modeling and simulation of dynamic systems. Wind energy conversion systems are for example such systems, containing subsystems with different ranges of the time constants: wind, turbine, generator, power electronics, transformer and grid. The electrical generator and the power converter need the smallest simulation step and therefore, these blocks decide the simulation speed. This paper presents a new and integrated simulation platform for modeling, optimizing and designing wind turbines. The platform contains different simulation tools: Matlab / Simulink - used as basic modeling tool, HAWC, DIgSilent and Saber.

  16. Traffic analysis toolbox volume XI : weather and traffic analysis, modeling and simulation.

    Science.gov (United States)

    2010-12-01

    This document presents a weather module for the traffic analysis tools program. It provides traffic engineers, transportation modelers and decisions makers with a guide that can incorporate weather impacts into transportation system analysis and mode...

  17. MOtoNMS : A MATLAB toolbox to process motion data for neuromusculoskeletal modeling and simulation

    NARCIS (Netherlands)

    Mantoan, Alice; Pizzolato, Claudio; Sartori, Massimo; Sawacha, Zimi; Cobelli, Claudio; Reggiani, Monica

    2015-01-01

    Background: Neuromusculoskeletal modeling and simulation enable investigation of the neuromusculoskeletal system and its role in human movement dynamics. These methods are progressively introduced into daily clinical practice. However, a major factor limiting this translation is the lack of robust

  18. Aeolus Toolbox for Dynamics Wind Farm Model, Simulation and Control

    DEFF Research Database (Denmark)

    Grunnet, Jacob Deleuran; Soltani, Mohsen; Knudsen, Torben

    2010-01-01

    This paper presents the wind farm simulation modeldeveloped in the EU-FP7 project, AEOLUS. Theidea is to provide a publicly available simulationpackage for researchers developing farm level controlsolutions. With the software it is possible toauto generate a wind farm simulation model in Matlab...

  19. A 3D Toolbox to Enhance Physiological Relevance of Human Tissue Models

    NARCIS (Netherlands)

    Picollet-D'hahan, N.; Dolega, M.E.; Liguori, L.; Marquette, C.; le Gac, Severine; Gidrol, X.; Martin, D.K.

    2016-01-01

    We discuss the current challenges and future prospects of flow-based organoid models and 3D self-assembling scaffolds. The existing paradigm of 3D culture suffers from a lack of control over organoid size and shape; can be an obstacle for cell harvesting and extended cellular and molecular analysis;

  20. Regensim – Matlab toolbox for renewable energy sources modelling and simulation

    Directory of Open Access Journals (Sweden)

    Cristian Dragoş Dumitru

    2011-12-01

    Full Text Available This paper deals with the implementation and development of a Matlab Simulink library named RegenSim designed for modeling, simulations and analysis of real hybrid solarwind-hydro systems connected to local grids. Blocks like wind generators, hydro generators, solar photovoltaic modules and accumulators are implemented. The main objective is the study of the hybrid power system behavior, which allows employing renewable and variable in time energy sources while providing a continuous supply.

  1. A Simulation Platform To Model, Optimize And Design Wind Turbines. The Matlab/Simulink Toolbox

    OpenAIRE

    Anca Daniela HANSEN; Frede BLAABJERG; Florin IOV

    2002-01-01

    In the last years Matlab / Simulink® has become the most used software for modeling and simulation of dynamic systems. Wind energy conversion systems are for example such systems, containing subsystems with different ranges of the time constants: wind, turbine, generator, power electronics, transformer and grid. The electrical generator and the power converter need the smallest simulation step and therefore, these blocks decide the simulation speed. This paper presents a new and integrated si...

  2. The NNSYSID Toolbox - A MATLAB Toolbox for System Identification with Neural Networks

    OpenAIRE

    Nørgård, Peter Magnus; Ravn, Ole; Hansen, Lars Kai; Poulsen, Niels Kjølstad

    1996-01-01

    To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms for determination of optimal network architectures. The toolbox should be regarded as a nonlinear extension to the system identification toolbox provided by The MathWorks, Inc. This paper gives a brief overview ...

  3. Complete scanpaths analysis toolbox.

    Science.gov (United States)

    Augustyniak, Piotr; Mikrut, Zbigniew

    2006-01-01

    This paper presents a complete open software environment for control, data processing and assessment of visual experiments. Visual experiments are widely used in research on human perception physiology and the results are applicable to various visual information-based man-machine interfacing, human-emulated automatic visual systems or scanpath-based learning of perceptual habits. The toolbox is designed for Matlab platform and supports infra-red reflection-based eyetracker in calibration and scanpath analysis modes. Toolbox procedures are organized in three layers: the lower one, communicating with the eyetracker output file, the middle detecting scanpath events on a physiological background and the one upper consisting of experiment schedule scripts, statistics and summaries. Several examples of visual experiments carried out with use of the presented toolbox complete the paper.

  4. A toolbox for representational similarity analysis.

    Directory of Open Access Journals (Sweden)

    Hamed Nili

    2014-04-01

    Full Text Available Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA, which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The

  5. Implementasi Fuzzy Logic Controller untuk Mengatur Ph Nutrisi pada Sistem Hidroponik Nutrient Film Technique (NFT

    Directory of Open Access Journals (Sweden)

    Dian Pancawati

    2016-07-01

    Full Text Available One solution to solve limited agricultural land is applying hydroponics Nutrient Film Technique (NFT. The advantage of NFT is using water circulated as a growing medium in order to obtain water, nutrients and oxygen to accelerate the growth of plants with good results. The most important parameter is the pH of nutrients. This article discusses how to design an automatic nutritional pH control system by implementing the method of Fuzzy Logic Controller. The control system use Arduino Mega2560, Analog pH Meter Kit as input, and the solenoid valve as actuators. The best response of the implementation of Fuzzy Logic Controller with the system which has 25 rules. The response shows that the system has in 1200 millisecond rise time and the steady state in 5530 milliseconds to increase the pH. While to decrease the pH system has response of rise time at 2000 milliseconds and steady state at the time of 3000 milliseconds. The system is able to maintain the pH at 5.5, with the result of the growth of lettuce as high as 20 cm and seven leaves for 54 days.

  6. The Neural Decoding Toolbox

    Directory of Open Access Journals (Sweden)

    Ethan eMeyers

    2013-05-01

    Full Text Available Population decoding is a powerful way to analyze neural data, however currently only a small percentage of systems neuroscience researchers use this method. In order to increase the use of population decoding, we have created the Neural Decoding Toolbox (NDT which is a Matlab package that makes it easy to apply population decoding analyses to neural activity. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and we give examples of how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. Overall this toolbox will make it much easier for neuroscientists to apply population decoding analyses to their data, which should help increase the pace of discovery in neuroscience.

  7. The neural decoding toolbox.

    Science.gov (United States)

    Meyers, Ethan M

    2013-01-01

    Population decoding is a powerful way to analyze neural data, however, currently only a small percentage of systems neuroscience researchers use this method. In order to increase the use of population decoding, we have created the Neural Decoding Toolbox (NDT) which is a Matlab package that makes it easy to apply population decoding analyses to neural activity. The design of the toolbox revolves around four abstract object classes which enables users to interchange particular modules in order to try different analyses while keeping the rest of the processing stream intact. The toolbox is capable of analyzing data from many different types of recording modalities, and we give examples of how it can be used to decode basic visual information from neural spiking activity and how it can be used to examine how invariant the activity of a neural population is to stimulus transformations. Overall this toolbox will make it much easier for neuroscientists to apply population decoding analyses to their data, which should help increase the pace of discovery in neuroscience.

  8. Broadview Radar Altimetry Toolbox

    Science.gov (United States)

    Garcia-Mondejar, Albert; Escolà, Roger; Moyano, Gorka; Roca, Mònica; Terra-Homem, Miguel; Friaças, Ana; Martinho, Fernando; Schrama, Ernst; Naeije, Marc; Ambrózio, Américo; Restano, Marco; Benveniste, Jérôme

    2017-04-01

    The universal altimetry toolbox, BRAT (Broadview Radar Altimetry Toolbox) which can read all previous and current altimetry missions' data, incorporates now the capability to read the upcoming Sentinel3 L1 and L2 products. ESA endeavoured to develop and supply this capability to support the users of the future Sentinel3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats. The BratGUI is the frontend for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with MATLAB/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the dataformatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as NetCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BRAT involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas. The Radar Altimeter Tutorial, that contains a strong introduction to altimetry, shows its applications in different fields such as Oceanography, Cryosphere, Geodesy, Hydrology among others. Included are also "use cases", with step-by-step examples, on how to use the toolbox in the different contexts. The Sentinel3 SAR Altimetry Toolbox shall benefit from the current BRAT version. While developing the toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific

  9. The GOCE User Toolbox (GUT) and Tutorial

    Science.gov (United States)

    Bingham, R. J.; Benveniste, J.; Knudsen, P.

    2015-12-01

    The GOCE User Toolbox (GUT) is an integrated suite of tools for the analysis and use of GOCE Level 2 gravity products. GUT supports applications in geodesy, oceanography and solid earth physics. The accompanying GUT tutorial provides information and guidance on how to use the toolbox for a variety of applications within each of these domains. An important motivation for the development of GUT has been the desire that users should be able to exploit the GOCE gravity products to calculate derived products relevant to their particular domains without necessarily needing to understand the technicalities of particular geodetic concepts and algorithms. As such, GUT is also suitable for use as an aid to the teaching of geophysics. A comprehensive and up-to-date set of a-priori data and models are supplied with the toolbox, together with a range of pre-defined workflows, allowing the user to immediately calculate useful geophysical quantities. The toolbox is supported by The GUT Algorithm Description and User Guide and The GUT Install Guide. GUT is cross-platform and may be used on Windows PCs, UNIX/Linux workstations and Macs. GUT version 2.2 was released in April 2014 and, besides some bug-fixes, the capability to calculate the simple Bouguer anomaly was added. Recently, GUT version 3 has been released. Through a collaborative effort between the relevant scientific communities, this version has built on earlier releases by further extending the functionality of the toolbox within the fields of geodesy, oceanography and solid earth physics. Additions include the ability to work directly with gravity gradients, anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies. The interface between the user and the toolbox has also been greatly improved and GUT version 3 now includes an attractive and intuitive Graphical User Interface. An associated GUT VCM tool for analysing the GOCE variance covariance matrices is also available.

  10. PESTO: Parameter EStimation TOolbox.

    Science.gov (United States)

    Stapor, Paul; Weindl, Daniel; Ballnus, Benjamin; Hug, Sabine; Loos, Carolin; Fiedler, Anna; Krause, Sabrina; Hroß, Sabrina; Fröhlich, Fabian; Hasenauer, Jan; Wren, Jonathan

    2018-02-15

    PESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers scalable algorithms for optimization, uncertainty and identifiability analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, for which the user can provide a deterministic objective function in MATLAB. PESTO is a MATLAB toolbox, freely available under the BSD license. The source code, along with extensive documentation and example code, can be downloaded from https://github.com/ICB-DCM/PESTO/. jan.hasenauer@helmholtz-muenchen.de. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  11. Feature selection toolbox

    Czech Academy of Sciences Publication Activity Database

    Somol, Petr; Pudil, Pavel

    2002-01-01

    Roč. 35, č. 12 (2002), s. 2749-2759 ISSN 0031-3203 R&D Projects: GA MŠk ME 187; GA ČR GA402/01/0981 Institutional research plan: CEZ:AV0Z1075907 Keywords : pattern recognition * feature selection * subset search Subject RIV: JC - Computer Hardware ; Software Impact factor: 1.038, year: 2002 http://library.utia.cas.cz/separaty/historie/somol- feature selection toolbox.pdf

  12. Development of a Twin-Spool Turbofan Engine Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Zinnecker, Alicia M.; Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Jonathan S.

    2014-01-01

    The Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) is a tool that has been developed to allow a user to build custom models of systems governed by thermodynamic principles using a template to model each basic process. Validation of this tool in an engine model application was performed through reconstruction of the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) (v2) using the building blocks from the T-MATS (v1) library. In order to match the two engine models, it was necessary to address differences in several assumptions made in the two modeling approaches. After these modifications were made, validation of the engine model continued by integrating both a steady-state and dynamic iterative solver with the engine plant and comparing results from steady-state and transient simulation of the T-MATS and C-MAPSS models. The results show that the T-MATS engine model was accurate within 3% of the C-MAPSS model, with inaccuracy attributed to the increased dimension of the iterative solver solution space required by the engine model constructed using the T-MATS library. This demonstrates that, given an understanding of the modeling assumptions made in T-MATS and a baseline model, the T-MATS tool provides a viable option for constructing a computational model of a twin-spool turbofan engine that may be used in simulation studies.

  13. Development of a Twin-spool Turbofan Engine Simulation Using the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

    Zinnecker, Alicia M.; Chapman, Jeffryes W.; Lavelle, Thomas M.; Litt, Johathan S.

    2014-01-01

    The Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS) is a tool that has been developed to allow a user to build custom models of systems governed by thermodynamic principles using a template to model each basic process. Validation of this tool in an engine model application was performed through reconstruction of the Commercial Modular Aero-Propulsion System Simulation (C-MAPSS) (v2) using the building blocks from the T-MATS (v1) library. In order to match the two engine models, it was necessary to address differences in several assumptions made in the two modeling approaches. After these modifications were made, validation of the engine model continued by integrating both a steady-state and dynamic iterative solver with the engine plant and comparing results from steady-state and transient simulation of the T-MATS and C-MAPSS models. The results show that the T-MATS engine model was accurate within 3 of the C-MAPSS model, with inaccuracy attributed to the increased dimension of the iterative solver solution space required by the engine model constructed using the T-MATS library. This demonstrates that, given an understanding of the modeling assumptions made in T-MATS and a baseline model, the T-MATS tool provides a viable option for constructing a computational model of a twin-spool turbofan engine that may be used in simulation studies.

  14. BioMet Toolbox: genome-wide analysis of metabolism

    DEFF Research Database (Denmark)

    Cvijovic, M.; Olivares Hernandez, Roberto; Agren, R.

    2010-01-01

    standardized simulations. Model files for various model organisms (fungi and bacteria) are included. Overall, the BioMet Toolbox serves as a valuable resource for exploring the capabilities of these metabolic networks. BioMet Toolbox is freely available at www.sysbio.se/BioMet/....... models. Systematic analysis of biological processes by means of modelling and simulations has made the identification of metabolic networks and prediction of metabolic capabilities under different conditions possible. For facilitating such systemic analysis, we have developed the BioMet Toolbox, a web......-based resource for stoichiometric analysis and for integration of transcriptome and interactome data, thereby exploiting the capabilities of genome-scale metabolic models. The BioMet Toolbox provides an effective user-friendly way to perform linear programming simulations towards maximized or minimized growth...

  15. Presentation of the International Building Physics Toolbox for Simulink

    DEFF Research Database (Denmark)

    Weitzmann, Peter; Sasic Kalagasidis, Angela; Nielsen, Toke Rammer

    2003-01-01

    The international building physics toolbox (IBPT) is a software library specially constructed for HAM system analysis in building physics. The toolbox is constructed as a modular structure of the standard building elements using the graphical programming language Simulink. Two research groups have...... participated in this project. In order to enable the development of the toolbox, a common modelling platform was defined: a set of unique communication signals, material database and documentation protocol. The IBPT is open source and publicly available on the Internet. Any researcher and student can use...

  16. DTU:Toolbox

    DEFF Research Database (Denmark)

    2002-01-01

    The DTU:Toolbox™ is a collection of machine learning algorithms implemented mainly for Matlab™. Currently it holds: *Independent component analysis (ICA) *Artificial neural networks (ANN) Focus is on developing easy to use algorithms with no or a minimum of parameter tuning. All algorithms come...... Institutes of Health's Human Brain Project. All code can be used freely in research and other non-profit applications. If you publish results obtained with the DTU:Toolbox we kindly ask that our and other relevant sources are properly cited. Description, citation and implementation notes for the individual...

  17. Ubuntu Linux toolbox

    CERN Document Server

    Negus, Christopher

    2012-01-01

    This bestseller from Linux guru Chris Negus is packed with an array of new and revised material As a longstanding bestseller, Ubuntu Linux Toolbox has taught you how to get the most out Ubuntu, the world?s most popular Linux distribution. With this eagerly anticipated new edition, Christopher Negus returns with a host of new and expanded coverage on tools for managing file systems, ways to connect to networks, techniques for securing Ubuntu systems, and a look at the latest Long Term Support (LTS) release of Ubuntu, all aimed at getting you up and running with Ubuntu Linux quickly.

  18. NEMO: A Stellar Dynamics Toolbox

    Science.gov (United States)

    Barnes, Joshua; Hut, Piet; Teuben, Peter

    2010-10-01

    NEMO is an extendible Stellar Dynamics Toolbox, following an Open-Source Software model. It has various programs to create, integrate, analyze and visualize N-body and SPH like systems, following the pipe and filter architecture. In addition there are various tools to operate on images, tables and orbits, including FITS files to export/import to/from other astronomical data reduction packages. A large growing fraction of NEMO has been contributed by a growing list of authors. The source code consist of a little over 4000 files and a little under 1,000,000 lines of code and documentation, mostly C, and some C++ and Fortran. NEMO development started in 1986 in Princeton (USA) by Barnes, Hut and Teuben. See also ZENO (ascl:1102.027) for the version that Barnes maintains.

  19. Impact of Low and Moderate Salinity Water on Plant Performance of Leafy Vegetables in a Recirculating NFT System

    OpenAIRE

    Genhua Niu; Youping Sun; Joseph G. Masabni

    2018-01-01

    Two greenhouse experiments were conducted to examine the growth and mineral nutrition of four leafy vegetables in a nutrient film technique (NFT) system with water with low to moderate salinity. In Expt. 1, a nutrient solution was prepared using reverse osmosis (RO) water and treatments consisted of supplementing with RO water, tap water, or nutrient solution. In Expt. 2, nutrient solution was prepared using three different water sources (treatments), namely, RO water, tap water, or tap water...

  20. The Eyelink Toolbox : Eye tracking with MATLAB and the psychophysics toolbox

    NARCIS (Netherlands)

    Cornelissen, FW; Peters, EM; Palmer, J

    2002-01-01

    The Eyelink Toolbox software supports the measurement of eye movements. The toolbox provides an interface between a high-level interpreted language (MATLAB), a visual display programming toolbox (Psychophysics Toolbox), and a video-based eyetracker (Eyelink). The Eyelink Toolbox enables

  1. ESA BRAT (Broadview Radar Altimetry Toolbox) and GUT (GOCE User Toolbox) toolboxes

    Science.gov (United States)

    Benveniste, J.; Ambrozio, A.; Restano, M.

    2016-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including the upcoming Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's future release (4.0.0) is planned for September 2016. Based on the community feedback, the frontend has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.0 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's VCM (Variance-Covariance Matrix) tool for analysing GOCE

  2. PENERAPAN PANJANG TALANG DAN JARAK TANAM DENGAN SISTEM HIDROPONIK NFT (Nutrient Film Technique PADA TANAMAN KAILAN (Brassica oleraceae var. alboglabra

    Directory of Open Access Journals (Sweden)

    Daviv Zali Vidianto

    2013-09-01

    Full Text Available Kailan vegetables is one kind of high economic value that can be grown in hydroponic NFT (Nutrient Film Technique. The purpose of this study to determine the effect of chamfer length and spacing of the system hydroponic NFT (Nutrient Film Technique on the growth and yield kailan (Brassica oleraceae var. Alboglabra. The research has been done in the greenhouse of the Faculty of Agriculture, University Department Agroekoteknologi Trunojoyo Madura District Kamal village Telang Bangkalan. Tat is was conducted in February-May 2012. Research using methods completely randomized design (CRD with non factorial treatment chamfer length 2 m with spacing of 15 cm (P1J1, chamfer length 2 m with spacing of 20 cm (P1J2, chamfer length of 4 m with spacing of 15 cm (P2J1 and chamfer length of 4 m with spacing of 20 cm (P2J2. The materials used are kailan seeds, fertilizers and hydroponics Goodplant acetic acid (CH3COOH. Observations were analyzed using analysis of variance and Duncan continued Test Distance (UJD level of 5%. P1J1 (chamfer length of 2 meters and 15 cm plant spacing gives the best effect on the variable root length, number of leaves and plant canopy wet weight. The treatment does’n effect to variable leaf area, root wet weight, dry weight, and root dry weight of the plant canopyKeyword : Brassica oleraceae var. Alboglabra, hydroponik NFT, chamfer length and spacing

  3. PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

    Science.gov (United States)

    Morales, Yeimy; Bosque, Gabriel; Vehí, Josep; Picó, Jesús; Llaneras, Francisco

    2016-07-11

    Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios. Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User's Guide with a thorough description of its functions and several examples. The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations.

  4. Development of a model using the MATLAB System identification toolbox to estimate (222)Rn equilibrium factor from CR-39 based passive measurements.

    Science.gov (United States)

    Abo-Elmagd, M; Sadek, A M

    2014-12-01

    Can and Bare method is a widely used passive method for measuring the equilibrium factor F through the determination of the track density ratio between bare (D) and filtered (Do) detectors. The dimensions of the used diffusion chamber are altering the deposition ratios of Po-isotopes on the chamber walls as well as the ratios of the existing alpha emitters in air. Then the measured filtered track density and therefore the resultant equilibrium factor is changed according to the diffusion chamber dimensions. For this reason, high uncertainty was expected in the measured F using different diffusion chambers. In the present work, F is derived as a function of both track density ratio (D/Do) and the dimensions of the used diffusion chambers (its volume to the total internal surface area; V/A). The accuracy of the derived formula was verified using the black-box modeling technique via the MATLAB System identification toolbox. The results show that the uncertainty of the calculated F by using the derived formula of F (D/Do, V/A) is only 5%. The obtained uncertainty ensures the quality of the derived function to calculate F using diffusion chambers with wide range of dimensions. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Integrated Budget Office Toolbox

    Science.gov (United States)

    Rushing, Douglas A.; Blakeley, Chris; Chapman, Gerry; Robertson, Bill; Horton, Allison; Besser, Thomas; McCarthy, Debbie

    2010-01-01

    The Integrated Budget Office Toolbox (IBOT) combines budgeting, resource allocation, organizational funding, and reporting features in an automated, integrated tool that provides data from a single source for Johnson Space Center (JSC) personnel. Using a common interface, concurrent users can utilize the data without compromising its integrity. IBOT tracks planning changes and updates throughout the year using both phasing and POP-related (program-operating-plan-related) budget information for the current year, and up to six years out. Separating lump-sum funds received from HQ (Headquarters) into separate labor, travel, procurement, Center G&A (general & administrative), and servicepool categories, IBOT creates a script that significantly reduces manual input time. IBOT also manages the movement of travel and procurement funds down to the organizational level and, using its integrated funds management feature, helps better track funding at lower levels. Third-party software is used to create integrated reports in IBOT that can be generated for plans, actuals, funds received, and other combinations of data that are currently maintained in the centralized format. Based on Microsoft SQL, IBOT incorporates generic budget processes, is transportable, and is economical to deploy and support.

  6. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    2005-01-01

    This paper presents a developed toolbox for space environment model in SIMULINK that facilitates development and design of Attitude Determination and Control Systems (ADCS) for a Low Earth Orbit (LEO) spacecraft. The toolbox includes, among others, models of orbit propagators, disturbances, Earth...

  7. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  8. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2016-01-01

    Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment, and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1) enumeration of the repertoire of model phenotypes, (2) prediction of values for the parameters for any model phenotype, and (3) analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3, and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between three stable states by transient stimulation through one of two input channels: a positive channel that increases the count

  9. Design Space Toolbox V2: Automated Software Enabling a Novel Phenotype-Centric Modeling Strategy for Natural and Synthetic Biological Systems

    Directory of Open Access Journals (Sweden)

    Jason Gunther Lomnitz

    2016-07-01

    Full Text Available Mathematical models of biochemical systems provide a means to elucidate the link between the genotype, environment and phenotype. A subclass of mathematical models, known as mechanistic models, quantitatively describe the complex non-linear mechanisms that capture the intricate interactions between biochemical components. However, the study of mechanistic models is challenging because most are analytically intractable and involve large numbers of system parameters. Conventional methods to analyze them rely on local analyses about a nominal parameter set and they do not reveal the vast majority of potential phenotypes possible for a given system design. We have recently developed a new modeling approach that does not require estimated values for the parameters initially and inverts the typical steps of the conventional modeling strategy. Instead, this approach relies on architectural features of the model to identify the phenotypic repertoire and then predict values for the parameters that yield specific instances of the system that realize desired phenotypic characteristics. Here, we present a collection of software tools, the Design Space Toolbox V2 based on the System Design Space method, that automates (1 enumeration of the repertoire of model phenotypes, (2 prediction of values for the parameters for any model phenotype and (3 analysis of model phenotypes through analytical and numerical methods. The result is an enabling technology that facilitates this radically new, phenotype-centric, modeling approach. We illustrate the power of these new tools by applying them to a synthetic gene circuit that can exhibit multi-stability. We then predict values for the system parameters such that the design exhibits 2, 3 and 4 stable steady states. In one example, inspection of the basins of attraction reveals that the circuit can count between 3 stable states by transient stimulation through one of two input channels: a positive channel that increases

  10. Efluente y té de vermicopost en la producción de hortalizas de hoja en sistema NFT.

    OpenAIRE

    González Solano, Karla Daniela

    2013-01-01

    El objetivo de la presente investigación fue determinar la calidad nutrimental del efluente y té de vermicompost en la producción de hortalizas de hoja producidas bajo un sistema NFT (Nutrient Film Technique). Para cumplir el objetivo se llevaron a cabo cinco investigaciones donde se incluye desde identificar el origen del vermicompost, las características químicas ideales para obtener un té de vermicompost hasta su evaluación nutrimental en hortalizas y aromáticas. Los resultados obtenidos ...

  11. Analisis sistem irigasi hidroponik NFT (nutrient film technique) pada tanaman budidaya tanaman selada (Lactuca sativa var crispa L.)

    OpenAIRE

    Sibarani, Sahat Muhtar

    2012-01-01

    Nutrient Film Technique (I\\FFT) is a new technological in hidroponics. In this system, a part of root deep on the water have fertilizers and other part upon the water which sirculating above 24 hours. The lining of the water is slight, about 3 mm, so its like film. The research of NFT irrigation was carried out to study on Electric Conductivity(EC) uniformity and pH of nutrient liquid as well as effectivity of gutters gradient application. The research was done with planting the plants in ...

  12. Experiencia de producción de lechuga americana (Lactuca sativa hidropónica, tipo NFT

    Directory of Open Access Journals (Sweden)

    Laura Brenes-Peralta

    2014-06-01

    En el Centro de Prácticas Docentes e Investigación Agropecuaria de la Escuela de Agronegocios del Instituto Tecnológico de Costa Rica (TEC se cuenta, actualmente, con un sistema de este tipo NFT donde estableció una actividad de fortalecimiento que ha resultado en la observación de ciertas características a partir de la experiencia generada, de la cual se espera fomentar el uso de la hidroponía, así como divulgar información técnica y de buenas prácticas en este tipo de cultivo entre usuarios interesados.

  13. Natter: A Python Natural Image Statistics Toolbox

    Directory of Open Access Journals (Sweden)

    Fabian H. Sinz

    2014-11-01

    Full Text Available The statistical analysis and modeling of natural images is an important branch of statistics with applications in image signaling, image compression, computer vision, and human perception. Because the space of all possible images is too large to be sampled exhaustively, natural image models must inevitably make assumptions in order to stay tractable. Subsequent model comparison can then ?lter out those models that best capture the statistical regularities in natural images. Proper model comparison, however, often requires that the models and the preprocessing of the data match down to the implementation details. Here we present the Natter, a statistical software toolbox for natural images models, that can provide such consistency. The Natter includes powerful but tractable baseline model as well as standardized data preprocessing steps. It has an extensive test suite to ensure correctness of its algorithms, it interfaces to the modular toolkit for data processing toolbox MDP, and provides simple ways to log the results of numerical experiments. Most importantly, its modular structure can be extended by new models with minimal coding e?ort, thereby providing a platform for the development and comparison of probabilistic models for natural image data.

  14. Particle Swarm Optimization Toolbox

    Science.gov (United States)

    Grant, Michael J.

    2010-01-01

    The Particle Swarm Optimization Toolbox is a library of evolutionary optimization tools developed in the MATLAB environment. The algorithms contained in the library include a genetic algorithm (GA), a single-objective particle swarm optimizer (SOPSO), and a multi-objective particle swarm optimizer (MOPSO). Development focused on both the SOPSO and MOPSO. A GA was included mainly for comparison purposes, and the particle swarm optimizers appeared to perform better for a wide variety of optimization problems. All algorithms are capable of performing unconstrained and constrained optimization. The particle swarm optimizers are capable of performing single and multi-objective optimization. The SOPSO and MOPSO algorithms are based on swarming theory and bird-flocking patterns to search the trade space for the optimal solution or optimal trade in competing objectives. The MOPSO generates Pareto fronts for objectives that are in competition. A GA, based on Darwin evolutionary theory, is also included in the library. The GA consists of individuals that form a population in the design space. The population mates to form offspring at new locations in the design space. These offspring contain traits from both of the parents. The algorithm is based on this combination of traits from parents to hopefully provide an improved solution than either of the original parents. As the algorithm progresses, individuals that hold these optimal traits will emerge as the optimal solutions. Due to the generic design of all optimization algorithms, each algorithm interfaces with a user-supplied objective function. This function serves as a "black-box" to the optimizers in which the only purpose of this function is to evaluate solutions provided by the optimizers. Hence, the user-supplied function can be numerical simulations, analytical functions, etc., since the specific detail of this function is of no concern to the optimizer. These algorithms were originally developed to support entry

  15. Speed management toolbox for rural communities.

    Science.gov (United States)

    2013-04-01

    The primary objective of this toolbox is to summarize various known traffic-calming treatments and their effectiveness. This toolbox focuses on roadway-based treatments for speed management, particularly for rural communities with transition zones. E...

  16. FIT3D toolbox: multiple view geometry and 3D reconstruction for Matlab

    NARCIS (Netherlands)

    Esteban, I.; Dijk, J.; Groen, F.

    2010-01-01

    FIT3D is a Toolbox built for Matlab that aims at unifying and distributing a set of tools that will allow the researcher to obtain a complete 3D model from a set of calibrated images. In this paper we motivate and present the structure of the toolbox in a tutorial and example based approach. Given

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

    Science.gov (United States)

    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.

  18. Expanding the methodological toolbox of HRM researchers : The added value of latent bathtub models and optimal matching analysis

    NARCIS (Netherlands)

    van der Laken, P.A.; Bakk, Zsuzsa; Giagkoulas, Vasileios; van Leeuwen, Linda; Bongenaar, Esther

    2018-01-01

    Researchers frequently rely on general linear models (GLMs) to investigate the impact of human resource management (HRM) decisions. However, the structure of organizations and recent technological advancements in the measurement of HRM processes cause contemporary HR data to be hierarchical and/or

  19. Extend your toolbox with R

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    R seems to be ideal tool for visualising your data as well as practically all other data-related tasks. Learn how to start with R as it is worth to be included not only in statistician's or data scientist's toolboxes.

  20. SSNN toolbox for non-linear system identification

    Science.gov (United States)

    Luzar, Marcel; Czajkowski, Andrzej

    2015-11-01

    The aim of this paper is to develop and design a State Space Neural Network toolbox for a non-linear system identification with an artificial state-space neural networks, which can be used in a model-based robust fault diagnosis and control. Such toolbox is implemented in the MATLAB environment and it uses some of its predefined functions. It is designed in the way that any non-linear multi-input multi-output system is identified and represented in the classical state-space form. The novelty of the proposed approach is that the final result of the identification process is the state, input and output matrices, not only the neural network parameters. Moreover, the toolbox is equipped with the graphical user interface, which makes it useful for the users not familiar with the neural networks theory.

  1. Lucretia A Matlab-Based Toolbox for the Modeling and Simulation of Single-Pass Electron Beam Transport Systems

    CERN Document Server

    Tenenbaum, P G

    2005-01-01

    We report on Lucretia, a new simulation tool for the study of single-pass electron beam transport systems. Lucretia supports a combination of analytic and tracking techniques to model the tuning and operation of bunch compressors, linear accelerators, and beam delivery systems of linear colliders and linac-driven Free Electron Laser (FEL) facilities. Extensive use of Matlab scripting, graphics, and numerical capabilities maximize the flexibility of the system, and emphasis has been placed on representing and preserving the fixed relationships between elements (common girders, power supplies, etc.) which must be respected in the design of tuning algorithms. An overview of the code organization, some simple examples, and plans for future development are discussed.

  2. NNSYSID - toolbox for system identification with neural networks

    DEFF Research Database (Denmark)

    Norgaard, M.; Ravn, Ole; Poulsen, Niels Kjølstad

    2002-01-01

    The NNSYSID toolset for System Identification has been developed as an add on to MATLAB(R). The NNSYSID toolbox has been designed to assist identification of nonlinear dynamic systems. It contains a number of nonlinear model structures based on neural networks, effective training algorithms...

  3. Wave data processing toolbox manual

    Science.gov (United States)

    Sullivan, Charlene M.; Warner, John C.; Martini, Marinna A.; Lightsom, Frances S.; Voulgaris, George; Work, Paul

    2006-01-01

    Researchers routinely deploy oceanographic equipment in estuaries, coastal nearshore environments, and shelf settings. These deployments usually include tripod-mounted instruments to measure a suite of physical parameters such as currents, waves, and pressure. Instruments such as the RD Instruments Acoustic Doppler Current Profiler (ADCP(tm)), the Sontek Argonaut, and the Nortek Aquadopp(tm) Profiler (AP) can measure these parameters. The data from these instruments must be processed using proprietary software unique to each instrument to convert measurements to real physical values. These processed files are then available for dissemination and scientific evaluation. For example, the proprietary processing program used to process data from the RD Instruments ADCP for wave information is called WavesMon. Depending on the length of the deployment, WavesMon will typically produce thousands of processed data files. These files are difficult to archive and further analysis of the data becomes cumbersome. More imperative is that these files alone do not include sufficient information pertinent to that deployment (metadata), which could hinder future scientific interpretation. This open-file report describes a toolbox developed to compile, archive, and disseminate the processed wave measurement data from an RD Instruments ADCP, a Sontek Argonaut, or a Nortek AP. This toolbox will be referred to as the Wave Data Processing Toolbox. The Wave Data Processing Toolbox congregates the processed files output from the proprietary software into two NetCDF files: one file contains the statistics of the burst data and the other file contains the raw burst data (additional details described below). One important advantage of this toolbox is that it converts the data into NetCDF format. Data in NetCDF format is easy to disseminate, is portable to any computer platform, and is viewable with public-domain freely-available software. Another important advantage is that a metadata

  4. The Linear Time Frequency Analysis Toolbox

    DEFF Research Database (Denmark)

    Søndergaard, Peter Lempel; Torrésani, Bruno; Balazs, Peter

    2011-01-01

    The Linear Time Frequency Analysis Toolbox is a Matlab/Octave toolbox for computational time-frequency analysis. It is intended both as an educational and computational tool. The toolbox provides the basic Gabor, Wilson and MDCT transform along with routines for constructing windows (lter...... prototypes) and routines for manipulating coe cients. It also provides a bunch of demo scripts devoted either to demonstrating the main functions of the toolbox, or to exemplify their use in specic signal processing applications. In this paper we describe the used algorithms, their mathematical background...

  5. Concentração e conteúdo de nutrientes em lisianto, cultivado em hidroponia, em sistema NFT = Concentration and nutrient content in lisianthus grown in a hydroponic NFT system

    Directory of Open Access Journals (Sweden)

    Fernanda Alice Antonello Londero Backes

    2008-10-01

    Full Text Available O diagnóstico nutricional é fundamental para determinar as exigências das plantas quanto aos nutrientes, de forma a se proceder a um manejo adequado, de acordo com a espécie. Assim, para determinar as concentrações e conteúdos nutricionais adequados à produção e qualidade de plantas de lisianto em cultivo hidropônico, instalou-se um experimento onde as plantas foram cultivadas em sistema NFT, em diferentes soluções nutritivas. O experimento foi conduzido, segundo delineamento experimental em blocos casualizados, em esquema fatorial 4x3, totalizando 12 tratamentos, com três repetições. Ostratamentos foram compostos de quatro cultivares (Echo Champagne, Mariachi Pure White, Balboa Yellow e Ávila Blue Rim e três soluções nutritivas (Teste, Steiner modificada e Barbosa. Foram avaliadas as concentrações e os conteúdos dos nutrientes nas folhas e conteúdos na parte aérea das plantas. As plantas cultivadas nas soluções Barbosa eTeste apresentaram resultados satisfatórios quanto às concentrações e aos conteúdos de nutrientes, enquanto a solução Steiner modificada produziu plantas com limitações nutricionais.The nutritional diagnosis is fundamental for determining plantnutrients, in order to correctly manage the nutritional requirements for each species. Thus, in order to determine the ideal nutrient amount and concentration for obtaining the best yield and quality of lisianthus grown hydroponically, an experiment was conducted inwhich the plants were grown under the NFT system in different nutrient solutions. The experiment was conducted according to a random block design arrangement in a 4x3 factorial scheme, totaling 12 treatments with three repetitions. The treatments werecomprised of four cultivars (Echo Champagne, Mariachi Pure White, Balboa Yellow and Ávila Blue Rim and three nutrient solutions (Test, modified Steiner and Barbosa. In the leaves, nutrient concentration and content were evaluated; in the aerial

  6. DeltaProt: a software toolbox for comparative genomics

    Directory of Open Access Journals (Sweden)

    Willassen Nils P

    2010-11-01

    Full Text Available Abstract Background Statistical bioinformatics is the study of biological data sets obtained by new micro-technologies by means of proper statistical methods. For a better understanding of environmental adaptations of proteins, orthologous sequences from different habitats may be explored and compared. The main goal of the DeltaProt Toolbox is to provide users with important functionality that is needed for comparative screening and studies of extremophile proteins and protein classes. Visualization of the data sets is also the focus of this article, since visualizations can play a key role in making the various relationships transparent. This application paper is intended to inform the reader of the existence, functionality, and applicability of the toolbox. Results We present the DeltaProt Toolbox, a software toolbox that may be useful in importing, analyzing and visualizing data from multiple alignments of proteins. The toolbox has been written in MATLAB™ to provide an easy and user-friendly platform, including a graphical user interface, while ensuring good numerical performance. Problems in genome biology may be easily stated thanks to a compact input format. The toolbox also offers the possibility of utilizing structural information from the SABLE or other structure predictors. Different sequence plots can then be viewed and compared in order to find their similarities and differences. Detailed statistics are also calculated during the procedure. Conclusions The DeltaProt package is open source and freely available for academic, non-commercial use. The latest version of DeltaProt can be obtained from http://services.cbu.uib.no/software/deltaprot/. The website also contains documentation, and the toolbox comes with real data sets that are intended for training in applying the models to carry out bioinformatical and statistical analyses of protein sequences. Equipped with the new algorithms proposed here, DeltaProt serves as an auxiliary

  7. The MultiAgent Decision Process toolbox: Software for decision-theoretic planning in multiagent-systems

    NARCIS (Netherlands)

    Spaan, M.T.J.; Oliehoek, F.A.; Shen, J.; Varakantham, P.; Maheswaran, R.

    2008-01-01

    This paper introduces the MultiAgent Decision Process software toolbox, an open source C++ library for decision-theoretic planning under uncertainty in multiagent systems. It provides support for several multiagent models, such as POSGs, Dec-POMDPs and MMDPs. The toolbox aims to reduce development

  8. Integrated system dynamics toolbox for water resources planning.

    Energy Technology Data Exchange (ETDEWEB)

    Reno, Marissa Devan; Passell, Howard David; Malczynski, Leonard A.; Peplinski, William J.; Tidwell, Vincent Carroll; Coursey, Don (University of Chicago, Chicago, IL); Hanson, Jason (University of New Mexico, Albuquerque, NM); Grimsrud, Kristine (University of New Mexico, Albuquerque, NM); Thacher, Jennifer (University of New Mexico, Albuquerque, NM); Broadbent, Craig (University of New Mexico, Albuquerque, NM); Brookshire, David (University of New Mexico, Albuquerque, NM); Chemak, Janie (University of New Mexico, Albuquerque, NM); Cockerill, Kristan (Cockeril Consulting, Boone, NC); Aragon, Carlos (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Hallett, Heather (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Vivoni, Enrique (New Mexico Univeristy of Technology and Mining (NM-TECH), Socorro, NM); Roach, Jesse

    2006-12-01

    Public mediated resource planning is quickly becoming the norm rather than the exception. Unfortunately, supporting tools are lacking that interactively engage the public in the decision-making process and integrate over the myriad values that influence water policy. In the pages of this report we document the first steps toward developing a specialized decision framework to meet this need; specifically, a modular and generic resource-planning ''toolbox''. The technical challenge lies in the integration of the disparate systems of hydrology, ecology, climate, demographics, economics, policy and law, each of which influence the supply and demand for water. Specifically, these systems, their associated processes, and most importantly the constitutive relations that link them must be identified, abstracted, and quantified. For this reason, the toolbox forms a collection of process modules and constitutive relations that the analyst can ''swap'' in and out to model the physical and social systems unique to their problem. This toolbox with all of its modules is developed within the common computational platform of system dynamics linked to a Geographical Information System (GIS). Development of this resource-planning toolbox represents an important foundational element of the proposed interagency center for Computer Aided Dispute Resolution (CADRe). The Center's mission is to manage water conflict through the application of computer-aided collaborative decision-making methods. The Center will promote the use of decision-support technologies within collaborative stakeholder processes to help stakeholders find common ground and create mutually beneficial water management solutions. The Center will also serve to develop new methods and technologies to help federal, state and local water managers find innovative and balanced solutions to the nation's most vexing water problems. The toolbox is an important step toward

  9. Audition assessment using the NIH Toolbox

    Science.gov (United States)

    Hoffman, Howard J.; Frisina, Robert; Dubno, Judy R.; Dhar, Sumitrajit; Wallhagen, Margaret; Kraus, Nina; Griffith, James W.; Walton, Joseph P.; Eddins, David A.; Newman, Craig; Victorson, David; Warrier, Catherine M.; Wilson, Richard H.

    2013-01-01

    The NIH Toolbox project has assembled measurement tools to assess a wide range of human perception and ability across the lifespan. As part of this initiative, a small but comprehensive battery of auditory tests has been assembled. The main tool of this battery, pure-tone thresholds, measures the ability of people to hear at specific frequencies. Pure-tone thresholds have long been considered the “gold standard” of auditory testing, and are normally obtained in a clinical setting by highly trained audiologists. For the purposes of the Toolbox project, an automated procedure (NIH Toolbox Threshold Hearing Test) was developed that allows nonspecialists to administer the test reliably. Three supplemental auditory tests are also included in the Toolbox auditory test battery: assessment of middle-ear function (tympanometry), speech perception in noise (the NIH Toolbox Words-in-Noise Test), and self-assessment of hearing impairment (the NIH Toolbox Hearing Handicap Inventory Ages 18–64 and the NIH Toolbox Hearing Handicap Inventory Ages 64+). Tympanometry can help differentiate conductive from sensorineural pathology. The NIH Toolbox Words-in-Noise Test measures a listener's ability to perceive words in noisy situations. This ability is not necessarily predicted by a person's pure-tone thresholds; some people with normal hearing have difficulty extracting meaning from speech sounds heard in a noisy context. The NIH Toolbox Hearing Handicap Inventory focuses on how a person's perceived hearing status affects daily life. The test was constructed to include emotional and social/situational subscales, with specific questions about how hearing impairment may affect one's emotional state or limit participation in specific activities. The 4 auditory tests included in the Toolbox auditory test battery cover a range of auditory abilities and provide a snapshot of a participant's auditory capacity. PMID:23479544

  10. A 'Toolbox' Equivalent Process for Safety Analysis Software

    International Nuclear Information System (INIS)

    O'Kula, K.R.; Eng, Tony

    2004-01-01

    Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 2002-1 (Quality Assurance for Safety-Related Software) identified a number of quality assurance issues on the use of software in Department of Energy (DOE) facilities for analyzing hazards, and designing and operating controls that prevent or mitigate potential accidents. The development and maintenance of a collection, or 'toolbox', of multiple-site use, standard solution, Software Quality Assurance (SQA)-compliant safety software is one of the major improvements identified in the associated DOE Implementation Plan (IP). The DOE safety analysis toolbox will contain a set of appropriately quality-assured, configuration-controlled, safety analysis codes, recognized for DOE-broad, safety basis applications. Currently, six widely applied safety analysis computer codes have been designated for toolbox consideration. While the toolbox concept considerably reduces SQA burdens among DOE users of these codes, many users of unique, single-purpose, or single-site software may still have sufficient technical justification to continue use of their computer code of choice, but are thwarted by the multiple-site condition on toolbox candidate software. The process discussed here provides a roadmap for an equivalency argument, i.e., establishing satisfactory SQA credentials for single-site software that can be deemed ''toolbox-equivalent''. The process is based on the model established to meet IP Commitment 4.2.1.2: Establish SQA criteria for the safety analysis ''toolbox'' codes. Implementing criteria that establish the set of prescriptive SQA requirements are based on implementation plan/procedures from the Savannah River Site, also incorporating aspects of those from the Waste Isolation Pilot Plant (SNL component) and the Yucca Mountain Project. The major requirements are met with evidence of a software quality assurance plan, software requirements and design documentation, user's instructions, test report, a

  11. Rhizofiltration of lead using an aromatic medicinal plant Plectranthus amboinicus cultured in a hydroponic nutrient film technique (NFT) system.

    Science.gov (United States)

    Ignatius, A; Arunbabu, V; Neethu, J; Ramasamy, E V

    2014-11-01

    Heavy metal contamination of water bodies and groundwater is a major concern of the modern world. Rhizofiltration--the use of plant root system to remove/extract pollutants from wastewater--has proven advantages over conventional methods of treatment. However, commercialization of this in situ remediation technology requires a better understanding of plant-metal interactions especially on the ability of different plant species to accumulate metals at different parts of the plant system which is critical for the successful remediation of contaminated medium. Many aquatic and terrestrial plants have been reported to accumulate heavy metals when grown hydroponically. Therefore, a batch experiment with different concentrations of lead and a nutrient film technique (NFT) experiment with recycling of wastewater were employed in this study in order to investigate the rhizofiltration of lead-containing wastewater using Plectranthus amboinicus, an aromatic medicinal plant. Results show that P. amboinicus is tolerant to a wide range of lead concentrations and nutrient deficiency. The plant accumulates considerable amount of lead, particularly in the roots, and translocation to the stem and leaf was limited, indicating that the use of leaves/above-ground parts of the plant for medicinal purposes is not hindered by its ability to remove lead from the soil or water. The study also suggests that the plant can be considered for the clean-up of lead-contaminated wastewater in combination with safe biomass disposal alternatives.

  12. DIAMOND: A graphical interface toolbox for comparative modal analysis and damage identification

    Energy Technology Data Exchange (ETDEWEB)

    Doebling, S.W.; Farrar, C.R. [Los Alamos National Lab., NM (United States). Engineering Sciences and Applications Div.; Cornwell, P.J. [Rose Hulman Inst. of Tech., Terre Haute, IN (United States)

    1997-06-01

    This paper introduces a new toolbox of graphical-interface software algorithms for the numerical simulation of vibration tests, analysis of modal data, finite element model correlation, and the comparison of both linear and nonlinear damage identification techniques. This toolbox is unique because it contains several different vibration-based damage identification algorithms, categorized as those which use only measured response and sensor location information (non-model-based techniques) and those which use finite element model correlation (model-based techniques). Another unique feature of this toolbox is the wide range of algorithms for experimental modal analysis. The toolbox also contains a unique capability that utilizes the measured coherence functions and Monte Carlo analysis to perform statistical uncertainty analysis on the modal parameters and damage identification results. This paper contains a detailed description of the various modal analysis, damage identification, and model correlation capabilities of toolbox, and also shows a sample application which uses the toolbox to analyze the statistical uncertainties on the results of a series of modal tests performed on a highway bridge.

  13. Sentinel-3 SAR Altimetry Toolbox

    Science.gov (United States)

    Benveniste, Jerome; Lucas, Bruno; DInardo, Salvatore

    2015-04-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage of ERS-2 and Envisat, and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the two Sentinels is expected to be launched in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth

  14. FALCON: a toolbox for the fast contextualization of logical networks.

    Science.gov (United States)

    De Landtsheer, Sébastien; Trairatphisan, Panuwat; Lucarelli, Philippe; Sauter, Thomas

    2017-11-01

    Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. thomas.sauter@uni.lu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  15. A computer toolbox for damage identification based on changes in vibration characteristics

    Energy Technology Data Exchange (ETDEWEB)

    Doebling, S.W.; Farrar, C.R. [Los Alamos National Lab., NM (United States); Cornwell, P.J. [Rose Hulman Institute of Technology, Terre Haute, IN (United States). Dept. of Mechanical Engineering

    1997-09-01

    This paper introduces a new toolbox of graphical-interface software algorithms for the numerical simulation of vibration tests, analysis of modal data, finite element model correlation, and the comparison of both linear and nonlinear damage identification techniques. This toolbox is unique because it contains several different vibration-based damage identification algorithms, categorized as those which use only measured response and sensor location information ({open_quotes}non-model-based{close_quotes} techniques) and those which use finite element model correlation ({open_quotes}model-based{close_quotes} techniques). Another unique feature of this toolbox is the wide range of algorithms for experimental modal analysis. The toolbox also contains a unique capability that utilizes the measured coherence functions and Monte Carlo analysis to perform statistical uncertainty analysis on the modal correlation capabilities of toolbox, and also shows a sample application which uses the toolbox to analyze the statistical uncertainties on the results of a series of modal tests performed on a highway bridge.

  16. Produção de alface em NFT e Floating aproveitando água salobra e o rejeito da dessalinização Lettuce production under NFT and Floating using brackish groundwater and the reject from its desalination

    Directory of Open Access Journals (Sweden)

    Alexandre Nascimento dos Santos

    2011-06-01

    Full Text Available Plantas de alface cv. Elba foram cultivadas em dois sistemas hidropônicos, Floating e NFT, com o objetivo de avaliar três tipos de água: a água salobra natural (2,47 dS m-1 obtida a partir de um poço profundo; água doce (0,11 dS m-1 produzido por dessalinização por osmose inversa, e o rejeito salino (5,15 dS m-1, um efluente do processo de dessalinização. Estas águas foram combinadas em seis tratamentos resultantes da sua utilização alternada para preparar a solução nutritiva (SN e/ou substituir as perdas por evapotranspiração (ETc. O experimento foi conduzido em casa de vegetação na região semiárida de Pernambuco, utilizando 48 unidades experimentais em blocos casualizados em esquema fatorial 6x2 com quatro repetições. O rendimento da alface (massa de matéria fresca foi maior nas condições do Floating. O uso exclusivo da água do poço profundo e do rejeito de dessalinizadores diminuiu 22,7 e 39,6% a produção de alface, respectivamente. Para uma melhor combinação de águas doces e salobras, o uso de água salobra para repor a perda por ETc pode aumentar a produção de alface em relação ao uso dessas águas para preparar a SN, estes resultados foram registrados para a água do poço profundo e o rejeito.Plants of lettuce cv. Elba were grown under two hydroponic systems, Floating and NFT, aiming to evaluate three water resources: natural brackish water (2,47 dS m-1 obtained from a deep well; fresh water (0,11 dS m-1 produced by reverse osmosis desalination; and reject brine (5,15 dS m-1, a wastewater from desalination process. These waters were combined in six treatments resulted from their alternated use to prepare nutrient solution (NS and/or replace the evapotranspiration loss (ETc. The experiment was carried out under a greenhouse condition in the semiarid region of Pernambuco State, Brazil; 48 experimental units were used for both hydroponic systems. The lettuce yield (shoot fresh matter was higher under

  17. Estratégias de uso de água salobra na produção de alface em hidroponia NFT Strategies for use of brackish water in NFT hydroponic lettuce production

    Directory of Open Access Journals (Sweden)

    Márcio S. Alves

    2011-05-01

    Full Text Available Plantas de alface crespa 'Verônica' foram cultivadas em condições hidropônicas, objetivando avaliar três diferentes estratégias de emprego de águas salobras: 1 águas salobras para reposição das perdas por evapotranspiração (ETc e água doce para o preparo da solução nutritiva (SN; 2 águas salobras para o preparo da SN e água doce para reposição da ETc; 3 águas salobras para o preparo da SN e reposição da ETc. Os níveis de salinidade da água foram obtidos pela adição de NaCl à água doce (0,27 dS m-1: 1,45; 2,51; 3,6; 5,41 e 7,5 dS m-1. O experimento foi conduzido em quatro blocos aleatorizados, com quatro repetições por tratamento. Uma estrutura de pesquisa foi construída com 72 parcelas que simulam a técnica do fluxo laminar de nutrientes (NFT. O uso de água salobra apenas para repor a ETc não produziu efeito sobre a produção da alface. Por outro lado, o uso de águas salobras para o preparo da SN e água doce para reposição da ETc, reduziu o rendimento da alface (massa de matéria fresca da parte aérea em 4,99% por (dS m-1. O rendimento foi reduzido em 7% por dS m-1 quando águas salobras foram usadas tanto para o preparo da SN quanto para reposição da ETc. Apesar da redução linear da produção da alface com o aumento da salinidade da água, sintomas depreciativos para a qualidade da alface hidropônica não foram registrados.Plants of crisphead lettuce cv. 'Verônica' were grown under hydroponic conditions aiming to evaluate three different strategies of brackish waters utilization: 1 brackish waters to replace the evapotranspiration loss (ETc and fresh water to prepare nutrient solution (NS; 2 brackish waters to prepare NS and fresh water to replace the ETc; 3 brackish waters to prepare NS and replace ETc. The levels of water salinity were obtained by addition of NaCl to fresh water (0.27 dS m-1: 1.45; 2.51; 3.6; 5.41 and 7.5 dS m-1. The experiment was conducted in randomized blocks with four

  18. Produção de girassol ornamental com uso de águas salobras em sistema hidropônico NFT Production of ornamental sunflower with use of brackish waters in NFT hydroponic system

    Directory of Open Access Journals (Sweden)

    Marlo P Maciel

    2012-02-01

    Full Text Available Plantas de girassol ornamental 'Sol Vermelho' foram cultivadas em hidroponia com o objetivo de avaliar o uso de águas salobras sobre seu rendimento e qualidade da inflorescência. As águas salobras foram usadas para preparar a solução nutritiva e repor as perdas por evapotranspiração. O experimento foi conduzido em delineamento inteiramente aleatorizado com cinco níveis de salinidade da água: 1,51; 2,56; 3,86 e 6,19 dS m-1, obtidos pela adição de NaCl na água doce local (0,47 dS m-1 que também foi usada como testemunha. Cada tratamento foi repetido quatro vezes e cada parcela (com quatro plantas foi construída para simular um sistema independente da técnica do fluxo laminar de nutrientes (NFT. Observou-se uma redução linear causada pelo aumento da salinidade da água sobre a altura das plantas, o diâmetro do caule e a massa da matéria seca da parte aérea. Tanto a altura da planta quanto o diâmetro do caule foram reduzidos em 3,2% e a massa de matéria seca da parte aérea foi reduzida em 5,78% (dS m-1-1, para cada acréscimo unitário da salinidade da água (dS m-1. Por outro lado, a salinidade da água não afetou o tamanho do capítulo do girassol e não foram registrados sintomas de toxicidade causados pela salinidade. Esses resultados sustentam a viabilidade técnica do uso de águas salobras para produção hidropônica de girassol ornamental.Plants of ornamental sunflower 'Sol Vermelho' were grown under hydroponic conditions aiming to evaluate the effects of use of brackish water on its yield and inflorescence (capitulum quality. The brackish waters were utilized to prepare nutrient solution and to replace water due to evapotranspiration loss. The experiment was carried out in a completely randomized experimental design with five levels of water salinity: 1.51; 2.56; 3.86 and 6.19 dS m-1, obtained by addition of NaCl to local fresh water; this fresh water (0.47 dS m-1 was also studied as control treatment. Each

  19. Competição de cultivares de alface sob cultivo hidropônico 'NFT' em três diferentes espaçamentos Butterhead lettuce cultivars under 'NFT' hydroponic cultivation in three different spacings

    Directory of Open Access Journals (Sweden)

    Ronan Gualberto

    1999-07-01

    Full Text Available Com o objetivo de avaliar o desempenho de seis cultivares de alface do tipo lisa (Babá de Verão, Brasil 303, Elisa, Karla, Lívia e Monalisa em três espaçamentos (25 x 20, 25 x 25 e 25 x 30 cm, cultivadas em sistema hidropônico 'NFT', realizou-se um experimento na Fazenda Experimental da Universidade de Marília (SP, no período de 23 de setembro a 21 de novembro de 1997. Foram avaliadas as características comprimento de caule, produção de matéria fresca por planta e por área e produção de matéria seca da parte aérea, da raiz e total. O delineamento experimental adotado foi o de blocos casualizados, em esquema fatorial 6 x 3, com três repetições. Não houve efeito significativo da interação entre cultivares e espaçamentos. As cultivares Babá de Verão, Lívia e Elisa se destacaram pela produção de matéria fresca e matéria seca total. As cultivares Monalisa e Karla mostraram-se menos suscetíveis ao pendoamento precoce, enquanto a 'Babá de Verão' foi a mais suscetível. Não foi verificada influência significativa dos espaçamentos sobre as características estudadas, exceto para a produção por área, onde independente das cultivares utilizadas, o espaçamento 25 x 20 propiciou uma produção de 4,465 Kg/m², superior aos demais espaçamentos utilizados. Assim. Produções significativamente inferiores foram obtidas nos tratamentos 25 x 25 cm e 25 x 30 cm: 3,583 e 3,304 Kg/m², respectivamente, devido à redução no número de plantas por m².An experiment was carried out at the Experimental Farm, of Marília University, from September 23th 1997 to November 21st 1997 with the objective of evaluating the performance of six butterhead lettuce cultivars (Babá de Verão, Brasil 303, Elisa, Karla, Lívia and Monalisa in three spacings (25 x 20, 25 x 25 and 25 x 30 cm, cultivated under a hydroponic system 'NFT'. Stem length, fresh matter yield per plant and per area, and aerial part and root dry matter weight were

  20. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    Energy Technology Data Exchange (ETDEWEB)

    Aarle, Wim van, E-mail: wim.vanaarle@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Palenstijn, Willem Jan, E-mail: willemjan.palenstijn@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); De Beenhouwer, Jan, E-mail: jan.debeenhouwer@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Altantzis, Thomas, E-mail: thomas.altantzis@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Bals, Sara, E-mail: sara.bals@uantwerpen.be [Electron Microscopy for Materials Science, University of Antwerp, Groenenborgerlaan 171, B-2020 Wilrijk (Belgium); Batenburg, K. Joost, E-mail: joost.batenburg@cwi.nl [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium); Centrum Wiskunde & Informatica, Science Park 123, NL-1098 XG Amsterdam (Netherlands); Mathematical Institute, Leiden University, P.O. Box 9512, NL-2300 RA Leiden (Netherlands); Sijbers, Jan, E-mail: jan.sijbers@uantwerpen.be [iMinds-Vision Lab, University of Antwerp, Universiteitsplein 1, B-2610 Wilrijk (Belgium)

    2015-10-15

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series.

  1. CAMELOT: Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox

    Science.gov (United States)

    Di Carlo, Marilena; Romero Martin, Juan Manuel; Vasile, Massimiliano

    2018-03-01

    Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox (CAMELOT) is a toolbox for the fast preliminary design and optimisation of low-thrust trajectories. It solves highly complex combinatorial problems to plan multi-target missions characterised by long spirals including different perturbations. To do so, CAMELOT implements a novel multi-fidelity approach combining analytical surrogate modelling and accurate computational estimations of the mission cost. Decisions are then made using two optimisation engines included in the toolbox, a single-objective global optimiser, and a combinatorial optimisation algorithm. CAMELOT has been applied to a variety of case studies: from the design of interplanetary trajectories to the optimal de-orbiting of space debris and from the deployment of constellations to on-orbit servicing. In this paper, the main elements of CAMELOT are described and two examples, solved using the toolbox, are presented.

  2. The ASTRA Toolbox: A platform for advanced algorithm development in electron tomography

    International Nuclear Information System (INIS)

    Aarle, Wim van; Palenstijn, Willem Jan; De Beenhouwer, Jan; Altantzis, Thomas; Bals, Sara; Batenburg, K. Joost; Sijbers, Jan

    2015-01-01

    We present the ASTRA Toolbox as an open platform for 3D image reconstruction in tomography. Most of the software tools that are currently used in electron tomography offer limited flexibility with respect to the geometrical parameters of the acquisition model and the algorithms used for reconstruction. The ASTRA Toolbox provides an extensive set of fast and flexible building blocks that can be used to develop advanced reconstruction algorithms, effectively removing these limitations. We demonstrate this flexibility, the resulting reconstruction quality, and the computational efficiency of this toolbox by a series of experiments, based on experimental dual-axis tilt series. - Highlights: • The ASTRA Toolbox is an open platform for 3D image reconstruction in tomography. • Advanced reconstruction algorithms can be prototyped using the fast and flexible building blocks. • This flexibility is demonstrated on a common use case: dual-axis tilt series reconstruction with prior knowledge. • The computational efficiency is validated on an experimentally measured tilt series

  3. What's in Your Teaching Toolbox?

    Science.gov (United States)

    Mormer, Elaine

    2018-02-01

    Educators are faced with an array of tools available to enhance learning outcomes in the classroom and clinic. These tools range from those that are very simple to those that are sufficiently complex to require an investment in learning time. This article summarizes a collection of teaching tools, ordered by the time involved in learning proficient use. Simple tools described include specific online blogs providing support for faculty and student writing and a simple method to capture and download videos from YouTube for classroom use. More complex tools described include a Web-based application for custom-created animated videos and an interactive audience polling system. Readers are encouraged to reflect on the tools most appropriate for use in their own teaching toolbox by considering the requisite time to proficiency and suitability to address desired learner outcomes.

  4. Impact of Low and Moderate Salinity Water on Plant Performance of Leafy Vegetables in a Recirculating NFT System

    Directory of Open Access Journals (Sweden)

    Genhua Niu

    2018-03-01

    Full Text Available Two greenhouse experiments were conducted to examine the growth and mineral nutrition of four leafy vegetables in a nutrient film technique (NFT system with water with low to moderate salinity. In Expt. 1, a nutrient solution was prepared using reverse osmosis (RO water and treatments consisted of supplementing with RO water, tap water, or nutrient solution. In Expt. 2, nutrient solution was prepared using three different water sources (treatments, namely, RO water, tap water, or tap water, plus sodium chloride (NaCl, and supplementing solution was prepared using the same three water sources at one third strength. For both of the experiments, seeds of pac choi ‘Tokyo Bekana’, ‘Mei Qing Choi’, and ‘Rosie’ (Brassica rapa var. chinensis and leaf lettuce ‘Tropicana’ (Lactuca sativa were sown and were grown in a growth chamber. Two weeks after sowing, seedlings were transplanted to the NFT systems. Expt. 1 was conducted from 19 April to 19 May 2016 and Expt. 2 from 6 September to 12 October 2016. In Expt. 1, nitrate (NO3− and phosphorus (P levels in the tanks decreased, and potassium (K+ levels reached almost zero at the end of the experiment when supplemented with RO or tap water. However, calcium (Ca2+, magnesium (Mg2+, and sulfate (SO42− either did not decrease or increased over time. Supplementing water type did not affect the growth of leaf lettuce and ‘Mei Qing Choi’ pac choi; however, fresh weight of ‘Rosie’ pac choi and both fresh and dry weight of ‘Tokyo Bekana’ pac choi were reduced when supplemented with RO water. Leaf sap NO3− was reduced in ‘Tokyo Bekana’ pac choi, but not in other varieties, when supplemented with RO or tap water. Leaf sap K+ decreased in ‘Tokyo Bekana’, but not in other varieties. The supplementing water type did not impact leaf sap Ca2+, regardless of vegetable varieties. In Expt. 2, NO3− in all of the treatments, P in RO water, and K+ in RO or tap water decreased in the

  5. Low Energy Mission Planning Toolbox, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — The Low Energy Mission Planning Toolbox is designed to significantly reduce the resources and time spent on designing missions in multi-body gravitational...

  6. Drinking Water Cyanotoxin Risk Communication Toolbox

    Science.gov (United States)

    The drinking water cyanotoxin risk communication toolbox is a ready-to-use, “one-stop-shop” to support public water systems, states, and local governments in developing, as they deem appropriate, their own risk communication materials.

  7. Air Sensor Toolbox: Resources and Funding

    Science.gov (United States)

    EPA’s Air Sensor Toolbox provides information and guidance on new low-cost compact technologies for measuring air quality. It provides information to help citizens more effectively and accurately collect air quality data in their community.

  8. Air Sensor Toolbox for Citizen Scientists

    Science.gov (United States)

    EPA’s Air Sensor Toolbox provides information and guidance on new low-cost compact technologies for measuring air quality. It provides information to help citizens more effectively and accurately collect air quality data in their community.

  9. Toolbox for multiloop Feynman diagrams calculations using $R^{*}$ operation

    OpenAIRE

    Batkovich, Dmitrii; Kompaniets, Mikhail

    2014-01-01

    We present the toolbox for analytical calculation of UV-counterterm of Feynman diagrams. It combines the power of $R^{*\\prime}$-operation with modern analytical methods. Written in pure Python our toolbox can be easily used and extended.

  10. Non-stationary Condition Monitoring of large diesel engines with the AEWATT toolbox

    DEFF Research Database (Denmark)

    Pontoppidan, Niels Henrik; Larsen, Jan; Sigurdsson, Sigurdur

    2005-01-01

    We are developing a specialized toolbox for non-stationary condition monitoring of large 2-stroke diesel engines based on acoustic emission measurements. The main contribution of this toolbox has so far been the utilization of adaptive linear models such as Principal and Independent Component...... Analysis, as combined modeling and feature reduction methods. These models describe the, say 1024 or 2048, acoustic emission samples per engine revolution, i.e. data are in the crank angle domain. In this framework we have applied unsupervised learning using only one feature – the log...

  11. A conceptual toolbox for designing CSCW applications

    DEFF Research Database (Denmark)

    Bødker, Susanne; Christiansen, Ellen

    1995-01-01

    This paper presents a conceptual toolbox, developed to support the design of CSCW applications in a large Esprit project, EuroCODE. Here, several groups of designers work to investigate computer support for cooperative work in large use organizations, at the same time as they work to develop...... an open development platform for CSCW applications. The conceptual toolbox has been developed to support communication in and among these design groups, between designers and users and in future use of the open development platform. Rejecting the idea that one may design from a framework describing CSCW......, the toolbox aims to support design by doing and help bridging between work with users, technical design, and insights gained from theoretical and empirical CSCW research....

  12. Effective and versatile software beamformation toolbox

    DEFF Research Database (Denmark)

    Kortbek, Jacob; Nikolov, Svetoslav; Jensen, Jørgen Arendt

    2007-01-01

    aperture to obtain a preferred constant F-number. An effective and versatile software toolbox for off-line beamformation designed to address all of these issues has been developed. It is capable of exploiting parallelization of computations on a Linux cluster and is written in C++ with a MATLAB (Math Works...... and stored in lookup-tables (LUT). Parametric beamforming can also be applied where calculations are done by demand, thus, reducing the storage demand dramatically. On a standard PC with a Pentium 4, 2.66 GHz processor running Linux the toolbox can beamform 100,000 points in lines of various directions in 20...

  13. Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox

    Directory of Open Access Journals (Sweden)

    Andre Santos Ribeiro

    2015-07-01

    Full Text Available Aim. In recent years, connectivity studies using neuroimaging data have increased the understanding of the organization of large-scale structural and functional brain networks. However, data analysis is time consuming as rigorous procedures must be assured, from structuring data and pre-processing to modality specific data procedures. Until now, no single toolbox was able to perform such investigations on truly multimodal image data from beginning to end, including the combination of different connectivity analyses. Thus, we have developed the Multimodal Imaging Brain Connectivity Analysis (MIBCA toolbox with the goal of diminishing time waste in data processing and to allow an innovative and comprehensive approach to brain connectivity.Materials and Methods. The MIBCA toolbox is a fully automated all-in-one connectivity toolbox that offers pre-processing, connectivity and graph theoretical analyses of multimodal image data such as diffusion-weighted imaging, functional magnetic resonance imaging (fMRI and positron emission tomography (PET. It was developed in MATLAB environment and pipelines well-known neuroimaging softwares such as Freesurfer, SPM, FSL, and Diffusion Toolkit. It further implements routines for the construction of structural, functional and effective or combined connectivity matrices, as well as, routines for the extraction and calculation of imaging and graph-theory metrics, the latter using also functions from the Brain Connectivity Toolbox. Finally, the toolbox performs group statistical analysis and enables data visualization in the form of matrices, 3D brain graphs and connectograms. In this paper the MIBCA toolbox is presented by illustrating its capabilities using multimodal image data from a group of 35 healthy subjects (19–73 years old with volumetric T1-weighted, diffusion tensor imaging, and resting state fMRI data, and 10 subjets with 18F-Altanserin PET data also.Results. It was observed both a high inter

  14. CONTINEX: A Toolbox for Continuation in Experiments

    DEFF Research Database (Denmark)

    Schilder, Frank; Bureau, Emil; Santos, Ilmar

    2014-01-01

    CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation-free mod......CONTINEX is a MATLAB toolbox for bifurcation analysis based on the development platform COCO (computational continuation core). CONTINEX is specifically designed for coupling to experimental test specimen via DSPACE, but provides also interfaces to SIMULINK-, ODE-, and so-called equation...

  15. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Looms, Majken Caroline

    2013-01-01

    We present an application of the SIPPI Matlab toolbox, to obtain a sample from the a posteriori probability density function for the classical tomographic inversion problem. We consider a number of different forward models, linear and non-linear, such as ray based forward models that rely...

  16. Tolkku - a toolbox for decision support from condition monitoring data

    International Nuclear Information System (INIS)

    Saarela, Olli; Lehtonen, Mikko; Halme, Jari; Aikala, Antti; Raivio, Kimmo

    2012-01-01

    This paper describes a software toolbox (a software library) designed for condition monitoring and diagnosis of machines. This toolbox implements both new methods and prior art and is aimed for practical down-to-earth data analysis work. The target is to improve knowledge of the operation and behaviour of machines and processes throughout their entire life-cycles. The toolbox supports different phases of condition based maintenance with tools that extract essential information and automate data processing. The paper discusses principles that have guided toolbox design and the implemented toolbox structure. Case examples are used to illustrate how condition monitoring applications can be built using the toolbox. In the first case study the toolbox is applied to fault detection of industrial centrifuges based on measured electrical current. The second case study outlines an application for centralized monitoring of a fleet of machines that supports organizational learning.

  17. SAFE(R): A Matlab/Octave Toolbox (and R Package) for Global Sensitivity Analysis

    Science.gov (United States)

    Pianosi, Francesca; Sarrazin, Fanny; Gollini, Isabella; Wagener, Thorsten

    2015-04-01

    Global Sensitivity Analysis (GSA) is increasingly used in the development and assessment of hydrological models, as well as for dominant control analysis and for scenario discovery to support water resource management under deep uncertainty. Here we present a toolbox for the application of GSA, called SAFE (Sensitivity Analysis For Everybody) that implements several established GSA methods, including method of Morris, Regional Sensitivity Analysis, variance-based sensitivity Analysis (Sobol') and FAST. It also includes new approaches and visualization tools to complement these established methods. The Toolbox is released in two versions, one running under Matlab/Octave (called SAFE) and one running in R (called SAFER). Thanks to its modular structure, SAFE(R) can be easily integrated with other toolbox and packages, and with models running in a different computing environment. Another interesting feature of SAFE(R) is that all the implemented methods include specific functions for assessing the robustness and convergence of the sensitivity estimates. Furthermore, SAFE(R) includes numerous visualisation tools for the effective investigation and communication of GSA results. The toolbox is designed to make GSA accessible to non-specialist users, and to provide a fully commented code for more experienced users to complement their own tools. The documentation includes a set of workflow scripts with practical guidelines on how to apply GSA and how to use the toolbox. SAFE(R) is open source and freely available from the following website: http://bristol.ac.uk/cabot/resources/safe-toolbox/ Ultimately, SAFE(R) aims at improving the diffusion and quality of GSA practice in the hydrological modelling community.

  18. PRoNTo: pattern recognition for neuroimaging toolbox.

    Science.gov (United States)

    Schrouff, J; Rosa, M J; Rondina, J M; Marquand, A F; Chu, C; Ashburner, J; Phillips, C; Richiardi, J; Mourão-Miranda, J

    2013-07-01

    In the past years, mass univariate statistical analyses of neuroimaging data have been complemented by the use of multivariate pattern analyses, especially based on machine learning models. While these allow an increased sensitivity for the detection of spatially distributed effects compared to univariate techniques, they lack an established and accessible software framework. The goal of this work was to build a toolbox comprising all the necessary functionalities for multivariate analyses of neuroimaging data, based on machine learning models. The "Pattern Recognition for Neuroimaging Toolbox" (PRoNTo) is open-source, cross-platform, MATLAB-based and SPM compatible, therefore being suitable for both cognitive and clinical neuroscience research. In addition, it is designed to facilitate novel contributions from developers, aiming to improve the interaction between the neuroimaging and machine learning communities. Here, we introduce PRoNTo by presenting examples of possible research questions that can be addressed with the machine learning framework implemented in PRoNTo, and cannot be easily investigated with mass univariate statistical analysis.

  19. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    2005-01-01

    gravity field, Earth magnetic field and eclipse. The structure and facilities within the toolbox are described and exemplified using a student satellite case (AAUSAT-II). The validity of developed models is confirmed by comparing the simulation results with the realistic data obtained from the Danish...... Ørsted satellite....

  20. Design and Implementation of a Space Environment Simulation Toolbox for Small Satellites

    DEFF Research Database (Denmark)

    Amini, Rouzbeh; Larsen, Jesper A.; Izadi-Zamanabadi, Roozbeh

    gravity field, Earth magnetic field and eclipse. The structure and facilities within the toolbox are described and exemplified using a student satellite case (AAUSAT-II). The validity of developed models is confirmed by comparing the simulation results with the realistic data obtained from the Danish...... Ørsted satellite....

  1. Construction of multi-functional open modulized Matlab simulation toolbox for imaging ladar system

    Science.gov (United States)

    Wu, Long; Zhao, Yuan; Tang, Meng; He, Jiang; Zhang, Yong

    2011-06-01

    Ladar system simulation is to simulate the ladar models using computer simulation technology in order to predict the performance of the ladar system. This paper presents the developments of laser imaging radar simulation for domestic and overseas studies and the studies of computer simulation on ladar system with different application requests. The LadarSim and FOI-LadarSIM simulation facilities of Utah State University and Swedish Defence Research Agency are introduced in details. This paper presents the low level of simulation scale, un-unified design and applications of domestic researches in imaging ladar system simulation, which are mostly to achieve simple function simulation based on ranging equations for ladar systems. Design of laser imaging radar simulation with open and modularized structure is proposed to design unified modules for ladar system, laser emitter, atmosphere models, target models, signal receiver, parameters setting and system controller. Unified Matlab toolbox and standard control modules have been built with regulated input and output of the functions, and the communication protocols between hardware modules. A simulation based on ICCD gain-modulated imaging ladar system for a space shuttle is made based on the toolbox. The simulation result shows that the models and parameter settings of the Matlab toolbox are able to simulate the actual detection process precisely. The unified control module and pre-defined parameter settings simplify the simulation of imaging ladar detection. Its open structures enable the toolbox to be modified for specialized requests. The modulization gives simulations flexibility.

  2. Segmentation Toolbox for Tomographic Image Data

    DEFF Research Database (Denmark)

    Einarsdottir, Hildur

    , techniques to automatically analyze such data becomes ever more important. Most segmentation methods for large datasets, such as CT images, deal with simple thresholding techniques, where intensity values cut offs are predetermined and hard coded. For data where the intensity difference is not sufficient......Motivation: Image acquisition has vastly improved over the past years, introducing techniques such as X-ray computed tomography (CT). CT images provide the means to probe a sample non-invasively to investigate its inner structure. Given the wide usage of this technique and massive data amounts......, and partial volume voxels occur frequently, thresholding methods do not suffice and more advanced methods are required. Contribution: To meet these requirements a toolbox has been developed, combining well known methods within the image analysis field. The toolbox includes cluster-based methods...

  3. ESA's Multi-mission Sentinel-1 Toolbox

    Science.gov (United States)

    Veci, Luis; Lu, Jun; Foumelis, Michael; Engdahl, Marcus

    2017-04-01

    The Sentinel-1 Toolbox is a new open source software for scientific learning, research and exploitation of the large archives of Sentinel and heritage missions. The Toolbox is based on the proven BEAM/NEST architecture inheriting all current NEST functionality including multi-mission support for most civilian satellite SAR missions. The project is funded through ESA's Scientific Exploitation of Operational Missions (SEOM). The Sentinel-1 Toolbox will strive to serve the SEOM mandate by providing leading-edge software to the science and application users in support of ESA's operational SAR mission as well as by educating and growing a SAR user community. The Toolbox consists of a collection of processing tools, data product readers and writers and a display and analysis application. A common architecture for all Sentinel Toolboxes is being jointly developed by Brockmann Consult, Array Systems Computing and C-S called the Sentinel Application Platform (SNAP). The SNAP architecture is ideal for Earth Observation processing and analysis due the following technological innovations: Extensibility, Portability, Modular Rich Client Platform, Generic EO Data Abstraction, Tiled Memory Management, and a Graph Processing Framework. The project has developed new tools for working with Sentinel-1 data in particular for working with the new Interferometric TOPSAR mode. TOPSAR Complex Coregistration and a complete Interferometric processing chain has been implemented for Sentinel-1 TOPSAR data. To accomplish this, a coregistration following the Spectral Diversity[4] method has been developed as well as special azimuth handling in the coherence, interferogram and spectral filter operators. The Toolbox includes reading of L0, L1 and L2 products in SAFE format, calibration and de-noising, slice product assembling, TOPSAR deburst and sub-swath merging, terrain flattening radiometric normalization, and visualization for L2 OCN products. The Toolbox also provides several new tools for

  4. The laboratory test utilization management toolbox.

    Science.gov (United States)

    Baird, Geoffrey

    2014-01-01

    Efficiently managing laboratory test utilization requires both ensuring adequate utilization of needed tests in some patients and discouraging superfluous tests in other patients. After the difficult clinical decision is made to define the patients that do and do not need a test, a wealth of interventions are available to the clinician and laboratorian to help guide appropriate utilization. These interventions are collectively referred to here as the utilization management toolbox. Experience has shown that some tools in the toolbox are weak and other are strong, and that tools are most effective when many are used simultaneously. While the outcomes of utilization management studies are not always as concrete as may be desired, what data is available in the literature indicate that strong utilization management interventions are safe and effective measures to improve patient health and reduce waste in an era of increasing financial pressure.

  5. The masked priming toolbox: an open-source MATLAB toolbox for masked priming researchers.

    Science.gov (United States)

    Wilson, Andrew D; Tresilian, James; Schlaghecken, Friederike

    2011-03-01

    The Masked Priming Toolbox is an open-source collection of MATLAB functions that utilizes the free third-party PsychToolbox-3 (PTB3: Brainard, Spatial Vision, 10, 433-436, 1997; Kleiner, Brainard & Pelli, Perception, 36, 2007; Pelli, Spatial Vision, 10, 437-442, 1997). It is designed to allow a researcher to run masked (and unmasked) priming experiments using a variety of response devices (including keyboards, graphics tablets and force transducers). Very little knowledge of MATLAB is required; experiments are generated by creating a text file with the required parameters, and raw and analyzed data are output to Excel (as well as MATLAB) files for further analysis. The toolbox implements a variety of stimuli for use as primes and targets, as well as a variety of masks. Timing, size, location, and orientation of stimuli are all parameterizable. The code is open-source and made available on the Web under a Creative Commons License.

  6. A toolbox for glider data processing and management

    OpenAIRE

    Troupin, Charles; Beltrán, Joan Pau; Heslop, Emma; Torner, Marc; Garau, Bartolomé; Allen, John T.; Ruiz, Simón; Tintoré, Joaquín

    2016-01-01

    We present a complete set of freely available MATLAB/Octave scripts called the SOCIB Glider Toolbox (https://github.com/socib/glider_toolbox). This new toolbox automates glider data processing functions, including thermal lag correction, quality control and graphical outputs. While the scientific value of the glider platform has been proven, the experience for the glider data user is far from perfect or routine. Over the last 10 years, ocean gliders have evolved such that they are now conside...

  7. Alternative Splicing Regulation of Cancer-Related Pathways in Caenorhabditis elegans: An In Vivo Model System with a Powerful Reverse Genetics Toolbox

    Directory of Open Access Journals (Sweden)

    Sergio Barberán-Soler

    2013-01-01

    Full Text Available Alternative splicing allows for the generation of protein diversity and fine-tunes gene expression. Several model systems have been used for the in vivo study of alternative splicing. Here we review the use of the nematode Caenorhabditis elegans to study splicing regulation in vivo. Recent studies have shown that close to 25% of genes in the worm genome undergo alternative splicing. A big proportion of these events are functional, conserved, and under strict regulation either across development or other conditions. Several techniques like genome-wide RNAi screens and bichromatic reporters are available for the study of alternative splicing in worms. In this review, we focus, first, on the main studies that have been performed to dissect alternative splicing in this system and later on examples from genes that have human homologs that are implicated in cancer. The significant advancement towards understanding the regulation of alternative splicing and cancer that the C. elegans system has offered is discussed.

  8. C%2B%2B tensor toolbox user manual.

    Energy Technology Data Exchange (ETDEWEB)

    Plantenga, Todd D.; Kolda, Tamara Gibson

    2012-04-01

    The C++ Tensor Toolbox is a software package for computing tensor decompositions. It is based on the Matlab Tensor Toolbox, and is particularly optimized for sparse data sets. This user manual briefly overviews tensor decomposition mathematics, software capabilities, and installation of the package. Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors in C++. The Toolbox compiles into libraries and is intended for use with custom applications written by users.

  9. BSMART: a Matlab/C toolbox for analysis of multichannel neural time series.

    Science.gov (United States)

    Cui, Jie; Xu, Lei; Bressler, Steven L; Ding, Mingzhou; Liang, Hualou

    2008-10-01

    We have developed a Matlab/C toolbox, Brain-SMART (System for Multivariate AutoRegressive Time series, or BSMART), for spectral analysis of continuous neural time series data recorded simultaneously from multiple sensors. Available functions include time series data importing/exporting, preprocessing (normalization and trend removal), AutoRegressive (AR) modeling (multivariate/bivariate model estimation and validation), spectral quantity estimation (auto power, coherence and Granger causality spectra), network analysis (including coherence and causality networks) and visualization (including data, power, coherence and causality views). The tools for investigating causal network structures in respect of frequency bands are unique functions provided by this toolbox. All functionality has been integrated into a simple and user-friendly graphical user interface (GUI) environment designed for easy accessibility. Although we have tested the toolbox only on Windows and Linux operating systems, BSMART itself is system independent. This toolbox is freely available (http://www.brain-smart.org) under the GNU public license for open source development.

  10. Interval Coded Scoring: a toolbox for interpretable scoring systems

    Directory of Open Access Journals (Sweden)

    Lieven Billiet

    2018-04-01

    Full Text Available Over the last decades, clinical decision support systems have been gaining importance. They help clinicians to make effective use of the overload of available information to obtain correct diagnoses and appropriate treatments. However, their power often comes at the cost of a black box model which cannot be interpreted easily. This interpretability is of paramount importance in a medical setting with regard to trust and (legal responsibility. In contrast, existing medical scoring systems are easy to understand and use, but they are often a simplified rule-of-thumb summary of previous medical experience rather than a well-founded system based on available data. Interval Coded Scoring (ICS connects these two approaches, exploiting the power of sparse optimization to derive scoring systems from training data. The presented toolbox interface makes this theory easily applicable to both small and large datasets. It contains two possible problem formulations based on linear programming or elastic net. Both allow to construct a model for a binary classification problem and establish risk profiles that can be used for future diagnosis. All of this requires only a few lines of code. ICS differs from standard machine learning through its model consisting of interpretable main effects and interactions. Furthermore, insertion of expert knowledge is possible because the training can be semi-automatic. This allows end users to make a trade-off between complexity and performance based on cross-validation results and expert knowledge. Additionally, the toolbox offers an accessible way to assess classification performance via accuracy and the ROC curve, whereas the calibration of the risk profile can be evaluated via a calibration curve. Finally, the colour-coded model visualization has particular appeal if one wants to apply ICS manually on new observations, as well as for validation by experts in the specific application domains. The validity and applicability

  11. UQTools: The Uncertainty Quantification Toolbox - Introduction and Tutorial

    Science.gov (United States)

    Kenny, Sean P.; Crespo, Luis G.; Giesy, Daniel P.

    2012-01-01

    UQTools is the short name for the Uncertainty Quantification Toolbox, a software package designed to efficiently quantify the impact of parametric uncertainty on engineering systems. UQTools is a MATLAB-based software package and was designed to be discipline independent, employing very generic representations of the system models and uncertainty. Specifically, UQTools accepts linear and nonlinear system models and permits arbitrary functional dependencies between the system s measures of interest and the probabilistic or non-probabilistic parametric uncertainty. One of the most significant features incorporated into UQTools is the theoretical development centered on homothetic deformations and their application to set bounding and approximating failure probabilities. Beyond the set bounding technique, UQTools provides a wide range of probabilistic and uncertainty-based tools to solve key problems in science and engineering.

  12. Matlab Stability and Control Toolbox: Trim and Static Stability Module

    Science.gov (United States)

    Crespo, Luis G.; Kenny, Sean P.

    2006-01-01

    This paper presents the technical background of the Trim and Static module of the Matlab Stability and Control Toolbox. This module performs a low-fidelity stability and control assessment of an aircraft model for a set of flight critical conditions. This is attained by determining if the control authority available for trim is sufficient and if the static stability characteristics are adequate. These conditions can be selected from a prescribed set or can be specified to meet particular requirements. The prescribed set of conditions includes horizontal flight, take-off rotation, landing flare, steady roll, steady turn and pull-up/ push-over flight, for which several operating conditions can be specified. A mathematical model was developed allowing for six-dimensional trim, adjustable inertial properties, asymmetric vehicle layouts, arbitrary number of engines, multi-axial thrust vectoring, engine(s)-out conditions, crosswind and gyroscopic effects.

  13. User's manual for Ecolego Toolbox and the Discretization Block

    Energy Technology Data Exchange (ETDEWEB)

    Broed, Robert (Facilia consulting AB (Sweden)); Shulan Xu (Swedish Radiation Protection Authority, Stockholm (Sweden))

    2008-03-15

    The CLIMB modelling team (Catchment LInked Models of radiological effects in the Biosphere) was instituted in 2004 to provide SSI with an independent modelling capability when reviewing SKB's assessment of long-term safety for a geological repository. Modelling in CLIMB covers all aspects of performance assessment (PA) from near-field releases to radiological consequences in the surface environment. Software used to implement assessment models has been developed within the project. The software comprises a toolbox based on the commercial packages Matlab and Simulink used to solve compartment based differential equation systems, but with an added user friendly graphical interface. This report documents the new simulation toolbox and a newly developed Discretisation Block, which is a powerful tool for solving problems involving a network of compartments in two dimensions

  14. A Panel Data Toolbox for MATLAB

    Directory of Open Access Journals (Sweden)

    Inmaculada C. Álvarez

    2017-01-01

    Full Text Available Panel Data Toolbox is a new package for MATLAB that includes functions to estimate the main econometric methods of balanced and unbalanced panel data analysis. The package includes code for the standard fixed, between and random effects estimation methods, as well as for the existing instrumental panels and a wide array of spatial panels. A full set of relevant tests is also included. This paper describes the methodology and implementation of the functions and illustrates their use with well-known examples. We perform numerical checks against other popular commercial and free software to show the validity of the results.

  15. Extending the COVAD toolbox to accommodate system non-linearities

    NARCIS (Netherlands)

    Bucco, D.; Weiss, M.

    2009-01-01

    The COVAD toolbox is a MATLAB/Simulink based tool conceived and developed for the rapid analysis and simulation of stochastically driven dynamic systems. In addition to a generic Monte Carlo capability, the toolbox is also supported by traditional analytical techniques such as the adjoint and

  16. Rapid Capability Fielding Toolbox Study

    Science.gov (United States)

    2010-03-01

    skipped  or  attenuated, depending on the specific effort) are as follows:   The  process  is  initiated  with  the  identification  and  careful ...O.L., “Modeling Methods and Conceptual Design Principles for Reconfigurable Systems”,  Journal  of Mechanical Design, 139, 101102, October 2008.  15...Motorola  Dennis Roberson is Vice Provost and Executive Director of the Institute of Business and  Interprofessional   Studies, as well as Acting

  17. Distributed Aerodynamic Sensing and Processing Toolbox

    Science.gov (United States)

    Brenner, Martin; Jutte, Christine; Mangalam, Arun

    2011-01-01

    A Distributed Aerodynamic Sensing and Processing (DASP) toolbox was designed and fabricated for flight test applications with an Aerostructures Test Wing (ATW) mounted under the fuselage of an F-15B on the Flight Test Fixture (FTF). DASP monitors and processes the aerodynamics with the structural dynamics using nonintrusive, surface-mounted, hot-film sensing. This aerodynamic measurement tool benefits programs devoted to static/dynamic load alleviation, body freedom flutter suppression, buffet control, improvement of aerodynamic efficiency through cruise control, supersonic wave drag reduction through shock control, etc. This DASP toolbox measures local and global unsteady aerodynamic load distribution with distributed sensing. It determines correlation between aerodynamic observables (aero forces) and structural dynamics, and allows control authority increase through aeroelastic shaping and active flow control. It offers improvements in flutter suppression and, in particular, body freedom flutter suppression, as well as aerodynamic performance of wings for increased range/endurance of manned/ unmanned flight vehicles. Other improvements include inlet performance with closed-loop active flow control, and development and validation of advanced analytical and computational tools for unsteady aerodynamics.

  18. Rad Toolbox User's Guide

    Energy Technology Data Exchange (ETDEWEB)

    Eckerman, Keith F. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Sjoreen, Andrea L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2013-05-01

    The Radiological Toolbox software developed by Oak Ridge National Laboratory (ORNL) for U. S. Nuclear Regulatory Commission (NRC) is designed to provide electronic access to the vast and varied data that underlies the field of radiation protection. These data represent physical, chemical, anatomical, physiological, and mathematical parameters detailed in various handbooks which a health physicist might consult while in his office. The initial motivation for the software was to serve the needs of the health physicist away from his office and without access to his handbooks; e.g., NRC inspectors. The earlier releases of the software were widely used and accepted around the world by not only practicing health physicist but also those within educational programs. This release updates the software to accommodate changes in Windows operating systems and, in some aspects, radiation protection. This release has been tested on Windows 7 and 8 and on 32- and 64-bit machines. The nuclear decay data has been updated and thermal neutron capture cross sections and cancer risk coefficients have been included. This document and the software’s user’s guide provide further details and documentation of the information captured within the Radiological Toolbox.

  19. BSMART: A Matlab/C toolbox for analysis of multichannel neural time series

    OpenAIRE

    Cui, Jie; Xu, Lei; Bressler, Steven L.; Ding, Mingzhou; Liang, Hualou

    2008-01-01

    We have developed a Matlab/C toolbox, Brain-SMART (System for Multivariate AutoRegressive Time series, or BSMART), for spectral analysis of continuous neural time series data recorded simultaneously from multiple sensors. Available functions include time series data importing/exporting, preprocessing (normalization and trend removal), AutoRegressive (AR) modeling (multivariate/bivariate model estimation and validation), spectral quantity estimation (auto power, coherence and Granger causality...

  20. A Bigger Toolbox: Biotechnology in Biodiversity Conservation.

    Science.gov (United States)

    Corlett, Richard T

    2017-01-01

    Conservation biology needs a bigger toolbox to meet unprecedented challenges. Genomics, fueled by declining sequencing costs, offers novel tools with increased precision for genetic questions previously answered with a few molecular markers, as well as completely new possibilities. Metabarcoding promises quicker, cheaper, and more accurate assessments of biodiversity in groups that are difficult to assess by traditional methods, while sequencing low-quality DNA extends the range of useable materials to include museum specimens, archeological remains, and environmental samples. Genomic and transcriptomic data can be used to assess the potential of populations to adapt to new challenges. In the near future, gene-editing tools may help endangered species cope with change, while gene drives control unwanted species and help wanted ones. De-extinction has become a serious prospect. Copyright © 2016 Elsevier Ltd. All rights reserved.

  1. Expanding the UniFrac Toolbox.

    Directory of Open Access Journals (Sweden)

    Ruth G Wong

    Full Text Available The UniFrac distance metric is often used to separate groups in microbiome analysis, but requires a constant sequencing depth to work properly. Here we demonstrate that unweighted UniFrac is highly sensitive to rarefaction instance and to sequencing depth in uniform data sets with no clear structure or separation between groups. We show that this arises because of subcompositional effects. We introduce information UniFrac and ratio UniFrac, two new weightings that are not as sensitive to rarefaction and allow greater separation of outliers than classic unweighted and weighted UniFrac. With this expansion of the UniFrac toolbox, we hope to empower researchers to extract more varied information from their data.

  2. Towards an integrated materials characterization toolbox

    DEFF Research Database (Denmark)

    Robertson, Ian M.; Schuh, Christopher A.; Vetrano, John S.

    2011-01-01

    The material characterization toolbox has recently experienced a number of parallel revolutionary advances, foreshadowing a time in the near future when material scientists can quantify material structure evolution across spatial and temporal space simultaneously. This will provide insight...... development. Electron microscopy; atom probe tomography; x-ray, neutron and electron tomography; serial sectioning tomography; and diffraction-based analysis methods are reviewed, and opportunities for their future development are highlighted. Advances in surface probe microscopy have been reviewed recently...... the state-of-the-art in characterization and suggest a trajectory for the continued development of the field. Based on this review, a set of grand challenges for characterization science is identified, including suggestions for instrumentation advances, scientific problems in microstructure analysis...

  3. SU-E-J-253: The Radiomics Toolbox in the Computational Environment for Radiological Research (CERR)

    International Nuclear Information System (INIS)

    Apte, A; Veeraraghavan, H; Oh, J; Kijewski, P; Deasy, J

    2015-01-01

    Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features and (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”

  4. Integration of a blood pressure controller and an infusion toolbox system using client-server technology.

    Science.gov (United States)

    Meijers, R H; Coussaert, E J; Cantraine, F R

    1998-05-01

    This paper shortly describes an Infusion Toolbox and a blood pressure (BP) control application. It explains how we applied an agent model and client-server technology to integrate them. We show that by using this framework and object oriented technologies the necessary changes to the existing applications are reduced. Many elements of the tested original systems could be re-used, which enhances safe development.

  5. Computing "anomalous" contaminant transport in porous media: the CTRW MATLAB toolbox.

    Science.gov (United States)

    Cortis, Andrea; Berkowitz, Brian

    2005-01-01

    We describe the continuous time random walk (CTRW) MATLAB toolbox, a collection of MATLAB scripts and functions that compute breakthrough curves (BTCs) and one-dimensional/two-dimensional (1D/2D) resident concentration profiles for passive tracer dispersion. The transport model is based on the CTRW theory. CTRW includes as special cases the classical Fickian dispersion based advection-dispersion equation, multirate and mobile-immobile models, and the fractional-in-time derivative transport equation. Several models for treating the memory effects responsible for the anomalous character of dispersion have been implemented in the CTRW toolbox. In the current version of the toolbox, it is possible to solve explicitly for the forward problem (concentration prediction) in 1D and 2D and for the inverse problem (parameter identification from experimental BTC data) in 1D. Future extensions will include explicit treatment of sorbing tracers, simple subroutines for treating radial flow from wells, introduction of arbitrary initial conditions, treatment of heterogeneous domains by use of the Fokker-Planck with Memory equation, and treatment of transport in multidimensional systems.

  6. The ABRAVIBE toolbox for teaching vibration analysis and structural dynamics

    DEFF Research Database (Denmark)

    Brandt, A.

    2013-01-01

    Vibration analysis is a subject where students often find it hard to comprehend the fundamental theory. The fact that we have, in general, almost no intuition for dynamic phenomena, means that students need to explore various dynamic phenomena in order to grasp the subject. For this reason......, a MATLAB toolbox (the ABRAVIBE toolbox) has been developed as an accompanying toolbox for the recent book "Noise and Vibration Analysis" by the author. This free, open software, published under GNU Public License, can be used with GNU Octave, if an entirely free software platform is wanted, with a few......). In this paper, an overview of the functionality is given and recommended use in teaching is discussed. It is also shown how the toolbox can be used for general vibration analysis using data from multichannel measurements. Finally, some laboratory exercises for structural dynamics teaching are discussed...

  7. Managing Fieldwork Data with Toolbox and the Natural Language Toolkit

    Directory of Open Access Journals (Sweden)

    Stuart Robinson

    2007-06-01

    Full Text Available This paper shows how fieldwork data can be managed using the program Toolbox together with the Natural Language Toolkit (NLTK for the Python programming language. It provides background information about Toolbox and describes how it can be downloaded and installed. The basic functionality of the program for lexicons and texts is described, and its strengths and weaknesses are reviewed. Its underlying data format is briefly discussed, and Toolbox processing capabilities of NLTK are introduced, showing ways in which it can be used to extend the functionality of Toolbox. This is illustrated with a few simple scripts that demonstrate basic data management tasks relevant to language documentation, such as printing out the contents of a lexicon as HTML.

  8. ARC Code TI: X-Plane Communications Toolbox (XPC)

    Data.gov (United States)

    National Aeronautics and Space Administration — The X-Plane Communications Toolbox (XPC) is an open source research tool used to interact with the commercial flight simulator software X-Plane. XPC allows users to...

  9. BASCO: a toolbox for task-related functional connectivity.

    Science.gov (United States)

    Göttlich, Martin; Beyer, Frederike; Krämer, Ulrike M

    2015-01-01

    BASCO (BetA Series COrrelation) is a user-friendly MATLAB toolbox with a graphical user interface (GUI) which allows investigating functional connectivity in event-related functional magnetic resonance imaging (fMRI) data. Connectivity analyses extend and compliment univariate activation analyses since the actual interaction between brain regions involved in a task can be explored. BASCO supports seed-based functional connectivity as well as brain network analyses. Although there are a multitude of advanced toolboxes for investigating resting-state functional connectivity, BASCO is the first toolbox for evaluating task-related whole-brain functional connectivity employing a large number of network nodes. Thus, BASCO allows investigating task-specific rather than resting-state networks. Here, we summarize the main features of the toolbox and describe the methods and algorithms.

  10. μ-diff: An open-source Matlab toolbox for computing multiple scattering problems by disks

    Science.gov (United States)

    Thierry, Bertrand; Antoine, Xavier; Chniti, Chokri; Alzubaidi, Hasan

    2015-07-01

    The aim of this paper is to describe a Matlab toolbox, called μ-diff, for modeling and numerically solving two-dimensional complex multiple scattering by a large collection of circular cylinders. The approximation methods in μ-diff are based on the Fourier series expansions of the four basic integral operators arising in scattering theory. Based on these expressions, an efficient spectrally accurate finite-dimensional solution of multiple scattering problems can be simply obtained for complex media even when many scatterers are considered as well as large frequencies. The solution of the global linear system to solve can use either direct solvers or preconditioned iterative Krylov subspace solvers for block Toeplitz matrices. Based on this approach, this paper explains how the code is built and organized. Some complete numerical examples of applications (direct and inverse scattering) are provided to show that μ-diff is a flexible, efficient and robust toolbox for solving some complex multiple scattering problems.

  11. Security Toolbox for Detecting Novel and Sophisticated Android Malware

    OpenAIRE

    Holland, Benjamin; Deering, Tom; Kothari, Suresh; Mathews, Jon; Ranade, Nikhil

    2015-01-01

    This paper presents a demo of our Security Toolbox to detect novel malware in Android apps. This Toolbox is developed through our recent research project funded by the DARPA Automated Program Analysis for Cybersecurity (APAC) project. The adversarial challenge ("Red") teams in the DARPA APAC program are tasked with designing sophisticated malware to test the bounds of malware detection technology being developed by the research and development ("Blue") teams. Our research group, a Blue team i...

  12. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    1997-01-01

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...... of multivariate time domain system identification of time-variant as well as time-invariant civil engineering structures from ambient testing data. A graphical user interface (GUI) is also developed to make the toolbox more user friendly....

  13. SNAP (Sentinel Application Platform) and the ESA Sentinel 3 Toolbox

    Science.gov (United States)

    Zuhlke, Marco; Fomferra, Norman; Brockmann, Carsten; Peters, Marco; Veci, Luis; Malik, Julien; Regner, Peter

    2015-12-01

    ESA is developing three new free open source Toolboxes for the scientific exploitation of the Sentinel-1, Sentinel-2 and Sentinel-3 missions. The Toolboxes are based on a common software platform, namely the Sentinel Application Platform (SNAP). SNAP is an evolution of the proven ESA BEAM/NEST architecture inheriting all current BEAM and NEST functionality including multi-mission support for SAR and optical missions to support ESA and third party missions for years to come. The Sentinel-3 Toolbox includes generic function for visualisation and analysis of Sentinel-3 OLCI and SLSTR Level 1 and Level 2 data, as well as specific processing tools such as cloud screening, water constituent retrieval and SST retrieval. The Toolbox will put emphasis on access to remote in-situ databases such as Felyx or MERMAID, and exploitation of the data-uncertainty information which is included in the Sentinel-3 data products. New image classification, segmentation and filtering methods, as well as interoperability with the ORFEO Toolbox and the GDAL libraries will be additional new tools. New challenges stemming from Sentinel-3 sensors, such as raster data in different resolutions within a single dataset, will be supported gracefully. The development of SNAP and the Sentinel Toolboxes is funded through the “Scientific Exploitation of Operational Missions (SEOM)” programme, a new programme element of ESA’s fourth period of the Earth Observation Envelope Programme (2013-2017).

  14. An open-source toolbox for automated phenotyping of mice in behavioral tasks

    Directory of Open Access Journals (Sweden)

    Tapan P Patel

    2014-10-01

    Full Text Available Classifying behavior patterns in mouse models of neurological, psychiatric and neurodevelopmental disorders is critical for understanding disease causality and treatment. However, complete characterization of behavior is time-intensive, prone to subjective scoring, and often requires specialized equipment. Although several reports describe automated home-cage monitoring and individual task scoring methods, we report the first open source, comprehensive toolbox for automating the scoring of several common behavior tasks used by the neuroscience community. We show this new toolbox is robust and achieves equal or better consistency when compared to manual scoring methods. We use this toolbox to study the alterations in behavior that occur following blast-induced traumatic brain injury (bTBI, and study if these behavior patterns are altered following genetic deletion of the transcription factor Ets-like kinase 1 (Elk-1. Due to the role of Elk-1 in neuronal survival and proposed role in synaptic plasticity, we hypothesized that Elk-1 deletion would improve some neurobehavioral deficits, while impairing others, following blast exposure. In Elk-1 knockout animals, deficits in open field, spatial object recognition and elevated zero maze performance after blast exposure disappeared, while new significant deficits appeared in spatial and associative memory. These are the first data suggesting a molecular mediator of anxiety deficits following blast-induced traumatic brain injury, and represent the utility of the broad screening tool we developed. More broadly, we envision this open-source toolbox will provide a more consistent and rapid analysis of behavior across many neurological diseases, promoting the rapid discovery of novel pathways mediating disease progression and treatment.

  15. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN

    Science.gov (United States)

    Lowder, Levi G.; Zhang, Dengwei; Baltes, Nicholas J.; Paul, Joseph W.; Tang, Xu; Zheng, Xuelian; Voytas, Daniel F.; Hsieh, Tzung-Fu; Zhang, Yong; Qi, Yiping

    2015-01-01

    The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas of molecular biosciences, including functional genomics, genetics, applied biomedical research, and agricultural biotechnology. In plant systems, however, a number of hurdles currently exist that limit this technology from reaching its full potential. For example, significant plant molecular biology expertise and effort is still required to generate functional expression constructs that allow simultaneous editing, and especially transcriptional regulation, of multiple different genomic loci or multiplexing, which is a significant advantage of CRISPR/Cas9 versus other genome-editing systems. To streamline and facilitate rapid and wide-scale use of CRISPR/Cas9-based technologies for plant research, we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 transfer DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco (Nicotiana benthamiana), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa), demonstrating its utility for basic and applied plant research. PMID:26297141

  16. A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation.

    Science.gov (United States)

    Lowder, Levi G; Zhang, Dengwei; Baltes, Nicholas J; Paul, Joseph W; Tang, Xu; Zheng, Xuelian; Voytas, Daniel F; Hsieh, Tzung-Fu; Zhang, Yong; Qi, Yiping

    2015-10-01

    The relative ease, speed, and biological scope of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated Protein9 (Cas9)-based reagents for genomic manipulations are revolutionizing virtually all areas of molecular biosciences, including functional genomics, genetics, applied biomedical research, and agricultural biotechnology. In plant systems, however, a number of hurdles currently exist that limit this technology from reaching its full potential. For example, significant plant molecular biology expertise and effort is still required to generate functional expression constructs that allow simultaneous editing, and especially transcriptional regulation, of multiple different genomic loci or multiplexing, which is a significant advantage of CRISPR/Cas9 versus other genome-editing systems. To streamline and facilitate rapid and wide-scale use of CRISPR/Cas9-based technologies for plant research, we developed and implemented a comprehensive molecular toolbox for multifaceted CRISPR/Cas9 applications in plants. This toolbox provides researchers with a protocol and reagents to quickly and efficiently assemble functional CRISPR/Cas9 transfer DNA constructs for monocots and dicots using Golden Gate and Gateway cloning methods. It comes with a full suite of capabilities, including multiplexed gene editing and transcriptional activation or repression of plant endogenous genes. We report the functionality and effectiveness of this toolbox in model plants such as tobacco (Nicotiana benthamiana), Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa), demonstrating its utility for basic and applied plant research. © 2015 American Society of Plant Biologists. All Rights Reserved.

  17. Hallmarks of Alzheimer disease are evolving relentlessly in Metropolitan Mexico City infants, children and young adults. APOE4 carriers have higher suicide risk and higher odds of reaching NFT stage V at ≤ 40 years of age.

    Science.gov (United States)

    Calderón-Garcidueñas, Lilian; Gónzalez-Maciel, Angélica; Reynoso-Robles, Rafael; Delgado-Chávez, Ricardo; Mukherjee, Partha S; Kulesza, Randy J; Torres-Jardón, Ricardo; Ávila-Ramírez, José; Villarreal-Ríos, Rodolfo

    2018-03-24

    Exposures to fine particulate matter (PM 2.5 ) and ozone (O 3 ) above USEPA standards are associated with Alzheimer's disease (AD) risk. Metropolitan Mexico City (MMC) residents have life time exposures to PM 2.5 and O 3 above USEPA standards. We investigated AD intra and extracellular protein aggregates and ultrastructural neurovascular pathology in 203 MMC residents age 25.36 ± 9.23 y. Immunohistochemical methods were used to identify AT8 hyperphosphorilated tau (Htau) and 4G8 (amyloid β 17-24). Primary outcomes: staging of Htau and amyloid, per decade and cumulative PM 2.5 (CPM 2.5 ) above standard. Apolipoprotein E allele 4 (APOE4), age and cause of death were secondary outcomes. Subcortical pretangle stage b was identified in an 11month old baby. Cortical tau pre-tangles, neurofibrillary tangles (NFT) Stages I-II, amyloid phases 1-2, Htau in substantia nigrae, auditory, oculomotor, trigeminal and autonomic systems were identified by the 2nd decade. Progression to NFT stages III-V was present in 24.8% of 30-40 y old subjects. APOE4 carriers have 4.92 times higher suicide odds (p = 0.0006), and 23.6 times higher odds of NFT V (p < 0.0001) v APOE4 non-carriers having similar CPM 2.5 exposure and age. Age (p = 0.0062) and CPM 2.5 (p = 0.0178) were significant for developing NFT V. Combustion-derived nanoparticles were associated with early and progressive damage to the neurovascular unit. Alzheimer's disease starting in the brainstem of young children and affecting 99.5% of young urbanites is a serious health crisis. Air pollution control should be prioritised. Childhood relentless Htau makes a fundamental target for neuroprotective interventions and the first two decades are critical. We recommend the concept of preclinical AD be revised and emphasize the need to define paediatric environmental, nutritional, metabolic and genetic risk factor interactions of paramount importance to prevent AD. AD evolving from childhood is threating the

  18. Streptomyces spp. in the biocatalysis toolbox.

    Science.gov (United States)

    Spasic, Jelena; Mandic, Mina; Djokic, Lidija; Nikodinovic-Runic, Jasmina

    2018-04-01

    About 20,100 research publications dated 2000-2017 were recovered searching the PubMed and Web of Science databases for Streptomyces, which are the richest known source of bioactive molecules. However, these bacteria with versatile metabolism are powerful suppliers of biocatalytic tools (enzymes) for advanced biotechnological applications such as green chemical transformations and biopharmaceutical and biofuel production. The recent technological advances, especially in DNA sequencing coupled with computational tools for protein functional and structural prediction, and the improved access to microbial diversity enabled the easier access to enzymes and the ability to engineer them to suit a wider range of biotechnological processes. The major driver behind a dramatic increase in the utilization of biocatalysis is sustainable development and the shift toward bioeconomy that will, in accordance to the UN policy agenda "Bioeconomy to 2030," become a global effort in the near future. Streptomyces spp. already play a significant role among industrial microorganisms. The intention of this minireview is to highlight the presence of Streptomyces in the toolbox of biocatalysis and to give an overview of the most important advances in novel biocatalyst discovery and applications. Judging by the steady increase in a number of recent references (228 for the 2000-2017 period), it is clear that biocatalysts from Streptomyces spp. hold promises in terms of valuable properties and applicative industrial potential.

  19. Design of a Toolbox of RNA Thermometers.

    Science.gov (United States)

    Sen, Shaunak; Apurva, Divyansh; Satija, Rohit; Siegal, Dan; Murray, Richard M

    2017-08-18

    Biomolecular temperature sensors can be used for efficient control of large-volume bioreactors, for spatiotemporal imaging and control of gene expression, and to engineer robustness to temperature in biomolecular circuit design. Although RNA-based sensors, called "thermometers", have been investigated in both natural and synthetic contexts, an important challenge is to design diverse responses to temperature differing in sensitivity and threshold. We address this issue by constructing a library of RNA thermometers based on thermodynamic computations and experimentally measuring their activities in cell-free biomolecular "breadboards". Using free energies of the minimum free energy structures as well as melt profile computations, we estimated that a diverse set of temperature responses were possible. We experimentally found a wide range of responses to temperature in the range 29-37 °C with fold-changes varying over 3-fold around the starting thermometer. The sensitivities of these responses ranged over 10-fold around the starting thermometer. We correlated these measurements with computational expectations, finding that although there was no strong correlation for the individual thermometers, overall trends of diversity, fold-changes, and sensitivities were similar. These results present a toolbox of RNA-based circuit elements with diverse temperature responses.

  20. Robotic inspection technology-process an toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, Markus [ROSEN Group (United States). R and D Dept.

    2005-07-01

    Pipeline deterioration grows progressively with ultimate aging of pipeline systems (on-plot and cross country). This includes both, very localized corrosion as well as increasing failure probability due to fatigue cracking. Limiting regular inspecting activities to the 'scrapable' part of the pipelines only, will ultimately result into a pipeline system with questionable integrity. The confidence level in the integrity of these systems will drop below acceptance levels. Inspection of presently un-inspectable sections of the pipeline system becomes a must. This paper provides information on ROSEN's progress on the 'robotic inspection technology' project. The robotic inspection concept developed by ROSEN is based on a modular toolbox principle. This is mandatory. A universal 'all purpose' robot would not be reliable and efficient in resolving the postulated inspection task. A preparatory Quality Function Deployment (QFD) analysis is performed prior to the decision about the adequate robotic solution. This enhances the serviceability and efficiency of the provided technology. The word 'robotic' can be understood in its full meaning of Recognition - Strategy - Motion - Control. Cooperation of different individual systems with an established communication, e.g. utilizing Bluetooth technology, support the robustness of the ROSEN robotic inspection approach. Beside the navigation strategy, the inspection strategy is also part of the QFD process. Multiple inspection technologies combined on a single carrier or distributed across interacting container must be selected with a clear vision of the particular goal. (author)

  1. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Science.gov (United States)

    Lawhern, Vernon; Hairston, W David; Robbins, Kay

    2013-01-01

    Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG) data as an additional illustration.

  2. DETECT: a MATLAB toolbox for event detection and identification in time series, with applications to artifact detection in EEG signals.

    Directory of Open Access Journals (Sweden)

    Vernon Lawhern

    Full Text Available Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG data as an additional illustration.

  3. A toolbox to visualise benefits resulting from flood hazard mitigation

    Science.gov (United States)

    Fuchs, Sven; Thaler, Thomas; Heiser, Micha

    2017-04-01

    , Keiler M, Sokratov SA, Shnyparkov A (2013) Spatiotemporal dynamics: the need for an innovative approach in mountain hazard risk management. Natural Hazards 68 (3):1217-1241 Papathoma-Köhle M, Zischg A, Fuchs S, Glade T, Keiler M (2015) Loss estimation for landslides in mountain areas - An integrated toolbox for vulnerability assessment and damage documentation. Environmental Modelling and Software 63:156-169 Totschnig R, Fuchs S (2013) Mountain torrents: quantifying vulnerability and assessing uncertainties. Engineering Geology 155:31-44

  4. Introduction to TAFI - A Matlab® toolbox for analysis of flexural isostasy

    Science.gov (United States)

    Jha, S.; Harry, D. L.; Schutt, D.

    2016-12-01

    The isostatic response of vertical tectonic loads emplaced on thin elastic plates overlying inviscid substrate and the corresponding gravity anomalies are commonly modeled using well established theories and methodologies of flexural analysis. However, such analysis requires some mathematical and coding expertise on part of users. With that in mind, we designed a new interactive Matlab® toolbox called Toolbox for Analysis of Flexural Isostasy (TAFI). TAFI allows users to create forward models (2-D and 3-D) of flexural deformation of the lithosphere and resulting gravity anomaly. TAFI computes Green's Functions for flexure of the elastic plate subjected to point or line loads, and analytical solution for harmonic loads. Flexure due to non-impulsive, distributed 2-D or 3-D loads are computed by convolving the appropriate Green's function with a user-supplied spatially discretized load function. The gravity anomaly associated with each density interface is calculated by using the Fourier Transform of flexural deflection of these interfaces and estimating the gravity in the wavenumber domain. All models created in TAFI are based on Matlab's intrinsic functions and do not require any specialized toolbox, function or library except those distributed with TAFI. Modeling functions within TAFI can be called from Matlab workspace, from within user written programs or from the TAFI's graphical user interface (GUI). The GUI enables the user to model the flexural deflection of lithosphere interactively, enabling real time comparison of model fit with observed data constraining the flexural deformation and gravity, facilitating rapid search for best fitting flexural model. TAFI is a very useful teaching and research tool and have been tested rigorously in graduate level teaching and basic research environment.

  5. Community 21: Digital toolbox for sustainable communities

    Directory of Open Access Journals (Sweden)

    Nick Gant

    2010-11-01

    Full Text Available This article will describe the 'Toolbox for the 21st Century Village' action research project and outline the critical research contexts that underpin its development as an online informatics and social engagement tool aimed at facilitating understanding, sharing and planning of integrated sustainability by individual communities. This will include exposing the context of ‘mis-communication’ of sustainability issues in society by visual culture, the media and politics. The article argues that this has served to alienate, demoralise and disenfranchise many individuals and communities. Being rural does not necessarily mean being ‘green’ and the article will describe the ‘green dichotomy’ and how rural behaviours are disproportionately dependent on natural resources and as a consequence are ‘less sustainable’, despite relative autonomy and community potential to make significant gains. The article will also unpack and explore how the loaded term sustainability only serves to divide and detract as a polemic and absolute term; whereas self-sufficiency is a demonstrable concern of vulnerable rural communities; a by-product of which can be genuine and valued, measurable and meaningful sustainable development. The above provides a contextual backdrop and rationale for the formation of a project that enables communities to frame their own concerns and envision themselves and their problems and responses as part of a larger system. The project is developed around an experimental online content management system (CMS platform that will facilitate sustainable development through envisioning, action planning and networking – connecting the ‘knots in the net’ of an active patchwork of ‘multi-local communities’. The platform design will provide methodology, process and capacity to enable reconciliation between the manifold concerns of social, economic and environmental sustainability whilst providing community facilitators with new

  6. System engineering toolbox for design-oriented engineers

    Science.gov (United States)

    Goldberg, B. E.; Everhart, K.; Stevens, R.; Babbitt, N., III; Clemens, P.; Stout, L.

    1994-01-01

    This system engineering toolbox is designed to provide tools and methodologies to the design-oriented systems engineer. A tool is defined as a set of procedures to accomplish a specific function. A methodology is defined as a collection of tools, rules, and postulates to accomplish a purpose. For each concept addressed in the toolbox, the following information is provided: (1) description, (2) application, (3) procedures, (4) examples, if practical, (5) advantages, (6) limitations, and (7) bibliography and/or references. The scope of the document includes concept development tools, system safety and reliability tools, design-related analytical tools, graphical data interpretation tools, a brief description of common statistical tools and methodologies, so-called total quality management tools, and trend analysis tools. Both relationship to project phase and primary functional usage of the tools are also delineated. The toolbox also includes a case study for illustrative purposes. Fifty-five tools are delineated in the text.

  7. A MATLAB toolbox for Granger causal connectivity analysis.

    Science.gov (United States)

    Seth, Anil K

    2010-02-15

    Assessing directed functional connectivity from time series data is a key challenge in neuroscience. One approach to this problem leverages a combination of Granger causality analysis and network theory. This article describes a freely available MATLAB toolbox--'Granger causal connectivity analysis' (GCCA)--which provides a core set of methods for performing this analysis on a variety of neuroscience data types including neuroelectric, neuromagnetic, functional MRI, and other neural signals. The toolbox includes core functions for Granger causality analysis of multivariate steady-state and event-related data, functions to preprocess data, assess statistical significance and validate results, and to compute and display network-level indices of causal connectivity including 'causal density' and 'causal flow'. The toolbox is deliberately small, enabling its easy assimilation into the repertoire of researchers. It is however readily extensible given proficiency with the MATLAB language. Copyright 2009 Elsevier B.V. All rights reserved.

  8. VQone MATLAB toolbox: A graphical experiment builder for image and video quality evaluations: VQone MATLAB toolbox.

    Science.gov (United States)

    Nuutinen, Mikko; Virtanen, Toni; Rummukainen, Olli; Häkkinen, Jukka

    2016-03-01

    This article presents VQone, a graphical experiment builder, written as a MATLAB toolbox, developed for image and video quality ratings. VQone contains the main elements needed for the subjective image and video quality rating process. This includes building and conducting experiments and data analysis. All functions can be controlled through graphical user interfaces. The experiment builder includes many standardized image and video quality rating methods. Moreover, it enables the creation of new methods or modified versions from standard methods. VQone is distributed free of charge under the terms of the GNU general public license and allows code modifications to be made so that the program's functions can be adjusted according to a user's requirements. VQone is available for download from the project page (http://www.helsinki.fi/psychology/groups/visualcognition/).

  9. SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

    Science.gov (United States)

    Konganti, Kranti; Wang, Gang; Yang, Ence; Cai, James J

    2013-01-01

    We present SBEToolbox (Systems Biology and Evolution Toolbox), an open-source Matlab toolbox for biological network analysis. It takes a network file as input, calculates a variety of centralities and topological metrics, clusters nodes into modules, and displays the network using different graph layout algorithms. Straightforward implementation and the inclusion of high-level functions allow the functionality to be easily extended or tailored through developing custom plugins. SBEGUI, a menu-driven graphical user interface (GUI) of SBEToolbox, enables easy access to various network and graph algorithms for programmers and non-programmers alike. All source code and sample data are freely available at https://github.com/biocoder/SBEToolbox/releases.

  10. Evidence for a common toolbox based on necrotrophy in a fungal lineage spanning necrotrophs, biotrophs, endophytes, host generalists and specialists.

    Directory of Open Access Journals (Sweden)

    Marion Andrew

    Full Text Available The Sclerotiniaceae (Ascomycotina, Leotiomycetes is a relatively recently evolved lineage of necrotrophic host generalists, and necrotrophic or biotrophic host specialists, some latent or symptomless. We hypothesized that they inherited a basic toolbox of genes for plant symbiosis from their common ancestor. Maintenance and evolutionary diversification of symbiosis could require selection on toolbox genes or on timing and magnitude of gene expression. The genes studied were chosen because their products have been previously investigated as pathogenicity factors in the Sclerotiniaceae. They encode proteins associated with cell wall degradation: acid protease 1 (acp1, aspartyl protease (asps, and polygalacturonases (pg1, pg3, pg5, pg6, and the oxalic acid (OA pathway: a zinc finger transcription factor (pac1, and oxaloacetate acetylhydrolase (oah, catalyst in OA production, essential for full symptom production in Sclerotinia sclerotiorum. Site-specific likelihood analyses provided evidence for purifying selection in all 8 pathogenicity-related genes. Consistent with an evolutionary arms race model, positive selection was detected in 5 of 8 genes. Only generalists produced large, proliferating disease lesions on excised Arabidopsis thaliana leaves and oxalic acid by 72 hours in vitro. In planta expression of oah was 10-300 times greater among the necrotrophic host generalists than necrotrophic and biotrophic host specialists; pac1 was not differentially expressed. Ability to amplify 6/8 pathogenicity related genes and produce oxalic acid in all genera are consistent with the common toolbox hypothesis for this gene sample. That our data did not distinguish biotrophs from necrotrophs is consistent with 1 a common toolbox based on necrotrophy and 2 the most conservative interpretation of the 3-locus housekeeping gene phylogeny--a baseline of necrotrophy from which forms of biotrophy emerged at least twice. Early oah overexpression likely expands the

  11. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    1997-01-01

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  12. Structural Time Domain Identification (STDI) Toolbox for Use with MATLAB

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Andersen, P.; Brincker, Rune

    The Structural Time Domain Identification (STDI) toolbox for use with MATLABTM is developed at Aalborg University, Denmark, based on the system identification research performed during recent years. By now, a reliable set of functions offers a wide spectrum of services for all the important steps...

  13. Adding quantitative muscle MRI to the FSHD clinical trial toolbox

    NARCIS (Netherlands)

    Mul, K.; Vincenten, S.C.C.; Voermans, N.C.; Lemmers, R.; Vliet, P.J.C. Van; Maarel, S.M. van der; Padberg, G.W.A.M.; Horlings, G.C.; Engelen, B.G.M. van

    2017-01-01

    OBJECTIVE: To add quantitative muscle MRI to the clinical trial toolbox for facioscapulohumeral muscular dystrophy (FSHD) by correlating it to clinical outcome measures in a large cohort of genetically and clinically well-characterized patients with FSHD comprising the entire clinical spectrum.

  14. Communication skills competencies: definitions and a teaching toolbox.

    Science.gov (United States)

    Rider, Elizabeth A; Keefer, Constance H

    2006-07-01

    Doctors' interpersonal and communication skills correlate with improved health care outcomes. International medical organisations require competency in communication skills. The Accreditation Council for Graduate Medical Education (ACGME) developed a toolbox for assessing this competency and 5 others, yet none initially for teaching these skills. The original focus in the development of the ACGME competencies was evaluation. This paper represents a significant step toward defining methods for teaching communication skills competencies. A total of 16 medical education leaders from medical schools worldwide, participating in the 2003 Harvard Macy Institute Program for Physician Educators, worked together to: (1) further define the ACGME competency in interpersonal and communication skills; (2) delineate teaching strategies for each level of medical education; and (3) create a teaching toolbox to integrate communication skills competencies into medical curricula. Four subgroups defined subcompetencies, identified teaching strategies for undergraduate, graduate and postgraduate medical training and brought their work to the larger group. The expanded communication competencies and teaching strategies were determined by a consensus of the larger group, presented to 80 Harvard Macy Scholars and Faculty for further discussion, then finalised by consensus. The teaching toolbox expands the ACGME core communication competencies, adds 20 subcompetencies and connects these competencies to teaching strategies at each level of medical training. It represents the collaboration and consensus of a diverse international group of medical education leaders in a variety of medical specialities and institutions, all involved in teaching communication skills. The toolbox is applicable globally across different settings and specialities, and is sensitive to different definitions of health care.

  15. Wyrm: A Brain-Computer Interface Toolbox in Python.

    Science.gov (United States)

    Venthur, Bastian; Dähne, Sven; Höhne, Johannes; Heller, Hendrik; Blankertz, Benjamin

    2015-10-01

    In the last years Python has gained more and more traction in the scientific community. Projects like NumPy, SciPy, and Matplotlib have created a strong foundation for scientific computing in Python and machine learning packages like scikit-learn or packages for data analysis like Pandas are building on top of it. In this paper we present Wyrm ( https://github.com/bbci/wyrm ), an open source BCI toolbox in Python. Wyrm is applicable to a broad range of neuroscientific problems. It can be used as a toolbox for analysis and visualization of neurophysiological data and in real-time settings, like an online BCI application. In order to prevent software defects, Wyrm makes extensive use of unit testing. We will explain the key aspects of Wyrm's software architecture and design decisions for its data structure, and demonstrate and validate the use of our toolbox by presenting our approach to the classification tasks of two different data sets from the BCI Competition III. Furthermore, we will give a brief analysis of the data sets using our toolbox, and demonstrate how we implemented an online experiment using Wyrm. With Wyrm we add the final piece to our ongoing effort to provide a complete, free and open source BCI system in Python.

  16. Wheat Rust Toolbox Related to New Initiatives on Yellow Rust

    DEFF Research Database (Denmark)

    Hansen, Jens Grønbech; Lassen, Poul

    A wheat rust toolbox was developed in the frame of the Borlaug Global Rust Initiative (BGRI) to support the early warning and monitoring of stem rust on a global scale. The toolbox consists of a number of databases and web applications for data management, quality control, dissemination and display...... of interactive maps; including information on surveillance (disease data over years and across countries for all three rusts) and graphs and maps indicating the distribution of UG99 and related pathotypes. Graphs and maps are integrated with, and disseminated, via the Rust SPORE web portal at FAO (http://www.fao.org/agriculture/crops/rust/stem/rust......-report/en/). The Wheat rust toolbox is one of several International research platforms hosted by Aarhus University, and it uses the same ICT framework and databases as EuroWheat (www.eurowheat.org) and EuroBlight (www.EuroBlight.net). The Wheat Rust Toolbox will also serve the Global Rust Reference Centre (GRRC) as well...

  17. ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data.

    Science.gov (United States)

    Minas, Giorgos; Momiji, Hiroshi; Jenkins, Dafyd J; Costa, Maria J; Rand, David A; Finkenstädt, Bärbel

    2017-06-26

    Given the development of high-throughput experimental techniques, an increasing number of whole genome transcription profiling time series data sets, with good temporal resolution, are becoming available to researchers. The ReTrOS toolbox (Reconstructing Transcription Open Software) provides MATLAB-based implementations of two related methods, namely ReTrOS-Smooth and ReTrOS-Switch, for reconstructing the temporal transcriptional activity profile of a gene from given mRNA expression time series or protein reporter time series. The methods are based on fitting a differential equation model incorporating the processes of transcription, translation and degradation. The toolbox provides a framework for model fitting along with statistical analyses of the model with a graphical interface and model visualisation. We highlight several applications of the toolbox, including the reconstruction of the temporal cascade of transcriptional activity inferred from mRNA expression data and protein reporter data in the core circadian clock in Arabidopsis thaliana, and how such reconstructed transcription profiles can be used to study the effects of different cell lines and conditions. The ReTrOS toolbox allows users to analyse gene and/or protein expression time series where, with appropriate formulation of prior information about a minimum of kinetic parameters, in particular rates of degradation, users are able to infer timings of changes in transcriptional activity. Data from any organism and obtained from a range of technologies can be used as input due to the flexible and generic nature of the model and implementation. The output from this software provides a useful analysis of time series data and can be incorporated into further modelling approaches or in hypothesis generation.

  18. Sentinel-2 data exploitation with ESA's Sentinel-2 Toolbox

    Science.gov (United States)

    Gascon, Ferran; Ramoino, Fabrizzio; deanos, Yves-louis

    2017-04-01

    The Sentinel-2 Toolbox is a project kicked off by ESA in early 2014, under the umbrella of the ESA SEOM programme with the aim to provide a tool for visualizing, analysing, and processing the Sentinel-2 datasets. The toolbox is an extension of the SeNtinel Application Platform (SNAP), a project resulting from the effort of the developers of the Sentinel-1, Sentinel-2 and Sentinel-3 toolbox to provide a single common application framework suited for the mixed exploitation of SAR, high resolution optical and medium resolution optical datasets. All three development teams collaborate to drive the evolution of the common SNAP framework in a developer forum. In this triplet, the Sentinel-2 toolbox is dedicated to enhance SNAP support for high resolution optical imagery. It is a multi-mission toolbox, already providing support for Sentinel-2, RapidEye, Deimos, SPOT 1 to SPOT 5 datasets. In terms of processing algorithms, SNAP provides tools specific to the Sentinel-2 mission : • An atmospheric correction module, Sen2Cor, is integrated into the toolbox, and provides scene classification, atmospheric correction, cirrus detection and correction. The output L2A products can be opened seamlessly in the toolbox. • A multitemporal synthesis processor (L3) • A biophysical products processor (L2B) • A water processor • A deforestation detector • OTB tools integration • SNAP Engine for Cloud Exploitation along with a set of more generic tools for high resolution optical data exploitation. Together with the generic functionalities of SNAP this provides an ideal environment for designing multi-missions processing chains and producing value-added products from raw datasets. The use of SNAP is manifold and the desktop tools provides a rich application for interactive visualization, analysis and processing of data. But all tools available from SNAP can be accessed via command-line through the Graph Processing Framework (GPT), the kernel of the SNAP processing engine. This

  19. CBP Toolbox Version 3.0 “Beta Testing” Performance Evaluation

    Energy Technology Data Exchange (ETDEWEB)

    Smith, III, F. G. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-07-29

    One function of the Cementitious Barriers Partnership (CBP) is to assess available models of cement degradation and to assemble suitable models into a “Toolbox” that would be made available to members of the partnership, as well as the DOE Complex. To this end, SRNL and Vanderbilt University collaborated to develop an interface using the GoldSim software to the STADIUM@ code developed by SIMCO Technologies, Inc. and LeachXS/ORCHESTRA developed by Energy research Centre of the Netherlands (ECN). Release of Version 3.0 of the CBP Toolbox is planned in the near future. As a part of this release, an increased level of quality assurance for the partner codes and the GoldSim interface has been developed. This report documents results from evaluation testing of the ability of CBP Toolbox 3.0 to perform simulations of concrete degradation applicable to performance assessment of waste disposal facilities. Simulations of the behavior of Savannah River Saltstone Vault 2 and Vault 1/4 concrete subject to sulfate attack and carbonation over a 500- to 1000-year time period were run using a new and upgraded version of the STADIUM@ code and the version of LeachXS/ORCHESTRA released in Version 2.0 of the CBP Toolbox. Running both codes allowed comparison of results from two models which take very different approaches to simulating cement degradation. In addition, simulations of chloride attack on the two concretes were made using the STADIUM@ code. The evaluation sought to demonstrate that: 1) the codes are capable of running extended realistic simulations in a reasonable amount of time; 2) the codes produce “reasonable” results; the code developers have provided validation test results as part of their code QA documentation; and 3) the two codes produce results that are consistent with one another. Results of the evaluation testing showed that the three criteria listed above were met by the CBP partner codes. Therefore, it is concluded that

  20. An open-source toolbox for multiphase flow in porous media

    Science.gov (United States)

    Horgue, P.; Soulaine, C.; Franc, J.; Guibert, R.; Debenest, G.

    2015-02-01

    Multiphase flow in porous media provides a wide range of applications: from the environmental understanding (aquifer, site-pollution) to industrial process improvements (oil production, waste management). Modeling of such flows involves specific volume-averaged equations and therefore specific computational fluid dynamics (CFD) tools. In this work, we develop a toolbox for modeling multiphase flow in porous media with OpenFOAM®, an open-source platform for CFD. The underlying idea of this approach is to provide an easily adaptable tool that can be used in further studies to test new mathematical models or numerical methods. The package provides the most common effective properties models of the literature (relative permeability, capillary pressure) and specific boundary conditions related to porous media flows. To validate this package, solvers based on the IMplicit Pressure Explicit Saturation (IMPES) method are developed in the toolbox. The numerical validation is performed by comparison with analytical solutions on academic cases. Then, a satisfactory parallel efficiency of the solver is shown on a more complex configuration.

  1. A Tol2 Gateway-Compatible Toolbox for the Study of the Nervous System and Neurodegenerative Disease.

    Science.gov (United States)

    Don, Emily K; Formella, Isabel; Badrock, Andrew P; Hall, Thomas E; Morsch, Marco; Hortle, Elinor; Hogan, Alison; Chow, Sharron; Gwee, Serene S L; Stoddart, Jack J; Nicholson, Garth; Chung, Roger; Cole, Nicholas J

    2017-02-01

    Currently there is a lack in fundamental understanding of disease progression of most neurodegenerative diseases, and, therefore, treatments and preventative measures are limited. Consequently, there is a great need for adaptable, yet robust model systems to both investigate elementary disease mechanisms and discover effective therapeutics. We have generated a Tol2 Gateway-compatible toolbox to study neurodegenerative disorders in zebrafish, which includes promoters for astrocytes, microglia and motor neurons, multiple fluorophores, and compatibility for the introduction of genes of interest or disease-linked genes. This toolbox will advance the rapid and flexible generation of zebrafish models to discover the biology of the nervous system and the disease processes that lead to neurodegeneration.

  2. Quantification of Storm Surge Using A Python-based ArcGIS Toolbox

    Science.gov (United States)

    Gao, S.; Siverd, C. G.; Bilskie, M. V.; Hagen, S. C.; Alizad, K.

    2016-12-01

    Geographic Information System (GIS) technology allows the organization, manipulation, analysis, and visualization of spatial data (Fischer, 2010). Although GIS provides some operations for spatial analysis, the methods are often only partially implemented and can be difficult to find and use effectively (Rigol-Sanchez et al., 2015). For coastal researchers, development of automated GIS tools is essential to efficiently analyze coastal flood risk from hurricanes. An adaptive GIS toolbox, Quantitative Surge Analysis Tool (QSAT), was developed and implements ArcGIS software and Python scripts to quantify attributes of hurricane storm surge (e.g., average water surface elevation). The python script provides a way to allow researchers to reduce the amount of time spent developing common solutions (Etherington, 2010) and repeating manual operations. The QSAT contains tools that run in the ArcGIS program. These tools compute average water surface elevation, average inundation depth, inundated area, total surge volume, percent of land inundated, and retention time for a given polygonal area. A new shapefile is created with a detail attribute table containing the various surge quantities. The toolbox is designed to directly read data files produced by an ADCIRC storm surge simulation as well as a polygon shapefile defining the areas of interest. The functionality of the QSAT toolbox was tested using Hydrologic Unit Code 12 (HUC 12) polygons of coastal Louisiana and ADCIRC model results from a simulation of Hurricane Gustav. The QSAT aids a streamlined transition of surge quantities across a local medium (i.e. HUC 12s) to better inform stakeholders and lead to improved regional and local decisions.

  3. Uso do rejeito da dessalinização de água salobra no cultivo da alface (Lactuca sativa L. em sistema hidropônico NFT Use of the desalted wastewater for lettuce (Lactuca sativa L. production in NFT hydroponic system

    Directory of Open Access Journals (Sweden)

    Rafaelly Suzanye da Silva Santos

    2010-08-01

    Full Text Available A dessalinização por osmose reversa tem sido bastante utilizada para o tratamento de água salobra, possibilitando a sua utilização para o consumo humano, especialmente em regiões semiáridas. Esse processo tem um fator limitante que é a produção de um rejeito de água com alta salinidade. Com o objetivo de avaliar os efeitos da utilização de água de rejeito da dessalinização no cultivo de alface cultivar Vera (Lactuca sativa L. em sistema hidropônico NFT foi conduzido um experimento em casa de vegetação no departamento de ciências ambientais da UFERSA, em delineamento em blocos casualizados, com seis tratamentos e quatro repetições. Os níveis de salinidade da água entre os tratamentos foram obtidos com, ou sem a necessidade de diluição da água de rejeito da dessalinização acrescido da solução nutritiva com salinidade de 1 dS m-1 (100% de água potável de abastecimento - 1,4 dS m-1; 85% abastecimento e 15% água de rejeito - 1,9 dS m-1; 75 % água de rejeito + 25 % água de abastecimento - 2,7 dS m-1; 50% água de rejeito e 50% água de abastecimento - 3,8 dS m-1; 25 % água de rejeito e 75 % água de abastecimento - 4,9 dS m-1 e água de rejeito coletada no dessalinizador - 5,5 dS m-1. Os parâmetros analisados foram área foliar, diâmetro do caule, número de folhas, peso de matéria fresca e o peso de matéria seca. Todas as variáveis estudadas foram influenciadas negativamente de forma linear pelo efeito da concentração de sais na água de irrigação, sendo que a área foliar e a matéria fresca da parte aérea são as que melhor representam a sensibilidade ao estresse salino na cultivar estudada, tendo a produção em termos de matéria fresca uma redução de 94,83%, ao se elevar a CEa de 1,4 a 5,5 dS m-1.The desalination process by reverse osmosis was used for the treatment of brackish water, making possible the usage human consume in semiarid zones. This process has a limiting factor: it produces

  4. The Bacillus BioBrick Box 2.0: expanding the genetic toolbox for the standardized work with Bacillus subtilis.

    Science.gov (United States)

    Popp, Philipp F; Dotzler, Mona; Radeck, Jara; Bartels, Julia; Mascher, Thorsten

    2017-11-08

    Standardized and well-characterized genetic building blocks allow the convenient assembly of novel genetic modules and devices, ensuring reusability of parts and reproducibility of experiments. In the first Bacillus subtilis-specific toolbox using the BioBrick standard, we presented integrative vectors, promoters, reporter genes and epitope tags for this Gram-positive model bacterium. With the Bacillus BioBrick Box 2.0, we significantly expand the range of our toolbox by providing new integrative vectors, introducing novel tools for fine-tuning protein expression, and carefully evaluating codon-adapted fluorescence proteins in B. subtilis, which cover the whole spectrum of visible light. Moreover, we developed new reporter systems to allow evaluating the strength of promoters and ribosome binding sites. This well-evaluated extension of our BioBrick-based toolbox increases the accessibility of B. subtilis and will therefore promote the use of this model bacterium and biotechnological workhorse as a host for fundamental and applied Synthetic Biology projects.

  5. The biopsychology-nonlinear analysis toolbox: a free, open-source Matlab-toolbox for the non-linear analysis of time series data.

    Science.gov (United States)

    Beste, Christian; Otto, Tobias; Hoffmann, Sven

    2010-10-01

    We provide a free, open-source toolbox for non-linear time series analyses. The major goal of this project was to provide a toolbox for nonlinear time series analyses that is easily accessible to a wide range of neuroscientists. The toolbox offers modular, powerful and flexible algorithms embedded in an easy to handle graphical user interface (GUI). The toolbox can be run within the Matlab environment, but also as stand-alone solution without reference to a programming environment that is also usable for different PC operating systems (Windows and Linux). The Biopsychology--Nonlinear Analysis Toolbox and documentation are available freely and open-source from http://biopsynltoolbox.sourceforge.net.

  6. Tadarida: A Toolbox for Animal Detection on Acoustic Recordings

    Directory of Open Access Journals (Sweden)

    Yves Bas

    2017-02-01

    Full Text Available Passive Acoustic Monitoring (PAM recently extended to a very wide range of animals, but no available open software has been sufficiently generic to automatically treat several taxonomic groups. Here we present Tadarida, a software toolbox allowing for the detection and labelling of recorded sound events, and to classify any new acoustic data into known classes. It is made up of three modules handling Detection, Labelling and Classification and running on either Linux or Windows. This development resulted in the first open software (1 allowing generic sound event detection (multi-taxa, (2 providing graphical sound labelling at a single-instance level and (3 covering the whole process from sound detection to classification. This generic and modular design opens numerous reuse opportunities among (bioacoustics researchers, especially for those managing and/or developing PAM schemes. The whole toolbox is openly developed in C++ (Detection and Labelling and R (Classification and stored at https://github.com/YvesBas.

  7. System design through Matlab, control toolbox and Simulink

    CERN Document Server

    Singh, Krishna K

    2001-01-01

    MATLAB , a software package developed by Math Works, Inc. is powerful, versatile and interactive software for scientific and technical computations including simulations. Specialised toolboxes provided with several built-in functions are a special feature of MATLAB . This book titled System Design through MATLAB , Control Toolbox and SIMULINK aims at getting the reader started with computations and simulations in system engineering quickly and easily and then proceeds to build concepts for advanced computations and simulations that includes the control and compensation of systems. Simulation through SIMULINK has also been described to allow the reader to get the feel of the real world situation. This book is appropriate for undergraduate students undergoing final semester of their project work, postgraduate students who have MATLAB integrated in their course or wish to take up simulation problem in the area of system engineering for their dissertation work and research scholars for whom MATLABÊ

  8. ecg-kit: a Matlab Toolbox for Cardiovascular Signal Processing

    Directory of Open Access Journals (Sweden)

    Andrés Julio Demski

    2016-04-01

    Full Text Available The electrocardiogram kit ('ecg-kit' for Matlab is an application-programming interface (API developed to provide users a common interface to access and process cardiovascular signals. In the current version, the toolbox supports several ECG recording formats, most of them used by the most popular databases, which allows access to more than 7 TB of information, stored in public databases such as those included in Physionet or the THEW project. The toolbox includes several algorithms frequently used in cardiovascular signal processing, such as heartbeat detectors and classifiers, pulse detectors for pulsatile signals and an ECG delineator. In addition, it provides a tool for manually reviewing and correcting the results produced by the automatic algorithms. The results obtained can be stored in a Matlab (.MAT file for backup or subsequent processing, or used to create a PDF report.

  9. PSYCHOACOUSTICS: a comprehensive MATLAB toolbox for auditory testing.

    Science.gov (United States)

    Soranzo, Alessandro; Grassi, Massimo

    2014-01-01

    PSYCHOACOUSTICS is a new MATLAB toolbox which implements three classic adaptive procedures for auditory threshold estimation. The first includes those of the Staircase family (method of limits, simple up-down and transformed up-down); the second is the Parameter Estimation by Sequential Testing (PEST); and the third is the Maximum Likelihood Procedure (MLP). The toolbox comes with more than twenty built-in experiments each provided with the recommended (default) parameters. However, if desired, these parameters can be modified through an intuitive and user friendly graphical interface and stored for future use (no programming skills are required). Finally, PSYCHOACOUSTICS is very flexible as it comes with several signal generators and can be easily extended for any experiment.

  10. An Open Source Pattern Recognition Toolbox for MATLAB

    OpenAIRE

    Morton Jr., Kenneth D.; Torrione, Peter; Collins, Leslie; Keene, Sam

    2014-01-01

    Pattern recognition and machine learning are becoming integral parts of algorithms in a wide range of applications. Different algorithms and approaches for machine learning include different tradeoffs between performance and computation, so during algorithm development it is often necessary to explore a variety of different approaches to a given task. A toolbox with a unified framework across multiple pattern recognition techniques enables algorithm developers the ability to rapidly evaluate ...

  11. Tensor Toolbox for MATLAB v. 3.0

    Energy Technology Data Exchange (ETDEWEB)

    2017-03-07

    Tensors (also known as multidimensional arrays or N-way arrays) are used in a variety of applications ranging from chemometrics to network analysis. The Tensor Toolbox provides classes for manipulating dense, sparse, and structured tensors using MATLAB's object-oriented features. It also provides algorithms for tensor decomposition and factorization, algorithms for computing tensor eigenvalues, and methods for visualization of results.

  12. Snag, a Toolbox for Gravitational Wave Data Analysis

    Science.gov (United States)

    Frasca, Sergio; Palomba, Cristiano; Ruffato, Roberto; Majorana, Ettore

    Snag is a MatLab toolbox, developed in the Rome Virgo group, to analyse gravitational data and develop detection methods. It is written using the OOP features of last versions of MatLab programming language and contains a large number of functions, most of which can be accessed by a GUI. Data_Browser is a GUI Snag application to access gravitational antenna sampled data in files.

  13. Cumulative Risk Assessment Toolbox: Methods and Approaches for the Practitioner

    Directory of Open Access Journals (Sweden)

    Margaret M. MacDonell

    2013-01-01

    Full Text Available The historical approach to assessing health risks of environmental chemicals has been to evaluate them one at a time. In fact, we are exposed every day to a wide variety of chemicals and are increasingly aware of potential health implications. Although considerable progress has been made in the science underlying risk assessments for real-world exposures, implementation has lagged because many practitioners are unaware of methods and tools available to support these analyses. To address this issue, the US Environmental Protection Agency developed a toolbox of cumulative risk resources for contaminated sites, as part of a resource document that was published in 2007. This paper highlights information for nearly 80 resources from the toolbox and provides selected updates, with practical notes for cumulative risk applications. Resources are organized according to the main elements of the assessment process: (1 planning, scoping, and problem formulation; (2 environmental fate and transport; (3 exposure analysis extending to human factors; (4 toxicity analysis; and (5 risk and uncertainty characterization, including presentation of results. In addition to providing online access, plans for the toolbox include addressing nonchemical stressors and applications beyond contaminated sites and further strengthening resource accessibility to support evolving analyses for cumulative risk and sustainable communities.

  14. A novel toolbox for E. coli lysis monitoring.

    Science.gov (United States)

    Rajamanickam, Vignesh; Wurm, David; Slouka, Christoph; Herwig, Christoph; Spadiut, Oliver

    2017-01-01

    The bacterium Escherichia coli is a well-studied recombinant host organism with a plethora of applications in biotechnology. Highly valuable biopharmaceuticals, such as antibody fragments and growth factors, are currently being produced in E. coli. However, the high metabolic burden during recombinant protein production can lead to cell death, consequent lysis, and undesired product loss. Thus, fast and precise analyzers to monitor E. coli bioprocesses and to retrieve key process information, such as the optimal time point of harvest, are needed. However, such reliable monitoring tools are still scarce to date. In this study, we cultivated an E. coli strain producing a recombinant single-chain antibody fragment in the cytoplasm. In bioreactor cultivations, we purposely triggered cell lysis by pH ramps. We developed a novel toolbox using UV chromatograms as fingerprints and chemometric techniques to monitor these lysis events and used flow cytometry (FCM) as reference method to quantify viability offline. Summarizing, we were able to show that a novel toolbox comprising HPLC chromatogram fingerprinting and data science tools allowed the identification of E. coli lysis in a fast and reliable manner. We are convinced that this toolbox will not only facilitate E. coli bioprocess monitoring but will also allow enhanced process control in the future.

  15. fMRI Artefact Rejection and Sleep Scoring Toolbox

    Directory of Open Access Journals (Sweden)

    Yves Leclercq

    2011-01-01

    Full Text Available We started writing the “fMRI artefact rejection and sleep scoring toolbox”, or “FAST”, to process our sleep EEG-fMRI data, that is, the simultaneous recording of electroencephalographic and functional magnetic resonance imaging data acquired while a subject is asleep. FAST tackles three crucial issues typical of this kind of data: (1 data manipulation (viewing, comparing, chunking, etc. of long continuous M/EEG recordings, (2 rejection of the fMRI-induced artefact in the EEG signal, and (3 manual sleep-scoring of the M/EEG recording. Currently, the toolbox can efficiently deal with these issues via a GUI, SPM8 batching system or hand-written script. The tools developed are, of course, also useful for other EEG applications, for example, involving simultaneous EEG-fMRI acquisition, continuous EEG eye-balling, and manipulation. Even though the toolbox was originally devised for EEG data, it will also gracefully handle MEG data without any problem. “FAST” is developed in Matlab as an add-on toolbox for SPM8 and, therefore, internally uses its SPM8-meeg data format. “FAST” is available for free, under the GNU-GPL.

  16. I. NIH TOOLBOX COGNITION BATTERY (CB): INTRODUCTION AND PEDIATRIC DATA*

    Science.gov (United States)

    Weintraub, Sandra; Bauer, Patricia J.; Zelazo, Philip David; Wallner-Allen, Kathleen; Dikmen, Sureyya S.; Heaton, Robert K.; Tulsky, David S.; Slotkin, Jerry; Blitz, David L.; Carlozzi, Noelle E.; Havlik, Richard J.; Beaumont, Jennifer L.; Mungas, Dan; Manly, Jennifer J.; Borosh, Beth G.; Nowinski, Cindy J.; Gershon, Richard C.

    2014-01-01

    This monograph presents the pediatric portion of the National Institutes of Health (NIH) Toolbox Cognition Battery (CB) of the NIH Toolbox for the Assessment of Neurological and Behavioral Function. The NIH Toolbox is an initiative of the Neuroscience Blueprint, a collaborative framework through which 16 NIH Institutes, Centers, and Offices jointly support neuroscience-related research, to accelerate discoveries and reduce the burden of nervous system disorders. The CB is one of four modules that measure cognitive, emotional, sensory, and motor health across the lifespan. The CB is unique in its continuity across childhood, adolescence, early adulthood, and old age, and in order to help create a common currency among disparate studies, it is also available at low cost to researchers for use in large-scale longitudinal and epidemiologic studies. This chapter describes the evolution of the CB; methods for selecting cognitive subdomains and instruments; the rationale for test design; and a validation study in children and adolescents, ages 3–15 years. Subsequent chapters feature detailed discussions of each test measure and its psychometric properties (Chapters 2–6), the factor structure of the test battery (Chapter 7), the effects of age and education on composite test scores (Chapter 8), and a final summary and discussion (Chapter 9). As the chapters in this monograph demonstrate, the CB has excellent psychometric properties, and the validation study provided evidence for the increasing differentiation of cognitive abilities with age. PMID:23952199

  17. RenderToolbox3: MATLAB tools that facilitate physically based stimulus rendering for vision research.

    Science.gov (United States)

    Heasly, Benjamin S; Cottaris, Nicolas P; Lichtman, Daniel P; Xiao, Bei; Brainard, David H

    2014-02-07

    RenderToolbox3 provides MATLAB utilities and prescribes a workflow that should be useful to researchers who want to employ graphics in the study of vision and perhaps in other endeavors as well. In particular, RenderToolbox3 facilitates rendering scene families in which various scene attributes and renderer behaviors are manipulated parametrically, enables spectral specification of object reflectance and illuminant spectra, enables the use of physically based material specifications, helps validate renderer output, and converts renderer output to physical units of radiance. This paper describes the design and functionality of the toolbox and discusses several examples that demonstrate its use. We have designed RenderToolbox3 to be portable across computer hardware and operating systems and to be free and open source (except for MATLAB itself). RenderToolbox3 is available at https://github.com/DavidBrainard/RenderToolbox3.

  18. SinCHet: a MATLAB toolbox for single cell heterogeneity analysis in cancer.

    Science.gov (United States)

    Li, Jiannong; Smalley, Inna; Schell, Michael J; Smalley, Keiran S M; Chen, Y Ann

    2017-09-15

    Single-cell technologies allow characterization of transcriptomes and epigenomes for individual cells under different conditions and provide unprecedented resolution for researchers to investigate cellular heterogeneity in cancer. The SinCHet ( gle ell erogeneity) toolbox is developed in MATLAB and has a graphical user interface (GUI) for visualization and user interaction. It analyzes both continuous (e.g. mRNA expression) and binary omics data (e.g. discretized methylation data). The toolbox does not only quantify cellular heterogeneity using S hannon P rofile (SP) at different clonal resolutions but also detects heterogeneity differences using a D statistic between two populations. It is defined as the area under the P rofile of S hannon D ifference (PSD). This flexible tool provides a default clonal resolution using the change point of PSD detected by multivariate adaptive regression splines model; it also allows user-defined clonal resolutions for further investigation. This tool provides insights into emerging or disappearing clones between conditions, and enables the prioritization of biomarkers for follow-up experiments based on heterogeneity or marker differences between and/or within cell populations. The SinCHet software is freely available for non-profit academic use. The source code, example datasets, and the compiled package are available at http://labpages2.moffitt.org/chen/software/ . ann.chen@moffitt.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  19. COMETS2: An advanced MATLAB toolbox for the numerical analysis of electric fields generated by transcranial direct current stimulation.

    Science.gov (United States)

    Lee, Chany; Jung, Young-Jin; Lee, Sang Jun; Im, Chang-Hwan

    2017-02-01

    Since there is no way to measure electric current generated by transcranial direct current stimulation (tDCS) inside the human head through in vivo experiments, numerical analysis based on the finite element method has been widely used to estimate the electric field inside the head. In 2013, we released a MATLAB toolbox named COMETS, which has been used by a number of groups and has helped researchers to gain insight into the electric field distribution during stimulation. The aim of this study was to develop an advanced MATLAB toolbox, named COMETS2, for the numerical analysis of the electric field generated by tDCS. COMETS2 can generate any sizes of rectangular pad electrodes on any positions on the scalp surface. To reduce the large computational burden when repeatedly testing multiple electrode locations and sizes, a new technique to decompose the global stiffness matrix was proposed. As examples of potential applications, we observed the effects of sizes and displacements of electrodes on the results of electric field analysis. The proposed mesh decomposition method significantly enhanced the overall computational efficiency. We implemented an automatic electrode modeler for the first time, and proposed a new technique to enhance the computational efficiency. In this paper, an efficient toolbox for tDCS analysis is introduced (freely available at http://www.cometstool.com). It is expected that COMETS2 will be a useful toolbox for researchers who want to benefit from the numerical analysis of electric fields generated by tDCS. Copyright © 2016. Published by Elsevier B.V.

  20. The iRoCS Toolbox--3D analysis of the plant root apical meristem at cellular resolution.

    Science.gov (United States)

    Schmidt, Thorsten; Pasternak, Taras; Liu, Kun; Blein, Thomas; Aubry-Hivet, Dorothée; Dovzhenko, Alexander; Duerr, Jasmin; Teale, William; Ditengou, Franck A; Burkhardt, Hans; Ronneberger, Olaf; Palme, Klaus

    2014-03-01

    To achieve a detailed understanding of processes in biological systems, cellular features must be quantified in the three-dimensional (3D) context of cells and organs. We described use of the intrinsic root coordinate system (iRoCS) as a reference model for the root apical meristem of plants. iRoCS enables direct and quantitative comparison between the root tips of plant populations at single-cell resolution. The iRoCS Toolbox automatically fits standardized coordinates to raw 3D image data. It detects nuclei or segments cells, automatically fits the coordinate system, and groups the nuclei/cells into the root's tissue layers. The division status of each nucleus may also be determined. The only manual step required is to mark the quiescent centre. All intermediate outputs may be refined if necessary. The ability to learn the visual appearance of nuclei by example allows the iRoCS Toolbox to be easily adapted to various phenotypes. The iRoCS Toolbox is provided as an open-source software package, licensed under the GNU General Public License, to make it accessible to a broad community. To demonstrate the power of the technique, we measured subtle changes in cell division patterns caused by modified auxin flux within the Arabidopsis thaliana root apical meristem. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  1. The Timeseries Toolbox - A Web Application to Enable Accessible, Reproducible Time Series Analysis

    Science.gov (United States)

    Veatch, W.; Friedman, D.; Baker, B.; Mueller, C.

    2017-12-01

    The vast majority of data analyzed by climate researchers are repeated observations of physical process or time series data. This data lends itself of a common set of statistical techniques and models designed to determine trends and variability (e.g., seasonality) of these repeated observations. Often, these same techniques and models can be applied to a wide variety of different time series data. The Timeseries Toolbox is a web application designed to standardize and streamline these common approaches to time series analysis and modeling with particular attention to hydrologic time series used in climate preparedness and resilience planning and design by the U. S. Army Corps of Engineers. The application performs much of the pre-processing of time series data necessary for more complex techniques (e.g. interpolation, aggregation). With this tool, users can upload any dataset that conforms to a standard template and immediately begin applying these techniques to analyze their time series data.

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

    Science.gov (United States)

    Clayson, Peter E; Miller, Gregory A

    2017-01-01

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

  3. UP Finder: A COBRA toolbox extension for identifying gene overexpression strategies for targeted overproduction

    Directory of Open Access Journals (Sweden)

    Xi Wang

    2017-12-01

    Full Text Available Overexpression of key genes is a basic strategy for overproducing target products via metabolic engineering. Traditionally, identifying those key genes/pathways largely relies on the knowledge of biochemistry and bioinformatics. In this study, a modeling tool named UP Finder was developed to facilitate the rapid identification of gene overexpression strategies. It was based on the COBRA toolbox under MATLAB environment. All the key gene/pathway targets are identified in one click after simply loading a Systems Biology Markup Language model and specifying a metabolite as the targeted product. The outputs are also quantitatively ranked to show the preference for determining overexpression strategies in pathway design. Analysis examples for overproducing lycopene precursor in Escherichia coli and fatty acyl-ACP in the cyanobacterium Synechocystis sp. PCC 6803 by the UP Finder showed high degree of agreement with the reported key genes in the literatures.

  4. Enhancing Organizational Performance: A Toolbox for Self ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Do you know if your organization is performing efficiently? If it isn't, do you know why? This guidebook presents an innovative and thoroughly tested model for organizational self-assessment. The tools and tips in Enhancing Organizational Performance go beyond measuring the impact of programs, products, and services.

  5. IMPROVEMENT TOOLBOX DESIGN FOR EFQM CRITERIA

    Directory of Open Access Journals (Sweden)

    Ipek Deveci Kocakoç

    2012-12-01

    Full Text Available The EFQM Excellence Model is a framework that helps organizations to achieve competitive advantage by measuring where they are on their path to excellence. However, it does not tell the organization what to do or how it should manage any of these areas. In this study, we suggest a structure to overcome this gap. We present a method, matrix reflections, to find a tool set that can be used for designing improvement approaches in order to reach desired results.

  6. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-01-01

    We present the software package MTpy that allows handling, processing, and imaging of magnetotelluric (MT) data sets. Written in Python, the code is open source, containing sub-packages and modules for various tasks within the standard MT data processing and handling scheme. Besides the independent definition of classes and functions, MTpy provides wrappers and convenience scripts to call standard external data processing and modelling software.

  7. Light sheet microscopes: Novel imaging toolbox for visualizing life's processes.

    Science.gov (United States)

    Heddleston, John M; Chew, Teng-Leong

    2016-11-01

    Capturing dynamic processes in live samples is a nontrivial task in biological imaging. Although fluorescence provides high specificity and contrast compared to other light microscopy techniques, the photophysical principles of this method can have a harmful effect on the sample. Current advances in light sheet microscopy have created a novel imaging toolbox that allows for rapid acquisition of high-resolution fluorescent images with minimal perturbation of the processes of interest. Each unique design has its own advantages and limitations. In this review, we describe several cutting edge light sheet microscopes and their optimal applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

    Ingrell, Christian Ravnsborg; Matthiesen, Rune; Jensen, Ole Nørregaard

    2006-01-01

    analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl......The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence...... inositol-anchored proteins....

  9. Evaluation Toolbox: Ex-Ante Impact Assessment and Value Network Analysis for SI

    NARCIS (Netherlands)

    Dhondt, S.; Ven, H. van de; Cressey, P.; Kaderabkova, A.; Luna, Á.; Moghadam Saman, S.; Castro Spila, J.; Ziauberyte, R.; Torre, W. van der; Terstriep, J.

    2016-01-01

    This report contains a toolbox for use with the Ex-Ante Impact Assessment for social innovations as was developed in the report D7.1. This toolbox proposes a series of convenient and useful tools to apply in an ex-ante assessment of social innovation within SIMPACT's policy areas unemployment,

  10. morphforge: a toolbox for simulating small networks of biologically detailed neurons in Python

    Directory of Open Access Journals (Sweden)

    Michael James Hull

    2014-01-01

    Full Text Available The broad structure of a modelling study can often be explained over a cup of coffee, butconverting this high-level conceptual idea into graphs of the final simulation results may requiremany weeks of sitting at a computer. Although models themselves can be complex, oftenmany mental resources are wasted working around complexities of the software ecosystemsuch as fighting to manage files, interfacing between tools and data formats, finding mistakesin code or working out the units of variables. morphforge is a high-level, Python toolboxfor building and managing simulations of small populations of multicompartmental biophysicalmodel neurons. An entire in silico experiment, including the definition of neuronal morphologies,channel descriptions, stimuli, visualisation and analysis of results can be written within a singleshort Python script using high-level objects. Multiple independent simulations can be createdand run from a single script, allowing parameter spaces to be investigated. Consideration hasbeen given to the reuse of both algorithmic and parameterisable components to allow bothspecific and stochastic parameter variations. Some other features of the toolbox include: theautomatic generation of human-readable documentation (e. g. PDF-files about a simulation; thetransparent handling of different biophysical units; a novel mechanism for plotting simulationresults based on a system of tags; and an architecture that supports both the use of establishedformats for defining channels and synapses (e. g. MODL files, and the possibility to supportother libraries and standards easily. We hope that this toolbox will allow scientists to quicklybuild simulations of multicompartmental model neurons for research and serve as a platform forfurther tool development.

  11. Spatial Data Mining Toolbox for Mapping Suitability of Landfill Sites Using Neural Networks

    Science.gov (United States)

    Abujayyab, S. K. M.; Ahamad, M. S. S.; Yahya, A. S.; Aziz, H. A.

    2016-09-01

    Mapping the suitability of landfill sites is a complex field and is involved with multidiscipline. The purpose of this research is to create an ArcGIS spatial data mining toolbox for mapping the suitability of landfill sites at a regional scale using neural networks. The toolbox is constructed from six sub-tools to prepare, train, and process data. The employment of the toolbox is straightforward. The multilayer perceptron (MLP) neural networks structure with a backpropagation learning algorithm is used. The dataset is mined from the north states in Malaysia. A total of 14 criteria are utilized to build the training dataset. The toolbox provides a platform for decision makers to implement neural networks for mapping the suitability of landfill sites in the ArcGIS environment. The result shows the ability of the toolbox to produce suitability maps for landfill sites.

  12. Parallel Sequential Monte Carlo for Efficient Density Combination: The Deco Matlab Toolbox

    DEFF Research Database (Denmark)

    Casarin, Roberto; Grassi, Stefano; Ravazzolo, Francesco

    This paper presents the Matlab package DeCo (Density Combination) which is based on the paper by Billio et al. (2013) where a constructive Bayesian approach is presented for combining predictive densities originating from different models or other sources of information. The combination weights...... for standard CPU computing and for Graphical Process Unit (GPU) parallel computing. For the GPU implementation we use the Matlab parallel computing toolbox and show how to use General Purposes GPU computing almost effortless. This GPU implementation comes with a speed up of the execution time up to seventy...... times compared to a standard CPU Matlab implementation on a multicore CPU. We show the use of the package and the computational gain of the GPU version, through some simulation experiments and empirical applications....

  13. STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB

    KAUST Repository

    Klingbeil, G.

    2011-02-25

    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.

  14. ParTIES: a toolbox for Paramecium interspersed DNA elimination studies.

    Science.gov (United States)

    Denby Wilkes, Cyril; Arnaiz, Olivier; Sperling, Linda

    2016-02-15

    Developmental DNA elimination occurs in a wide variety of multicellular organisms, but ciliates are the only single-celled eukaryotes in which this phenomenon has been reported. Despite considerable interest in ciliates as models for DNA elimination, no standard methods for identification and characterization of the eliminated sequences are currently available. We present the Paramecium Toolbox for Interspersed DNA Elimination Studies (ParTIES), designed for Paramecium species, that (i) identifies eliminated sequences, (ii) measures their presence in a sequencing sample and (iii) detects rare elimination polymorphisms. ParTIES is multi-threaded Perl software available at https://github.com/oarnaiz/ParTIES. ParTIES is distributed under the GNU General Public Licence v3. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  15. GMAC: a Matlab toolbox for spectral Granger causality analysis of fMRI data.

    Science.gov (United States)

    Tana, Maria Gabriella; Sclocco, Roberta; Bianchi, Anna Maria

    2012-10-01

    Investigation of causal interactions within brain networks using Granger causality analysis (GCA) is a key challenge in studying neural activity on the basis of functional magnetic resonance imaging (fMRI). The article describes an open-source software toolbox GMAC (Granger multivariate autoregressive connectivity) implementing multivariate spectral GCA. Available features are: fMRI data importing/exporting, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions have been integrated into a user-friendly graphical interface developed in the Matlab environment, easily accessible to both technical and clinical users. Copyright © 2012 Elsevier Ltd. All rights reserved.

  16. A Sommerfeld toolbox for colored dark sectors

    Science.gov (United States)

    El Hedri, Sonia; Kaminska, Anna; de Vries, Maikel

    2017-09-01

    We present analytical formulas for the Sommerfeld corrections to the annihilation of massive colored particles into quarks and gluons through the strong interaction. These corrections are essential to accurately compute the dark matter relic density for coannihilation with colored partners. Our formulas allow us to compute the Sommerfeld effect, not only for the lowest term in the angular momentum expansion of the amplitude, but for all orders in the partial wave expansion. In particular, we carefully account for the effects of the spin of the annihilating particle on the symmetry of the two-particle wave function. This work focuses on strongly interacting particles of arbitrary spin in the triplet, sextet and octet color representations. For typical velocities during freeze-out, we find that including Sommerfeld corrections on the next-to-leading order partial wave leads to modifications of up to 10 to 20 percent on the total annihilation cross section. Complementary to QCD, we generalize our results to particles charged under an arbitrary unbroken SU( N) gauge group, as encountered in dark glueball models. In connection with this paper a Mathematica notebook is provided to compute the Sommerfeld corrections for colored particles up to arbitrary order in the angular momentum expansion.

  17. A Sommerfeld toolbox for colored dark sectors

    Energy Technology Data Exchange (ETDEWEB)

    El Hedri, Sonia; Kaminska, Anna; Vries, Maikel de [Mainz Univ., PRISMA Cluster of Excellence and Mainz Inst. for Theoretical Physics (Germany)

    2017-09-15

    We present analytical formulas for the Sommerfeld corrections to the annihilation of massive colored particles into quarks and gluons through the strong interaction. These corrections are essential to accurately compute the dark matter relic density for coannihilation with colored partners. Our formulas allow us to compute the Sommerfeld effect, not only for the lowest term in the angular momentum expansion of the amplitude, but for all orders in the partial wave expansion. In particular, we carefully account for the effects of the spin of the annihilating particle on the symmetry of the two-particle wave function. This work focuses on strongly interacting particles of arbitrary spin in the triplet, sextet and octet color representations. For typical velocities during freeze-out, we find that including Sommerfeld corrections on the next-to-leading order partial wave leads to modifications of up to 10 to 20 percent on the total annihilation cross section. Complementary to QCD, we generalize our results to particles charged under an arbitrary unbroken SU(N) gauge group, as encountered in dark glueball models. In connection with this paper a Mathematica notebook is provided to compute the Sommerfeld corrections for colored particles up to arbitrary order in the angular momentum expansion. (orig.)

  18. Cementitious Barriers Partnership (CBP): Training and Release of CBP Toolbox Software, Version 1.0 - 13480

    International Nuclear Information System (INIS)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S.; Flach, G.; Langton, C.; Smith, F.G. III; Burns, H.; Van der Sloot, H.; Meeussen, J.C.L.; Samson, E.; Mallick, P.; Suttora, L.; Esh, D.; Fuhrmann, M.; Philip, J.

    2013-01-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS TM /ORCHESTRA, STADIUM R , and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS TM /ORCHESTRA and STADIUM R codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed by discussions

  19. Cementitious Barriers Partnership (CBP): Training and Release of CBP Toolbox Software, Version 1.0 - 13480

    Energy Technology Data Exchange (ETDEWEB)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S. [Vanderbilt University, School of Engineering, CRESP, Nashville, TN 37235 (United States); Flach, G.; Langton, C.; Smith, F.G. III; Burns, H. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Van der Sloot, H. [Hans Van der Sloot Consultancy, Dorpsstraat 216, 1721BV Langedijk (Netherlands); Meeussen, J.C.L. [Nuclear Research and Consultancy Group, Westerduinweg 3, Petten (Netherlands); Samson, E. [SIMCO Technologies, Inc., Quebec (Canada); Mallick, P.; Suttora, L. [U.S. Department of Energy, Washington, DC (United States); Esh, D.; Fuhrmann, M.; Philip, J. [U.S. Nuclear Regulatory Commission, Washington, DC (United States)

    2013-07-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS{sup TM}/ORCHESTRA, STADIUM{sup R}, and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed

  20. The BRAT and GUT Couple: Broadview Radar Altimetry and GOCE User Toolboxes

    Science.gov (United States)

    Benveniste, J.; Restano, M.; Ambrózio, A.

    2017-12-01

    The Broadview Radar Altimetry Toolbox (BRAT) is a collection of tools designed to facilitate the processing of radar altimetry data from previous and current altimetry missions, including Sentinel-3A L1 and L2 products. A tutorial is included providing plenty of use cases. BRAT's next release (4.2.0) is planned for October 2017. Based on the community feedback, the front-end has been further improved and simplified whereas the capability to use BRAT in conjunction with MATLAB/IDL or C/C++/Python/Fortran, allowing users to obtain desired data bypassing the data-formatting hassle, remains unchanged. Several kinds of computations can be done within BRAT involving the combination of data fields, that can be saved for future uses, either by using embedded formulas including those from oceanographic altimetry, or by implementing ad-hoc Python modules created by users to meet their needs. BRAT can also be used to quickly visualise data, or to translate data into other formats, e.g. from NetCDF to raster images. The GOCE User Toolbox (GUT) is a compilation of tools for the use and the analysis of GOCE gravity field models. It facilitates using, viewing and post-processing GOCE L2 data and allows gravity field data, in conjunction and consistently with any other auxiliary data set, to be pre-processed by beginners in gravity field processing, for oceanographic and hydrologic as well as for solid earth applications at both regional and global scales. Hence, GUT facilitates the extensive use of data acquired during GRACE and GOCE missions. In the current 3.1 version, GUT has been outfitted with a graphical user interface allowing users to visually program data processing workflows. Further enhancements aiming at facilitating the use of gradients, the anisotropic diffusive filtering, and the computation of Bouguer and isostatic gravity anomalies have been introduced. Packaged with GUT is also GUT's Variance-Covariance Matrix tool (VCM). BRAT and GUT toolboxes can be freely

  1. Adding to the Mercury Speciation Toolbox

    Science.gov (United States)

    Fitts, J. P.; Northrup, P. A.; Chidambaram, D.; Kalb, P. D.

    2007-12-01

    Mercury was used to separate lithium-6 isotope for weapons production at the Y-12 Plant in Oak Ridge, TN in the 1950s and 1960s. A large portion of the waste Hg entered the environment and continues to move throughout the sub-surface and surface waters in the area. Environmental management of Hg contamination within this complex hydrologic system, where Hg speciation and the mobile fraction have been found to vary widely, will require ongoing characterization and predictive modeling of Hg speciation. State-of-the-art spectroscopic tools that can directly probe Hg speciation in preserved aqueous and sediment samples with greater sensitivity, however, are required to determine rates and mechanisms of biogeochemical reactions. We will present the first results demonstrating the use of x-ray absorption spectroscopy (XAS) at the Hg M5 edge (2295 eV) to fingerprint Hg species. Heavy-metal M5 absorption edges can have very sharp features due to local electron transitions, and therefore, we are developing this edge as a tool for quantitative measurement of Hg species. In addition, sulfur speciation using the sulfur K absorption edge, which is at a similar energy (2472 eV), can be measured in the same scan as the Hg M5 edge. Potentially important organic and inorganic sulfur species (sulfide, disulfide, elemental sulfur, sulfite and sulfate) are readily differentiated, and thereby, provides an independent method for monitoring the redox state of the system along with changes in S-Hg bonding. We will also present x-ray microprobe 2-D concentration maps of Hg and other elements at the grain and pore scales to identify its microscopic distribution and chemical associations. When used in combination with established sequential extraction and direct spectroscopic methods, the addition of XAS at the Hg M5 edge should provide a significant advancement in the determination of Hg speciation in complex biogeochemical environments.

  2. The Expanded Capabilities Of The Cementitious Barriers Partnership Software Toolbox Version 2.0 - 14331

    Energy Technology Data Exchange (ETDEWEB)

    Burns, Heather; Flach, Greg; Smith, Frank; Langton, Christine; Brown, Kevin; Kosson, David; Samson, Eric; Mallick, Pramod

    2014-01-10

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. The CBP Software Toolbox – “Version 1.0” was released early in FY2013 and was used to support DOE-EM performance assessments in evaluating various degradation mechanisms that included sulfate attack, carbonation and constituent leaching. The sulfate attack analysis predicted the extent and damage that sulfate ingress will have on concrete vaults over extended time (i.e., > 1000 years) and the carbonation analysis provided concrete degradation predictions from rebar corrosion. The new release “Version 2.0” includes upgraded carbonation software and a new software module to evaluate degradation due to chloride attack. Also included in the newer version are a dual regime module allowing evaluation of contaminant release in two regimes – both fractured and un-fractured. The integrated software package has also been upgraded with new plotting capabilities and many other features that increase the “user-friendliness” of the package. Experimental work has been generated to provide data to calibrate the models to improve the credibility of the analysis and reduce the uncertainty. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to or longer than 100 years for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox is and will continue to produce tangible benefits to the working DOE

  3. Signal processing and neural network toolbox and its application to failure diagnosis and prognosis

    Science.gov (United States)

    Tu, Fang; Wen, Fang; Willett, Peter K.; Pattipati, Krishna R.; Jordan, Eric H.

    2001-07-01

    Many systems are comprised of components equipped with self-testing capability; however, if the system is complex involving feedback and the self-testing itself may occasionally be faulty, tracing faults to a single or multiple causes is difficult. Moreover, many sensors are incapable of reliable decision-making on their own. In such cases, a signal processing front-end that can match inference needs will be very helpful. The work is concerned with providing an object-oriented simulation environment for signal processing and neural network-based fault diagnosis and prognosis. In the toolbox, we implemented a wide range of spectral and statistical manipulation methods such as filters, harmonic analyzers, transient detectors, and multi-resolution decomposition to extract features for failure events from data collected by data sensors. Then we evaluated multiple learning paradigms for general classification, diagnosis and prognosis. The network models evaluated include Restricted Coulomb Energy (RCE) Neural Network, Learning Vector Quantization (LVQ), Decision Trees (C4.5), Fuzzy Adaptive Resonance Theory (FuzzyArtmap), Linear Discriminant Rule (LDR), Quadratic Discriminant Rule (QDR), Radial Basis Functions (RBF), Multiple Layer Perceptrons (MLP) and Single Layer Perceptrons (SLP). Validation techniques, such as N-fold cross-validation and bootstrap techniques, are employed for evaluating the robustness of network models. The trained networks are evaluated for their performance using test data on the basis of percent error rates obtained via cross-validation, time efficiency, generalization ability to unseen faults. Finally, the usage of neural networks for the prediction of residual life of turbine blades with thermal barrier coatings is described and the results are shown. The neural network toolbox has also been applied to fault diagnosis in mixed-signal circuits.

  4. UbiGate: a synthetic biology toolbox to analyse ubiquitination.

    Science.gov (United States)

    Kowarschik, Kathrin; Hoehenwarter, Wolfgang; Marillonnet, Sylvestre; Trujillo, Marco

    2018-03-01

    Ubiquitination is mediated by an enzymatic cascade that results in the modification of substrate proteins, redefining their fate. This post-translational modification is involved in most cellular processes, yet its analysis faces manifold obstacles due to its complex and ubiquitous nature. Reconstitution of the ubiquitination cascade in bacterial systems circumvents several of these problems and was shown to faithfully recapitulate the process. Here, we present UbiGate - a synthetic biology toolbox, together with an inducible bacterial expression system - to enable the straightforward reconstitution of the ubiquitination cascades of different organisms in Escherichia coli by 'Golden Gate' cloning. This inclusive toolbox uses a hierarchical modular cloning system to assemble complex DNA molecules encoding the multiple genetic elements of the ubiquitination cascade in a predefined order, to generate polycistronic operons for expression. We demonstrate the efficiency of UbiGate in generating a variety of expression elements to reconstitute autoubiquitination by different E3 ligases and the modification of their substrates, as well as its usefulness for dissecting the process in a time- and cost-effective manner. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  5. Comparison of ArcToolbox and Terrain Tiles processing procedures for inundation mapping in mountainous terrain.

    Science.gov (United States)

    Darnell, Andrew; Wise, Richard; Quaranta, John

    2013-01-01

    Floodplain management consists of efforts to reduce flood damage to critical infrastructure and to protect the life and health of individuals from flooding. A major component of this effort is the monitoring of flood control structures such as dams because the potential failure of these structures may have catastrophic consequences. To prepare for these threats, engineers use inundation maps that illustrate the flood resulting from high river stages. To create the maps, the structure and river systems are modeled using engineering software programs, and hydrologic events are used to simulate the conditions leading to the failure of the structure. The output data are then exported to other software programs for the creation of inundation maps. Although the computer programs for this process have been established, the processing procedures vary and yield inconsistent results. Thus, these processing methods need to be examined to determine the functionality of each in floodplain management practices. The main goal of this article is to present the development of a more integrated, accurate, and precise graphical interface tool for interpretation by emergency managers and floodplain engineers. To accomplish this purpose, a potential dam failure was simulated and analyzed for a candidate river system using two processing methods: ArcToolbox and Terrain Tiles. The research involved performing a comparison of the outputs, which revealed that both procedures yielded similar inundations for single river reaches. However, the results indicated key differences when examining outputs for large river systems. On the basis of criteria involving the hydrologic accuracy and effects on infrastructure, the Terrain Tiles inundation surpassed the ArcToolbox inundation in terms of following topography and depicting flow rates and flood extents at confluences, bends, and tributary streams. Thus, the Terrain Tiles procedure is a more accurate representation of flood extents for use by

  6. Technical skills assessment toolbox: a review using the unitary framework of validity.

    Science.gov (United States)

    Ghaderi, Iman; Manji, Farouq; Park, Yoon Soo; Juul, Dorthea; Ott, Michael; Harris, Ilene; Farrell, Timothy M

    2015-02-01

    The purpose of this study was to create a technical skills assessment toolbox for 35 basic and advanced skills/procedures that comprise the American College of Surgeons (ACS)/Association of Program Directors in Surgery (APDS) surgical skills curriculum and to provide a critical appraisal of the included tools, using contemporary framework of validity. Competency-based training has become the predominant model in surgical education and assessment of performance is an essential component. Assessment methods must produce valid results to accurately determine the level of competency. A search was performed, using PubMed and Google Scholar, to identify tools that have been developed for assessment of the targeted technical skills. A total of 23 assessment tools for the 35 ACS/APDS skills modules were identified. Some tools, such as Operative Performance Rating System (OSATS) and Objective Structured Assessment of Technical Skill (OPRS), have been tested for more than 1 procedure. Therefore, 30 modules had at least 1 assessment tool, with some common surgical procedures being addressed by several tools. Five modules had none. Only 3 studies used Messick's framework to design their validity studies. The remaining studies used an outdated framework on the basis of "types of validity." When analyzed using the contemporary framework, few of these studies demonstrated validity for content, internal structure, and relationship to other variables. This study provides an assessment toolbox for common surgical skills/procedures. Our review shows that few authors have used the contemporary unitary concept of validity for development of their assessment tools. As we progress toward competency-based training, future studies should provide evidence for various sources of validity using the contemporary framework.

  7. FracPaQ: a MATLAB™ toolbox for the quantification of fracture patterns

    Science.gov (United States)

    Healy, David; Rizzo, Roberto; Farrell, Natalie; Watkins, Hannah; Cornwell, David; Gomez-Rivas, Enrique; Timms, Nick

    2017-04-01

    The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, shapes and spatial distributions often exhibit some kind of order. In detail, there may be relationships among the different fracture attributes e.g. small fractures dominated by one orientation, larger fractures by another. These relationships are important because the mechanical (e.g. strength, anisotropy) and transport (e.g. fluids, heat) properties of rock depend on these fracture patterns and fracture attributes. This presentation describes an open source toolbox to quantify fracture patterns, including distributions in fracture attributes and their spatial variation. Software has been developed to quantify fracture patterns from 2-D digital images, such as thin section micrographs, geological maps, outcrop or aerial photographs or satellite images. The toolbox comprises a suite of MATLAB™ scripts based on published quantitative methods for the analysis of fracture attributes: orientations, lengths, intensity, density and connectivity. An estimate of permeability in 2-D is made using a parallel plate model. The software provides an objective and consistent methodology for quantifying fracture patterns and their variations in 2-D across a wide range of length scales. Our current focus for the application of the software is on quantifying crack and fracture patterns in and around fault zones. There is a large body of published work on the quantification of relatively simple joint patterns, but fault zones present a bigger, and arguably more important, challenge. The methods presented are inherently scale independent, and a key task will be to analyse and integrate quantitative fracture pattern data from micro- to macro-scales. New features in this release include multi-scale analyses based on a wavelet method to look for scale transitions, support for multi-colour traces in the input file processed as separate fracture sets, and combining fracture traces

  8. Simulating electron energy loss spectroscopy with the MNPBEM toolbox

    Science.gov (United States)

    Hohenester, Ulrich

    2014-03-01

    Within the MNPBEM toolbox, we show how to simulate electron energy loss spectroscopy (EELS) of plasmonic nanoparticles using a boundary element method approach. The methodology underlying our approach closely follows the concepts developed by García de Abajo and coworkers (Garcia de Abajo, 2010). We introduce two classes eelsret and eelsstat that allow in combination with our recently developed MNPBEM toolbox for a simple, robust, and efficient computation of EEL spectra and maps. The classes are accompanied by a number of demo programs for EELS simulation of metallic nanospheres, nanodisks, and nanotriangles, and for electron trajectories passing by or penetrating through the metallic nanoparticles. We also discuss how to compute electric fields induced by the electron beam and cathodoluminescence. Catalogue identifier: AEKJ_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKJ_v2_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 38886 No. of bytes in distributed program, including test data, etc.: 1222650 Distribution format: tar.gz Programming language: Matlab 7.11.0 (R2010b). Computer: Any which supports Matlab 7.11.0 (R2010b). Operating system: Any which supports Matlab 7.11.0 (R2010b). RAM:≥1 GB Classification: 18. Catalogue identifier of previous version: AEKJ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 183 (2012) 370 External routines: MESH2D available at www.mathworks.com Does the new version supersede the previous version?: Yes Nature of problem: Simulation of electron energy loss spectroscopy (EELS) for plasmonic nanoparticles. Solution method: Boundary element method using electromagnetic potentials. Reasons for new version: The new version of the toolbox includes two additional classes for the simulation of electron energy

  9. HINT: A Toolbox for Hierarchical Modeling of Neuroimaging Data

    OpenAIRE

    Lukemire, Joshua; Wang, Yikai; Verma, Amit; Guo, Ying

    2018-01-01

    The modular behavior of the human brain is commonly investigated using independent component analysis (ICA) to identify spatially or temporally distinct functional networks. Investigators are commonly interested not only in the networks themselves, but in how the networks differ in the presence of clinical or demographic covariates. To date, group ICA methods do not directly incorporate these effects during the ICA decomposition. Instead, two-stage approaches are used to attempt to identify c...

  10. CRONE control system design toolbox for the control engineering community: tutorial and case study.

    Science.gov (United States)

    Lanusse, Patrick; Malti, Rachid; Melchior, Pierre

    2013-05-13

    Fractional-order differentiation offers new degrees of freedom that simplify the design of high-performance dynamic controllers. The CRONE control system design (CSD) methodology proposes the design of robust controllers by using fractional-order operators. A software toolbox has been developed based on this methodology and is freely available for the international scientific and industrial communities. This paper presents both the CRONE CSD methodology and its implementation using the toolbox. The design of two robust controllers for irrigation canals shows how to use the toolbox.

  11. An object-oriented multi-threaded software beamformation toolbox

    DEFF Research Database (Denmark)

    Hansen, Jens Munk; Hemmsen, Martin Christian; Jensen, Jørgen Arendt

    2011-01-01

    - mial, or cubic splines. Apodization can be specied by a number of window functions of xed size applied on the individual elements as a function of distance to a reference point, or it can be dynamic with an expanding or contracting aperture to obtain a constant F-number, or both. On a standard PC....... On a single computer, it mimics the parallization in a scanner containing multiple beam formers. The focusing is determined using the positions of the transducer elements, presence of virtual sources, and the focus points. For interpolation, a number of interpolation schemes can be chosen, e.g. linear, polyno...... with an Intel Quad-Core Xeon E5520 processor running at 2.26 GHz, the toolbox can beamform 300:000 points using 700:000 data samples in 3 seconds using a transducer with 192 elements, dynamic apodization in transmit and receive, and cubic splines for interpolation. This is 19 times faster than our previous...

  12. The influence of industrial applications on a control system toolbox

    International Nuclear Information System (INIS)

    Clout, P.

    1992-01-01

    Vsystem is as an open, advanced software application toolbox for rapidly creating fast, efficient and cost-effective control and data-acquisition systems. Vsystem's modular architecture is designed for single computers, networked computers and workstations running under VAX/VMS or VAX/ELN. At the heart of Vsystem lies Vaccess, a user extendible real-time database and library of access routines. The application database provides the link to the hardware of the application and can be organized as one database or separate database installed in different computers on the network. Vsystem has found application in charged-particle accelerator control, tokamak control, and industrial research, as well as its more recent industrial applications. This paper describes the broad feature of Vsystem and the influence that recent industrial applications have had on the software. (author)

  13. Tracking the Sources of Fecal Contaminations: an Interdisciplinary Toolbox

    Science.gov (United States)

    Jeanneau, L.; Jarde, E.; Derrien, M.; Gruau, G.; Solecki, O.; Pourcher, A.; Marti, R.; Wéry, N.; Caprais, M.; Gourmelon, M.; Mieszkin, S.; Jadas-Hécart, A.; Communal, P.

    2011-12-01

    Fecal contaminations of inland and coastal waters induce risks to human health and economic losses. In order to improve water management, it is necessary to identify the sources of contamination, which implies the development of specific markers. In order to be considered as a valuable host-specific marker, one must (1) be source specific, (2) occur in high concentration in polluting matrices, (3) exhibit extra-intestinal persistence similar to fecal indicator bacteria (FIB) and (4) not grow out of the host. However, up to day no single marker has fulfilled all those criteria. Thus, it has been suggested to use a combination of markers in order to generate more reliable data. This has lead to the development of a Microbial Source Tracking (MST) toolbox including FIB and microbial and chemical specific markers in order to differentiate between human, bovine and porcine fecal contaminations. Those specific markers are, (1) genotypes of F-specific RNA bacteriophages, (2) bacterial markers belonging to the Bacteroidales (human-specific HF183, ruminant-specific Rum-2-Bac and pig-specific Pig-2-Bac markers), to the Bifidobacterium (Bifidobacterium adolescentis) and pig-specific Lactobacillus amylovorus, (3) fecal stanols and (4) caffeine. The development of this MST toolbox was composed of four steps, from the molecular scale to the watershed scale. At the molecular scale, the specificity and the concentration of those markers were studied in cattle and pig manures and in waste water treatment plant (WWTP) effluents and influents. At the microcosm scale, the transfer of bovine and porcine specific markers was investigated by rainfall simulations on agricultural plots amended with cattle or pig manure. Moreover, the relative persistence of FIB and human, porcine and bovine specific markers was investigated in freshwater and seawater microcosms inoculated with a WWTP influent, pig manure and cow manure. Finally, the aforementioned MST toolbox has been validated at the

  14. Toolbox of Molecular Techniques for Studying Leptospira Spp.

    Science.gov (United States)

    Picardeau, Mathieu

    2017-08-29

    This chapter covers the progress made in the Leptospira field since the application of mutagenesis techniques and how they have allowed the study of virulence factors and, more generally, the biology of Leptospira. The last decade has seen advances in our ability to perform molecular genetic analysis of Leptospira. Major achievements include the generation of large collections of mutant strains and the construction of replicative plasmids, enabling complementation of mutations. However, there are still no practical tools for routine genetic manipulation of pathogenic Leptospira strains, slowing down advances in pathogenesis research. This review summarizes the status of the molecular genetic toolbox for Leptospira species and highlights new challenges in the nascent field of Leptospira genetics.

  15. DYNAMIC SYSTEM ANALYSIS WITH pplane8.m (MATLAB® toolbox

    Directory of Open Access Journals (Sweden)

    Alejandro Regalado-Méndez

    2013-12-01

    Full Text Available In this work, four dynamic systems were analyzed (physical, chemical, ecological and economical, represented by autonomous systems of two ordinary differential equations. Main objective is proving that pplane8.m is an adequate and efficient computer tool. The analysis of autonomous systems was given by characterization of their critical points according to Coughanowr & LeBlanc (2009, with the MATLAB® toolbox pplane8.m. The main results are that pplane8.m (Polking, 2009 can quickly and precisely draw trajectories of each phase plane, it easily computes each critical point, and correctly characterize each equilibrium point of all autonomous studied systems. Finally, we can say that pplane8.m is a powerful tool to help the teaching-learning process for engineering students.

  16. Development of an Ontology-Directed Signal Processing Toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Stephen W. Lang

    2011-05-27

    This project was focused on the development of tools for the automatic configuration of signal processing systems. The goal is to develop tools that will be useful in a variety of Government and commercial areas and useable by people who are not signal processing experts. In order to get the most benefit from signal processing techniques, deep technical expertise is often required in order to select appropriate algorithms, combine them into a processing chain, and tune algorithm parameters for best performance on a specific problem. Therefore a significant benefit would result from the assembly of a toolbox of processing algorithms that has been selected for their effectiveness in a group of related problem areas, along with the means to allow people who are not signal processing experts to reliably select, combine, and tune these algorithms to solve specific problems. Defining a vocabulary for problem domain experts that is sufficiently expressive to drive the configuration of signal processing functions will allow the expertise of signal processing experts to be captured in rules for automated configuration. In order to test the feasibility of this approach, we addressed a lightning classification problem, which was proposed by DOE as a surrogate for problems encountered in nuclear nonproliferation data processing. We coded a toolbox of low-level signal processing algorithms for extracting features of RF waveforms, and demonstrated a prototype tool for screening data. We showed examples of using the tool for expediting the generation of ground-truth metadata, for training a signal recognizer, and for searching for signals with particular characteristics. The public benefits of this approach, if successful, will accrue to Government and commercial activities that face the same general problem - the development of sensor systems for complex environments. It will enable problem domain experts (e.g. analysts) to construct signal and image processing chains without

  17. Expanding access to rheumatology care: the rheumatology general practice toolbox.

    LENUS (Irish Health Repository)

    Conway, R

    2015-02-01

    Management guidelines for many rheumatic diseases are published in specialty rheumatology literature but rarely in general medical journals. Musculoskeletal disorders comprise 14% of all consultations in primary care. Formal post-graduate training in rheumatology is limited or absent for many primary care practitioners. Primary care practitioners can be trained to effectively treat complex diseases and have expressed a preference for interactive educational courses. The Rheumatology General Practice (GP) Toolbox is an intensive one day course designed to offer up to date information to primary care practitioners on the latest diagnostic and treatment guidelines for seven common rheumatic diseases. The course structure involves a short lecture on each topic and workshops on arthrocentesis, joint injection and DXA interpretation. Participants evaluated their knowledge and educational experience before, during and after the course. Thirty-two primary care practitioners attended, who had a median of 13 (IQR 6.5, 20) years experience in their specialty. The median number of educational symposia attended in the previous 5 years was 10 (IQR-5, 22.5), with a median of 0 (IQR 0, 1) in rheumatology. All respondents agreed that the course format was appropriate. Numerical improvements were demonstrated in participant\\'s confidence in diagnosing and managing all seven common rheumatologic conditions, with statistically significant improvements (p < 0.05) in 11 of the 14 aspects assessed. The Rheumatology Toolbox is an effective educational method for disseminating current knowledge in rheumatology to primary care physicians and improved participant\\'s self-assessed competence in diagnosis and management of common rheumatic diseases.

  18. GRETNA: a graph theoretical network analysis toolbox for imaging connectomics

    Directory of Open Access Journals (Sweden)

    Jinhui eWang

    2015-06-01

    Full Text Available Recent studies have suggested that the brain’s structural and functional networks (i.e., connectomics can be constructed by various imaging technologies (e.g., EEG/MEG; structural, diffusion and functional MRI and further characterized by graph theory. Given the huge complexity of network construction, analysis and statistics, toolboxes incorporating these functions are largely lacking. Here, we developed the GRaph thEoreTical Network Analysis (GRETNA toolbox for imaging connectomics. The GRETNA contains several key features as follows: (i an open-source, Matlab-based, cross-platform (Windows and UNIX OS package with a graphical user interface; (ii allowing topological analyses of global and local network properties with parallel computing ability, independent of imaging modality and species; (iii providing flexible manipulations in several key steps during network construction and analysis, which include network node definition, network connectivity processing, network type selection and choice of thresholding procedure; (iv allowing statistical comparisons of global, nodal and connectional network metrics and assessments of relationship between these network metrics and clinical or behavioral variables of interest; and (v including functionality in image preprocessing and network construction based on resting-state functional MRI (R-fMRI data. After applying the GRETNA to a publicly released R-fMRI dataset of 54 healthy young adults, we demonstrated that human brain functional networks exhibit efficient small-world, assortative, hierarchical and modular organizations and possess highly connected hubs and that these findings are robust against different analytical strategies. With these efforts, we anticipate that GRETNA will accelerate imaging connectomics in an easy, quick and flexible manner. GRETNA is freely available on the NITRC website (http://www.nitrc.org/projects/gretna/.

  19. PANDA: a pipeline toolbox for analyzing brain diffusion images

    Directory of Open Access Journals (Sweden)

    Zaixu eCui

    2013-02-01

    Full Text Available Diffusion magnetic resonance imaging (dMRI is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named Pipeline for Analyzing braiN Diffusion imAges (PANDA for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL, Pipeline System for Octave and Matlab (PSOM, Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics (e.g., FA and MD that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI, allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  20. GRETNA: a graph theoretical network analysis toolbox for imaging connectomics.

    Science.gov (United States)

    Wang, Jinhui; Wang, Xindi; Xia, Mingrui; Liao, Xuhong; Evans, Alan; He, Yong

    2015-01-01

    Recent studies have suggested that the brain's structural and functional networks (i.e., connectomics) can be constructed by various imaging technologies (e.g., EEG/MEG; structural, diffusion and functional MRI) and further characterized by graph theory. Given the huge complexity of network construction, analysis and statistics, toolboxes incorporating these functions are largely lacking. Here, we developed the GRaph thEoreTical Network Analysis (GRETNA) toolbox for imaging connectomics. The GRETNA contains several key features as follows: (i) an open-source, Matlab-based, cross-platform (Windows and UNIX OS) package with a graphical user interface (GUI); (ii) allowing topological analyses of global and local network properties with parallel computing ability, independent of imaging modality and species; (iii) providing flexible manipulations in several key steps during network construction and analysis, which include network node definition, network connectivity processing, network type selection and choice of thresholding procedure; (iv) allowing statistical comparisons of global, nodal and connectional network metrics and assessments of relationship between these network metrics and clinical or behavioral variables of interest; and (v) including functionality in image preprocessing and network construction based on resting-state functional MRI (R-fMRI) data. After applying the GRETNA to a publicly released R-fMRI dataset of 54 healthy young adults, we demonstrated that human brain functional networks exhibit efficient small-world, assortative, hierarchical and modular organizations and possess highly connected hubs and that these findings are robust against different analytical strategies. With these efforts, we anticipate that GRETNA will accelerate imaging connectomics in an easy, quick and flexible manner. GRETNA is freely available on the NITRC website.

  1. PANDA: a pipeline toolbox for analyzing brain diffusion images.

    Science.gov (United States)

    Cui, Zaixu; Zhong, Suyu; Xu, Pengfei; He, Yong; Gong, Gaolang

    2013-01-01

    Diffusion magnetic resonance imaging (dMRI) is widely used in both scientific research and clinical practice in in-vivo studies of the human brain. While a number of post-processing packages have been developed, fully automated processing of dMRI datasets remains challenging. Here, we developed a MATLAB toolbox named "Pipeline for Analyzing braiN Diffusion imAges" (PANDA) for fully automated processing of brain diffusion images. The processing modules of a few established packages, including FMRIB Software Library (FSL), Pipeline System for Octave and Matlab (PSOM), Diffusion Toolkit and MRIcron, were employed in PANDA. Using any number of raw dMRI datasets from different subjects, in either DICOM or NIfTI format, PANDA can automatically perform a series of steps to process DICOM/NIfTI to diffusion metrics [e.g., fractional anisotropy (FA) and mean diffusivity (MD)] that are ready for statistical analysis at the voxel-level, the atlas-level and the Tract-Based Spatial Statistics (TBSS)-level and can finish the construction of anatomical brain networks for all subjects. In particular, PANDA can process different subjects in parallel, using multiple cores either in a single computer or in a distributed computing environment, thus greatly reducing the time cost when dealing with a large number of datasets. In addition, PANDA has a friendly graphical user interface (GUI), allowing the user to be interactive and to adjust the input/output settings, as well as the processing parameters. As an open-source package, PANDA is freely available at http://www.nitrc.org/projects/panda/. This novel toolbox is expected to substantially simplify the image processing of dMRI datasets and facilitate human structural connectome studies.

  2. GISMO: A MATLAB toolbox for seismic research, monitoring, & education

    Science.gov (United States)

    Thompson, G.; Reyes, C. G.; Kempler, L. A.

    2017-12-01

    GISMO is an open-source MATLAB toolbox which provides an object-oriented framework to build workflows and applications that read, process, visualize and write seismic waveform, catalog and instrument response data. GISMO can retrieve data from a variety of sources (e.g. FDSN web services, Earthworm/Winston servers) and data formats (SAC, Seisan, etc.). It can handle waveform data that crosses file boundaries. All this alleviates one of the most time consuming part for scientists developing their own codes. GISMO simplifies seismic data analysis by providing a common interface for your data, regardless of its source. Several common plots are built-in to GISMO, such as record section plots, spectrograms, depth-time sections, event count per unit time, energy release per unit time, etc. Other visualizations include map views and cross-sections of hypocentral data. Several common processing methods are also included, such as an extensive set of tools for correlation analysis. Support is being added to interface GISMO with ObsPy. GISMO encourages community development of an integrated set of codes and accompanying documentation, eliminating the need for seismologists to "reinvent the wheel". By sharing code the consistency and repeatability of results can be enhanced. GISMO is hosted on GitHub with documentation both within the source code and in the project wiki. GISMO has been used at the University of South Florida and University of Alaska Fairbanks in graduate-level courses including Seismic Data Analysis, Time Series Analysis and Computational Seismology. GISMO has also been tailored to interface with the common seismic monitoring software and data formats used by volcano observatories in the US and elsewhere. As an example, toolbox training was delivered to researchers at INETER (Nicaragua). Applications built on GISMO include IceWeb (e.g. web-based spectrograms), which has been used by Alaska Volcano Observatory since 1998 and became the prototype for the USGS

  3. Switch of sensitivity dynamics revealed with DyGloSA toolbox for dynamical global sensitivity analysis as an early warning for system's critical transition.

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA - a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits.

  4. Switch of Sensitivity Dynamics Revealed with DyGloSA Toolbox for Dynamical Global Sensitivity Analysis as an Early Warning for System's Critical Transition

    Science.gov (United States)

    Baumuratova, Tatiana; Dobre, Simona; Bastogne, Thierry; Sauter, Thomas

    2013-01-01

    Systems with bifurcations may experience abrupt irreversible and often unwanted shifts in their performance, called critical transitions. For many systems like climate, economy, ecosystems it is highly desirable to identify indicators serving as early warnings of such regime shifts. Several statistical measures were recently proposed as early warnings of critical transitions including increased variance, autocorrelation and skewness of experimental or model-generated data. The lack of automatized tool for model-based prediction of critical transitions led to designing DyGloSA – a MATLAB toolbox for dynamical global parameter sensitivity analysis (GPSA) of ordinary differential equations models. We suggest that the switch in dynamics of parameter sensitivities revealed by our toolbox is an early warning that a system is approaching a critical transition. We illustrate the efficiency of our toolbox by analyzing several models with bifurcations and predicting the time periods when systems can still avoid going to a critical transition by manipulating certain parameter values, which is not detectable with the existing SA techniques. DyGloSA is based on the SBToolbox2 and contains functions, which compute dynamically the global sensitivity indices of the system by applying four main GPSA methods: eFAST, Sobol's ANOVA, PRCC and WALS. It includes parallelized versions of the functions enabling significant reduction of the computational time (up to 12 times). DyGloSA is freely available as a set of MATLAB scripts at http://bio.uni.lu/systems_biology/software/dyglosa. It requires installation of MATLAB (versions R2008b or later) and the Systems Biology Toolbox2 available at www.sbtoolbox2.org. DyGloSA can be run on Windows and Linux systems, -32 and -64 bits. PMID:24367574

  5. FRACOR-software toolbox for deterministic mapping of fracture corridors in oil fields on AutoCAD platform

    Science.gov (United States)

    Ozkaya, Sait I.

    2018-03-01

    Fracture corridors are interconnected large fractures in a narrow sub vertical tabular array, which usually traverse entire reservoir vertically and extended for several hundreds of meters laterally. Fracture corridors with their huge conductivities constitute an important element of many fractured reservoirs. Unlike small diffuse fractures, actual fracture corridors must be mapped deterministically for simulation or field development purposes. Fracture corridors can be identified and quantified definitely with borehole image logs and well testing. However, there are rarely sufficient image logs or well tests, and it is necessary to utilize various fracture corridor indicators with varying degrees of reliability. Integration of data from many different sources, in turn, requires a platform with powerful editing and layering capability. Available commercial reservoir characterization software packages, with layering and editing capabilities, can be cost intensive. CAD packages are far more affordable and may easily acquire the versatility and power of commercial software packages with addition of a small software toolbox. The objective of this communication is to present FRACOR, a software toolbox which enables deterministic 2D fracture corridor mapping and modeling on AutoCAD platform. The FRACOR toolbox is written in AutoLISPand contains several independent routines to import and integrate available fracture corridor data from an oil field, and export results as text files. The resulting fracture corridor maps consists mainly of fracture corridors with different confidence levels from combination of static and dynamic data and exclusion zones where no fracture corridor can exist. The exported text file of fracture corridors from FRACOR can be imported into an upscaling programs to generate fracture grid for dual porosity simulation or used for field development and well planning.

  6. SplitRFLab: A MATLAB GUI toolbox for receiver function analysis based on SplitLab

    Science.gov (United States)

    Xu, Mijian; Huang, Hui; Huang, Zhouchuan; Wang, Liangshu

    2016-02-01

    We add new modules for receiver function (RF) analysis in SplitLab toolbox, which includes the manual RF analysis module, automatic RF analysis and related quality control modules, and H- k stacking module. The updated toolbox (named SplitRFLab toolbox), especially its automatic RF analysis module, could calculate the RFs quickly and efficiently, which is very useful in RF analysis with huge amount of seismic data. China is now conducting the ChinArray project that plans to deploy thousands of portable stations across Chinese mainland. Our SplitRFLab toolbox may obtain reliable RF results quickly at the first time, which provide essentially new constraint to the crustal and mantle structures.

  7. A microfluidic toolbox for the development of in-situ product removal strategies in biocatalysis

    DEFF Research Database (Denmark)

    Heintz, Søren; Mitic, Aleksandar; Ringborg, Rolf Hoffmeyer

    2016-01-01

    A microfluidic toolbox for accelerated development of biocatalytic processes has great potential. This is especially the case for the development of advanced biocatalytic process concepts, where reactors and product separation methods are closely linked together to intensify the process performan...

  8. A toolbox for safety instrumented system evaluation based on improved continuous-time Markov chain

    Science.gov (United States)

    Wardana, Awang N. I.; Kurniady, Rahman; Pambudi, Galih; Purnama, Jaka; Suryopratomo, Kutut

    2017-08-01

    Safety instrumented system (SIS) is designed to restore a plant into a safe condition when pre-hazardous event is occur. It has a vital role especially in process industries. A SIS shall be meet with safety requirement specifications. To confirm it, SIS shall be evaluated. Typically, the evaluation is calculated by hand. This paper presents a toolbox for SIS evaluation. It is developed based on improved continuous-time Markov chain. The toolbox supports to detailed approach of evaluation. This paper also illustrates an industrial application of the toolbox to evaluate arch burner safety system of primary reformer. The results of the case study demonstrates that the toolbox can be used to evaluate industrial SIS in detail and to plan the maintenance strategy.

  9. Review of Qualitative Approaches for the Construction Industry: Designing a Risk Management Toolbox

    Directory of Open Access Journals (Sweden)

    David M. Zalk

    2011-06-01

    Conclusion: The Construction Toolbox presents a review-generated format to harness multiple solutions-based national programs and publications for controlling construction-related risks with simplified approaches across the occupational safety, health and hygiene professions.

  10. A new impetus for guideline development and implementation: construction and evaluation of a toolbox

    NARCIS (Netherlands)

    Hilbink, M.A.; Ouwens, M.M.T.J.; Burgers, J.S.; Kool, R.B.

    2014-01-01

    BACKGROUND: In the last decade, guideline organizations faced a number of problems, including a lack of standardization in guideline development methods and suboptimal guideline implementation. To contribute to the solution of these problems, we produced a toolbox for guideline development,

  11. Developing an intervention toolbox for common health problems in the workplace

    OpenAIRE

    Kendall, Nick; Burton, Kim; Lunt, Jennifer; Mellor, Nadine; Daniels, Kevin

    2015-01-01

    The project brief was to develop the content for an intervention toolbox for common health problems in the workplace - musculoskeletal, mental health and stress complaints. The intention was to develop a prototype toolbox that can be taken forward to (1) minimise the occurrence of work-relevant common health problems (CHPs) and (2) reduce avoidable sickness absence, healthcare use and long-term disability for CHP complaints that inevitably occur in the workplace

  12. The NNSYSID Toolbox - A MATLAB Toolbox for System Identification with Neural Networks

    DEFF Research Database (Denmark)

    Nørgård, Peter Magnus; Ravn, Ole; Hansen, Lars Kai

    1996-01-01

    To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms for determi......To assist the identification of nonlinear dynamic systems, a set of tools has been developed for the MATLAB(R) environment. The tools include a number of different model structures, highly effective training algorithms, functions for validating trained networks, and pruning algorithms...

  13. Facade Refurbishment Toolbox. Supporting the Design of Residential Energy Upgrades

    Directory of Open Access Journals (Sweden)

    Thaleia Konstantinou

    2014-07-01

    strategies be integrated in the early design phase, in order to support decision-making? The objective of the research is to enable the design of refurbishment strategies that acknowledge the potential of energy savings. Having available an assessment of the energy performance results in informed decisions that improve the efficiency of the strategy and the final refurbished building. The answer to the research question is given by the Façade Refurbishment Toolbox (FRT approach. It consists of three different types of information that can support the decision-making of residential façade refurbishment strategies. Firstly, the building envelope components that need to be addressed in an integrated refurbishment strategy are identified and different retrofitting measures for each one are proposed, composing the façade refurbishment toolbox. Secondly, the measures are quantified in terms of energy upgrade potential, expressed by the simulated energy demand reduction after the application of the measure. Finally, a roadmap to the key decision aspects in the refurbishment strategy development indicates when the toolbox information can be used. The methodology used to develop the FRT approach includes organising and calculating information about component retrofitting measures. The steps of the methodology were developed in the different chapters of the thesis. The first three chapters (Chapters 2-4 comprise the theoretical background that shapes the research question, discussion of the residential building stock, energy performance and refurbishment practice. Chapters 5 and 6 describe the process of the composition of the toolbox. Finally, Chapters 7 and 8 are concerned with its further applicability, regarding the approach validation and usability. This thesis concludes with an approach to enable informed and energy-efficiency conscious decisions in the early stage of the design of refurbishment strategies. To improve the design process, the Façade Refurbishment Toolbox

  14. Crescimento e produtividade do tomateiro em cultivo hidropônico NFT em função da concentração iônica da solução nutritiva Growing and yield of tomato in hydroponic cultivation as a result of the ionic concentration of the nutritive solution

    Directory of Open Access Journals (Sweden)

    Gláucio da C Genúncio

    2006-06-01

    Full Text Available O cultivo hidropônico do tomateiro é uma técnica com a qual pode-se obter maior produtividade e melhoria no controle de diversos fatores durante o ciclo produtivo. Entretanto, essa técnica ainda requer aprimoramento em vários aspectos, dentre eles, as doses de nutrientes na solução nutritiva. Neste sentido, um experimento foi conduzido em casa de vegetação equipada com sistema hidropônico tipo fluxo contínuo de nutrientes (nutrient film technique; NFT. Foram utilizadas as cultivares de tomate UC-82, Saladinha e T-93 supridas com solução nutritiva de Hoagland nas concentrações iônicas 50%; 75% e 100%. Na última coleta de frutos, aos 138 dias após a transferência para o sistema NFT, colheram-se as plantas e avaliaram-se o acúmulo de massa na parte aérea, massa fresca de fruto, número de frutos por planta, massa fresca total de frutos por planta, teor de sólidos solúveis totais (ºBrix e produtividade. As características genotípicas das cultivares influenciaram fortemente a produtividade. De modo geral, as diferentes concentrações iônicas das soluções nutritivas, nas condições em que foi desenvolvido o trabalho, não influenciaram a produtividade e o acúmulo de massa dos tomateiros. Portanto é recomendável o uso de soluções de menor concentração iônica para o cultivo de tomateiros UC-82, Saladinha e T-93 em sistema hidropônico NFT, nas condições climáticas de Seropédica, Rio de Janeiro.The tomato hydroponics cultivation is a technique that provides high productivity and a better control of several factors during the production cycle. However, this technique needs improvements such as adequate dosage of nutrients in the nutritive solution. An experiment was carried out in a greenhouse equipped with a nutrient film technique system (NFT. Three commercial cvs. of tomato, UC-82, Saladinha, and T-93, were grown with three Hoagland's solution concentrations, 50%; 75%; and 100%. In the last fruit harvest, 138

  15. The Basic Radar Altimetry Toolbox for Sentinel 3 Users

    Science.gov (United States)

    Lucas, Bruno; Rosmorduc, Vinca; Niemeijer, Sander; Bronner, Emilie; Dinardo, Salvatore; Benveniste, Jérôme

    2013-04-01

    The Basic Radar Altimetry Toolbox (BRAT) is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2006 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales). The latest version of the software, 3.1, was released on March 2012. The tools enable users to interact with the most common altimetry data formats, being the most used way, the Graphical User Interface (BratGui). This GUI is a front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. The BratDisplay (graphic visualizer) can be launched from BratGui, or used as a stand-alone tool to visualize netCDF files - it is distributed with another ESA toolbox (GUT) as the visualizer. The most frequent uses of BRAT are teaching remote sensing, altimetry data reading (all missions from ERS-1 to Saral and soon Sentinel-3), quick data visualization/export and simple computation on the data fields. BRAT can be used for importing data and having a quick look at his contents, with several different types of plotting available. One can also use it to translate the data into other formats such as netCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BratGui involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas (MSS, -SSH, MSLA, editing of spurious data, etc.). The documentation collection includes the standard user manual explaining all the ways to interact with the set of software tools but the most important item is the Radar Altimeter Tutorial, that contains a strong introduction to

  16. Blueprint XAS: a Matlab-based toolbox for the fitting and analysis of XAS spectra.

    Science.gov (United States)

    Delgado-Jaime, Mario Ulises; Mewis, Craig Philip; Kennepohl, Pierre

    2010-01-01

    Blueprint XAS is a new Matlab-based program developed to fit and analyse X-ray absorption spectroscopy (XAS) data, most specifically in the near-edge region of the spectrum. The program is based on a methodology that introduces a novel background model into the complete fit model and that is capable of generating any number of independent fits with minimal introduction of user bias [Delgado-Jaime & Kennepohl (2010), J. Synchrotron Rad. 17, 119-128]. The functions and settings on the five panels of its graphical user interface are designed to suit the needs of near-edge XAS data analyzers. A batch function allows for the setting of multiple jobs to be run with Matlab in the background. A unique statistics panel allows the user to analyse a family of independent fits, to evaluate fit models and to draw statistically supported conclusions. The version introduced here (v0.2) is currently a toolbox for Matlab. Future stand-alone versions of the program will also incorporate several other new features to create a full package of tools for XAS data processing.

  17. European Studies and Public Engagement: A Conceptual Toolbox

    Directory of Open Access Journals (Sweden)

    Andreas Müllerleile

    2014-11-01

    Full Text Available Journal of Contemporary European Research User Username Password Remember me Subscribe... Sign up for issue alerts Follow JCER on Twitter Font Size Make font size smaller Make font size default Make font size larger Journal Content Search Search Scope Browse By Issue By Author By Title Information For Readers For Authors For Librarians Journal Help Keywords CFSP Communication ESDP EU EU enlargement EU trade policy Energy, EU, External Policy Europe European Commission European Parliament European Union European integration Europeanisation First Enlargement Germany Liberty Lisbon Treaty Poland Russia Security teaching European studies The UACES Blog The Commission after the 2014 EP... Power shift? The EU’s pivot to Asia 100 Books on Europe to be Remembered For a Global European Studies? EU Member State Building in the... Open Journal Systems Home About Login Register Search Current Archives Announcements UACES Home > Vol 10, No 4 (2014 > Müllerleile European Studies and Public Engagement: A Conceptual Toolbox Andreas Müllerleile Abstract This article examines public engagement strategies for academics working in the field of European Studies. Should academics engage with the public? What are the most effective outreach strategies? And what are the implications for universities and departments? The article argues that engaging with the public should be considered an integral part for academics working on topics that relate to the European Union or European politics. The article has a theoretical and a practical dimension. The first part of the paper deals with the nature of public engagement, explaining why it is an important issue and how it differs from the mainstream understanding of public engagement. The practical part of the paper presents the idea of building an online presence through which academics can engage with the public debate both during periods of low issue salience and high issue salience. The final section includes a toolbox

  18. ObsPy - A Python Toolbox for Seismology - and Applications

    Science.gov (United States)

    Krischer, L.; Megies, T.; Barsch, R.; MacCarthy, J.; Lecocq, T.; Koymans, M. R.; Carothers, L.; Eulenfeld, T.; Reyes, C. G.; Falco, N.; Sales de Andrade, E.

    2017-12-01

    Recent years witnessed the evolution of Python's ecosystem into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community driven, open-source project dedicated to provide a bridge for seismology into that ecosystem. It is a Python toolbox offering: Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, SC3ML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than eight years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. Newest features include: Full interoperability of SEED and StationXML/Inventory objects Access to the Nominal Response Library (NRL) for easy and quick creation of station metadata from scratch Support for the IRIS Federated Catalog Service Improved performance of the EarthWorm client Several improvements to MiniSEED read/write module Improved plotting capabilities for PPSD (spectrograms, PSD of discrete frequencies over time, ..) Support for.. Reading ArcLink Inventory XML Reading Reftek data format Writing SeisComp3 ML (SC3ML) Writing StationTXT format This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases and show-case some projects that are based on ObsPy, e.g.: seismo

  19. Software Toolbox for Low-Frequency Conductivity and Current Density Imaging Using MRI.

    Science.gov (United States)

    Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-11-01

    Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in transcranial direct current stimulation (tDCS), deep brain stimulation (DBS), and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the MATLAB environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html . Its functions were tested by using several experimental datasets, which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes. Low-frequency conductivity and current density imaging using MRI includes

  20. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave.

    Science.gov (United States)

    Silva, Ikaro; Moody, George B

    The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox provides access over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by metadata such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  1. MANIA-a pattern classification toolbox for neuroimaging data.

    Science.gov (United States)

    Grotegerd, Dominik; Redlich, Ronny; Almeida, Jorge R C; Riemenschneider, Mona; Kugel, Harald; Arolt, Volker; Dannlowski, Udo

    2014-07-01

    Conventional univariate statistics are common and widespread in neuroimaging research. However, functional and structural MRI data reveal a multivariate nature, since neighboring voxels are highly correlated and different localized brain regions activate interdependently. Multivariate pattern classification techniques are capable of overcoming shortcomings of univariate statistics. A rising interest in such approaches on neuroimaging data leads to an increasing demand of appropriate software and tools in this field. Here, we introduce and release MANIA-Machine learning Application for NeuroImaging Analyses. MANIA is a Matlab based software toolbox enabling easy pattern classification of neuroimaging data and offering a broad assortment of machine learning algorithms and feature selection methods. Between groups classifications are the main scope of this software, for instance the differentiation between patients and controls. A special emphasis was placed on an intuitive and easy to use graphical user interface allowing quick implementation and guidance also for clinically oriented researchers. MANIA is free and open source, published under GPL3 license. This work will give an overview regarding the functionality and the modular software architecture as well as a comparison between other software packages.

  2. Enhancing the genome editing toolbox: genome wide CRISPR arrayed libraries.

    Science.gov (United States)

    Metzakopian, Emmanouil; Strong, Alex; Iyer, Vivek; Hodgkins, Alex; Tzelepis, Konstantinos; Antunes, Liliana; Friedrich, Mathias J; Kang, Qiaohua; Davidson, Teresa; Lamberth, Jacob; Hoffmann, Christina; Davis, Gregory D; Vassiliou, George S; Skarnes, William C; Bradley, Allan

    2017-05-22

    CRISPR-Cas9 technology has accelerated biological research becoming routine for many laboratories. It is rapidly replacing conventional gene editing techniques and has high utility for both genome-wide and gene-focussed applications. Here we present the first individually cloned CRISPR-Cas9 genome wide arrayed sgRNA libraries covering 17,166 human and 20,430 mouse genes at a complexity of 34,332 sgRNAs for human and 40,860 sgRNAs for the mouse genome. For flexibility in generating stable cell lines the sgRNAs have been cloned in a lentivirus backbone containing PiggyBac transposase recognition elements together with fluorescent and drug selection markers. Over 95% of tested sgRNA induced specific DNA cleavage as measured by CEL-1 assays. Furthermore, sgRNA targeting GPI anchor protein pathway genes induced loss of function mutations in human and mouse cell lines measured by FLAER labelling. These arrayed libraries offer the prospect for performing screens on individual genes, combinations as well as larger gene sets. They also facilitate rapid deconvolution of signals from genome-wide screens. This set of vectors provide an organized comprehensive gene editing toolbox of considerable scientific value.

  3. Towards a Toolbox for a Process Innovation Laboratory

    DEFF Research Database (Denmark)

    Gong, Jie; Møller, Charles

    2011-01-01

    Driven by the global competition, process Innovation has been a challenge to large enterprises for many years. The research in this paper discusses about the theory and methods of Business Process Innovation (BPI) in designing Intelligent Supply Chains (ISC) in inter-organizations. We first revie...... control/process improvement. Then we present the case study of Genpact, and based on the findings we formulate the challenges towards a toolbox for a process innovation laboratory. These guidelines are the main contributions of this paper.......Driven by the global competition, process Innovation has been a challenge to large enterprises for many years. The research in this paper discusses about the theory and methods of Business Process Innovation (BPI) in designing Intelligent Supply Chains (ISC) in inter-organizations. We first review...... the BPI concepts, compare it with Business Process Improvement (BPIm) and Business Process Reengineering (BPR), and then build an analytical framework to define business process innovation from four different perspectives: management science, knowledge management, information technology and quality...

  4. Towards a Toolbox for a Process Innovation Laboratory

    DEFF Research Database (Denmark)

    Gong, Jie; Møller, Charles

    2012-01-01

    Driven by the global competition, process Innovation has been a challenge to large enterprises for many years. The research in this paper discusses about the theory and methods of Business Process Innovation (BPI) in designing Intelligent Supply Chains (ISC) in inter-organizations. We first revie...... control/process improvement. Then we present the case study of Genpact, and based on the findings we formulate the challenges towards a toolbox for a process innovation laboratory. These guidelines are the main contribution of this paper.......Driven by the global competition, process Innovation has been a challenge to large enterprises for many years. The research in this paper discusses about the theory and methods of Business Process Innovation (BPI) in designing Intelligent Supply Chains (ISC) in inter-organizations. We first review...... the BPI concepts, compare it with Business Process Improvement (BPIm) and Business Process Reengineering (BPR), and then build an analytical framework to define business process innovation from four different perspectives: management science, knowledge management, information technology and quality...

  5. ObsPy: A Python Toolbox for Seismology

    Science.gov (United States)

    Krischer, Lion; Megies, Tobias; Sales de Andrade, Elliott; Barsch, Robert; MacCarthy, Jonathan

    2017-04-01

    In recent years the Python ecosystem evolved into one of the most powerful and productive scientific environments across disciplines. ObsPy (https://www.obspy.org) is a fully community-driven, open-source project dedicated to providing a bridge for seismology into that ecosystem. It does so by offering Read and write support for essentially every commonly used data format in seismology with a unified interface and automatic format detection. This includes waveform data (MiniSEED, SAC, SEG-Y, Reftek, …) as well as station (SEED, StationXML, …) and event meta information (QuakeML, ZMAP, …). Integrated access to the largest data centers, web services, and real-time data streams (FDSNWS, ArcLink, SeedLink, ...). A powerful signal processing toolbox tuned to the specific needs of seismologists. Utility functionality like travel time calculations with the TauP method, geodetic functions, and data visualizations. ObsPy has been in constant development for more than seven years and is developed and used by scientists around the world with successful applications in all branches of seismology. Additionally it nowadays serves as the foundation for a large number of more specialized packages. This presentation will give a short overview of the capabilities of ObsPy and point out several representative or new use cases. Additionally we will discuss the road ahead as well as the long-term sustainability of open-source scientific software.

  6. Molecular toolbox for studying diatom biology in Phaeodactylum tricornutum.

    Science.gov (United States)

    Siaut, Magali; Heijde, Marc; Mangogna, Manuela; Montsant, Anton; Coesel, Sacha; Allen, Andrew; Manfredonia, Alessandro; Falciatore, Angela; Bowler, Chris

    2007-12-30

    Research into diatom biology has now entered the post-genomics era, following the recent completion of the Thalassiosira pseudonana and Phaeodactylum tricornutum whole genome sequences and the establishment of Expressed Sequence Tag (EST) databases. The thorough exploitation of these resources will require the development of molecular tools to analyze and modulate the function of diatom genes in vivo. Towards this objective, we report here the identification of several reference genes that can be used as internal standards for gene expression studies by quantitative real-time PCR (qRT-PCR) in P. tricornutum cells grown over a diel cycle. In addition, we describe a series of diatom expression vectors based on Invitrogen Gateway technology for high-throughput protein tagging and overexpression studies in P. tricornutum. We demonstrate the utility of the diatom Destination vectors for determining the subcellular localization of a protein of interest and for immunodetection. The availability of these new resources significantly enriches the molecular toolbox for P. tricornutum and provides the diatom research community with well defined high-throughput methods for the analysis of diatom genes and proteins in vivo.

  7. SELANSI: a toolbox for simulation of stochastic gene regulatory networks.

    Science.gov (United States)

    Pájaro, Manuel; Otero-Muras, Irene; Vázquez, Carlos; Alonso, Antonio A

    2018-03-01

    Gene regulation is inherently stochastic. In many applications concerning Systems and Synthetic Biology such as the reverse engineering and the de novo design of genetic circuits, stochastic effects (yet potentially crucial) are often neglected due to the high computational cost of stochastic simulations. With advances in these fields there is an increasing need of tools providing accurate approximations of the stochastic dynamics of gene regulatory networks (GRNs) with reduced computational effort. This work presents SELANSI (SEmi-LAgrangian SImulation of GRNs), a software toolbox for the simulation of stochastic multidimensional gene regulatory networks. SELANSI exploits intrinsic structural properties of gene regulatory networks to accurately approximate the corresponding Chemical Master Equation with a partial integral differential equation that is solved by a semi-lagrangian method with high efficiency. Networks under consideration might involve multiple genes with self and cross regulations, in which genes can be regulated by different transcription factors. Moreover, the validity of the method is not restricted to a particular type of kinetics. The tool offers total flexibility regarding network topology, kinetics and parameterization, as well as simulation options. SELANSI runs under the MATLAB environment, and is available under GPLv3 license at https://sites.google.com/view/selansi. antonio@iim.csic.es. © The Author(s) 2017. Published by Oxford University Press.

  8. MATLAB Stability and Control Toolbox Trim and Static Stability Module

    Science.gov (United States)

    Kenny, Sean P.; Crespo, Luis

    2012-01-01

    MATLAB Stability and Control Toolbox (MASCOT) utilizes geometric, aerodynamic, and inertial inputs to calculate air vehicle stability in a variety of critical flight conditions. The code is based on fundamental, non-linear equations of motion and is able to translate results into a qualitative, graphical scale useful to the non-expert. MASCOT was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental nonlinear equations of motion, MASCOT then calculates vehicle trim and static stability data for the desired flight condition(s). Available flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind, and sideslip, plus three take-off rotation conditions. Results are displayed through a unique graphical interface developed to provide the non-stability and control expert conceptual design engineer a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. If desired, the user can also examine the detailed, quantitative results.

  9. Dem Generation from Close-Range Photogrammetry Using Extended Python Photogrammetry Toolbox

    Science.gov (United States)

    Belmonte, A. A.; Biong, M. M. P.; Macatulad, E. G.

    2017-10-01

    Digital elevation models (DEMs) are widely used raster data for different applications concerning terrain, such as for flood modelling, viewshed analysis, mining, land development, engineering design projects, to name a few. DEMs can be obtained through various methods, including topographic survey, LiDAR or photogrammetry, and internet sources. Terrestrial close-range photogrammetry is one of the alternative methods to produce DEMs through the processing of images using photogrammetry software. There are already powerful photogrammetry software that are commercially-available and can produce high-accuracy DEMs. However, this entails corresponding cost. Although, some of these software have free or demo trials, these trials have limits in their usable features and usage time. One alternative is the use of free and open-source software (FOSS), such as the Python Photogrammetry Toolbox (PPT), which provides an interface for performing photogrammetric processes implemented through python script. For relatively small areas such as in mining or construction excavation, a relatively inexpensive, fast and accurate method would be advantageous. In this study, PPT was used to generate 3D point cloud data from images of an open pit excavation. The PPT was extended to add an algorithm converting the generated point cloud data into a usable DEM.

  10. Interpolation and Inversion - New Features in the Matlab Sesimic Anisotropy Toolbox

    Science.gov (United States)

    Walker, A.; Wookey, J. M.

    2015-12-01

    A key step in studies of seismic anisotropy in the mantle is often the creation of models designed to explain its physical origin. We previously released MSAT (the Matlab Seismic Anisotropy Toolbox), which includes a range of functions that can be used together to build these models and provide geological or geophysical insight given measurements of, for example, shear-wave splitting. Here we describe some of the new features of MSAT that will be included in a new release timed to coincide with the 2015 Fall Meeting. A critical step in testing models of the origin of seismic anisotropy is the determination of the misfit between shear-wave splitting parameters predicted from a model and measured from seismic observations. Is a model that correctly reproduces the delay time "better" than a model that correctly reproduces the fast polarization? We have introduced several new methods that use both parameters to calculate the misfit in a meaningful way and these can be used as part of an inversion scheme in order to find a model that best matches measured shear wave splitting. Our preferred approach involves the creation, "splitting", and "unsplitting" of a test wavelet. A measure of the misfit is then provided by the normalized second eigenvalue of the covariance matrix of particle motion for the two wavelets in a way similar to that used to find splitting parameters from data. This can be used as part of an inverse scheme to find a model that can reproduce a set of shear-wave splitting observations. A second challenge is the interpolation of elastic constants between two known points. Naive element-by-element interpolation can result in anomalous seismic velocities from the interpolated tensor. We introduce an interpolation technique involving both the orientation (defined in terms of the eigenvectors of the dilatational or Voigt stiffness tensor) and magnitude of the two end-member elastic tensors. This permits changes in symmetry between the end-members and removes

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

    Science.gov (United States)

    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

  12. The Handover Toolbox: a knowledge exchange and training platform for improving patient care.

    Science.gov (United States)

    Drachsler, Hendrik; Kicken, Wendy; van der Klink, Marcel; Stoyanov, Slavi; Boshuizen, Henny P A; Barach, Paul

    2012-12-01

    Safe and effective patient handovers remain a global organisational and training challenge. Limited evidence supports available handover training programmes. Customisable training is a promising approach to improve the quality and sustainability of handover training and outcomes. We present a Handover Toolbox designed in the context of the European HANDOVER Project. The Toolbox aims to support physicians, nurses, individuals in health professions training, medical educators and handover experts by providing customised handover training tools for different clinical needs and contexts. The Handover Toolbox uses the Technology Enhanced Learning Design Process (TEL-DP), which encompasses user requirements analysis; writing personas; group concept mapping; analysis of suitable software; plus, minus, interesting rating; and usability testing. TEL-DP is aligned with participatory design approaches and ensures development occurs in close collaboration with, and engagement of, key stakeholders. Application of TEL-DP confirmed that the ideal formats of handover training differs for practicing professionals versus individuals in health profession education programmes. Training experts from different countries differed in their views on the optimal content and delivery of training. Analysis of suitable software identified ready-to-use systems that provide required functionalities and can be further customised to users' needs. Interest rating and usability testing resulted in improved usability, navigation and uptake of the Handover Toolbox. The design of the Handover Toolbox was based on a carefully led stakeholder participatory design using the TEL-DP approach. The Toolbox supports a customisable learning approach that allows trainers to design training that addresses the specific information needs of the various target groups. We offer recommendations regarding the application of the Handover Toolbox to medical educators.

  13. Toolbox for the design of LiNbO3-based passive and active integrated quantum circuits

    Science.gov (United States)

    Sharapova, P. R.; Luo, K. H.; Herrmann, H.; Reichelt, M.; Meier, T.; Silberhorn, C.

    2017-12-01

    We present and discuss perspectives of current developments on advanced quantum optical circuits monolithically integrated in the lithium niobate platform. A set of basic components comprising photon pair sources based on parametric down conversion (PDC), passive routing elements and active electro-optically controllable switches and polarisation converters are building blocks of a toolbox which is the basis for a broad range of diverse quantum circuits. We review the state-of-the-art of these components and provide models that properly describe their performance in quantum circuits. As an example for applications of these models we discuss design issues for a circuit providing on-chip two-photon interference. The circuit comprises a PDC section for photon pair generation followed by an actively controllable modified mach–Zehnder structure for observing Hong–Ou–Mandel interference. The performance of such a chip is simulated theoretically by taking even imperfections of the properties of the individual components into account.

  14. The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data.

    Science.gov (United States)

    Hebart, Martin N; Görgen, Kai; Haynes, John-Dylan

    2014-01-01

    The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns.

  15. The Decoding Toolbox (TDT: A versatile software package for multivariate analyses of functional imaging data

    Directory of Open Access Journals (Sweden)

    Martin Nikolai Hebart

    2015-01-01

    Full Text Available The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns.

  16. Neural Parallel Engine: A toolbox for massively parallel neural signal processing.

    Science.gov (United States)

    Tam, Wing-Kin; Yang, Zhi

    2018-05-01

    Large-scale neural recordings provide detailed information on neuronal activities and can help elicit the underlying neural mechanisms of the brain. However, the computational burden is also formidable when we try to process the huge data stream generated by such recordings. In this study, we report the development of Neural Parallel Engine (NPE), a toolbox for massively parallel neural signal processing on graphical processing units (GPUs). It offers a selection of the most commonly used routines in neural signal processing such as spike detection and spike sorting, including advanced algorithms such as exponential-component-power-component (EC-PC) spike detection and binary pursuit spike sorting. We also propose a new method for detecting peaks in parallel through a parallel compact operation. Our toolbox is able to offer a 5× to 110× speedup compared with its CPU counterparts depending on the algorithms. A user-friendly MATLAB interface is provided to allow easy integration of the toolbox into existing workflows. Previous efforts on GPU neural signal processing only focus on a few rudimentary algorithms, are not well-optimized and often do not provide a user-friendly programming interface to fit into existing workflows. There is a strong need for a comprehensive toolbox for massively parallel neural signal processing. A new toolbox for massively parallel neural signal processing has been created. It can offer significant speedup in processing signals from large-scale recordings up to thousands of channels. Copyright © 2018 Elsevier B.V. All rights reserved.

  17. MATLAB Toolboxes for Reference Electrode Standardization Technique (REST) of Scalp EEG.

    Science.gov (United States)

    Dong, Li; Li, Fali; Liu, Qiang; Wen, Xin; Lai, Yongxiu; Xu, Peng; Yao, Dezhong

    2017-01-01

    Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies.

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

    Science.gov (United States)

    Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka

    2017-09-15

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

  19. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    Science.gov (United States)

    Li, R. N.; Liu, X.; Liu, S. J.

    2013-12-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission.

  20. EXTERNAL VERIFICATION OF THE BUNDLE ADJUSTMENT IN PHOTOGRAMMETRIC SOFTWARE USING THE DAMPED BUNDLE ADJUSTMENT TOOLBOX

    Directory of Open Access Journals (Sweden)

    N. Börlin

    2016-06-01

    Full Text Available The aim of this paper is to investigate whether the Matlab-based Damped Bundle Adjustment Toolbox (DBAT can be used to provide independent verification of the BA computation of two popular software—PhotoModeler (PM and PhotoScan (PS. For frame camera data sets with lens distortion, DBAT is able to reprocess and replicate subsets of PM results with high accuracy. For lens-distortion-free data sets, DBAT can furthermore provide comparative results between PM and PS. Data sets for the discussed projects are available from the authors. The use of an external verification tool such as DBAT will enable users to get an independent verification of the computations of their software. In addition, DBAT can provide computation of quality parameters such as estimated standard deviations, correlation between parameters, etc., something that should be part of best practice for any photogrammetric software. Finally, as the code is free and open-source, users can add computations of their own.

  1. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803.

    Science.gov (United States)

    Immethun, Cheryl M; DeLorenzo, Drew M; Focht, Caroline M; Gupta, Dinesh; Johnson, Charles B; Moon, Tae Seok

    2017-07-01

    Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  2. Optimization design of wind turbine drive train based on Matlab genetic algorithm toolbox

    International Nuclear Information System (INIS)

    Li, R N; Liu, X; Liu, S J

    2013-01-01

    In order to ensure the high efficiency of the whole flexible drive train of the front-end speed adjusting wind turbine, the working principle of the main part of the drive train is analyzed. As critical parameters, rotating speed ratios of three planetary gear trains are selected as the research subject. The mathematical model of the torque converter speed ratio is established based on these three critical variable quantity, and the effect of key parameters on the efficiency of hydraulic mechanical transmission is analyzed. Based on the torque balance and the energy balance, refer to hydraulic mechanical transmission characteristics, the transmission efficiency expression of the whole drive train is established. The fitness function and constraint functions are established respectively based on the drive train transmission efficiency and the torque converter rotating speed ratio range. And the optimization calculation is carried out by using MATLAB genetic algorithm toolbox. The optimization method and results provide an optimization program for exact match of wind turbine rotor, gearbox, hydraulic mechanical transmission, hydraulic torque converter and synchronous generator, ensure that the drive train work with a high efficiency, and give a reference for the selection of the torque converter and hydraulic mechanical transmission

  3. ToolConnect: a functional connectivity toolbox for in vitro networks

    Directory of Open Access Journals (Sweden)

    Vito Paolo Pastore

    2016-03-01

    Full Text Available Nowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent introduction of high-density large-scale Micro-Electrode Arrays (MEAs which have favored the mapping of functional connections and the recordings of the neuronal electrical activity. Although several toolboxes have been implemented to characterize network dynamics and derive functional links, no specifically dedicated software for the management of huge amount of data and direct estimation of functional connectivity maps has been developed. TOOLCONNECT offers the implementation of up to date algorithms and a user-friendly Graphical User Interface (GUI to analyze recorded data from large scale networks. It has been specifically conceived as a computationally efficient open-source software tailored to infer functional connectivity by analyzing the spike trains acquired from in vitro networks coupled to MEAs. In the current version, TOOLCONNECT implements correlation- (cross-correlation, partial-correlation and information theory (joint entropy, transfer entropy based core algorithms, as well as useful and practical add-ons to visualize functional connectivity graphs and extract some topological features. In this work, we present the software, its main features and capabilities together with some demonstrative applications on hippocampal recordings.

  4. ToolConnect: A Functional Connectivity Toolbox for In vitro Networks.

    Science.gov (United States)

    Pastore, Vito Paolo; Poli, Daniele; Godjoski, Aleksandar; Martinoia, Sergio; Massobrio, Paolo

    2016-01-01

    Nowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent introduction of high-density large-scale Micro-Electrode Arrays (MEAs) which have favored the mapping of functional connections and the recordings of the neuronal electrical activity. Although, several toolboxes have been implemented to characterize network dynamics and derive functional links, no specifically dedicated software for the management of huge amount of data and direct estimation of functional connectivity maps has been developed. toolconnect offers the implementation of up to date algorithms and a user-friendly Graphical User Interface (GUI) to analyze recorded data from large scale networks. It has been specifically conceived as a computationally efficient open-source software tailored to infer functional connectivity by analyzing the spike trains acquired from in vitro networks coupled to MEAs. In the current version, toolconnect implements correlation- (cross-correlation, partial-correlation) and information theory (joint entropy, transfer entropy) based core algorithms, as well as useful and practical add-ons to visualize functional connectivity graphs and extract some topological features. In this work, we present the software, its main features and capabilities together with some demonstrative applications on hippocampal recordings.

  5. Travel demand management : a toolbox of strategies to reduce single\\0x2010occupant vehicle trips and increase alternate mode usage in Arizona.

    Science.gov (United States)

    2012-02-01

    The report provides a suite of recommended strategies to reduce single-occupant vehicle traffic in the urban : areas of Phoenix and Tucson, Arizona, which are presented as a travel demand management toolbox. The : toolbox includes supporting research...

  6. LivBioSig: development of a toolbox for online bio-signals processing and experimentation.

    Science.gov (United States)

    Lorrain, T; Niazi, I K; Thibergien, O; Jiang, N; Farina, D

    2011-01-01

    Various research fields, such as brain computer interface, requires online acquisition and analysis of biological data to validate assumptions or to help obtaining insights into the physiological processes of the human body. In this paper we introduce the LivBioSig toolbox for online bio-signals processing and experimentation. This open source and modularized MATLAB toolbox allows performing various experiment paradigms involving online signal processing. These currently include synchronous and asynchronous BCI experiments, and event related stimulation experiments. The use of Graphic User Interfaces (GUI) makes the system suitable even for beginner Matlab users, and the experiments easily configurable. The modularized structure allows advanced users to develop the toolbox further to adapt it to the needs of the research fields.

  7. CerebroMatic: A Versatile Toolbox for Spline-Based MRI Template Creation.

    Science.gov (United States)

    Wilke, Marko; Altaye, Mekibib; Holland, Scott K

    2017-01-01

    Brain image spatial normalization and tissue segmentation rely on prior tissue probability maps. Appropriately selecting these tissue maps becomes particularly important when investigating "unusual" populations, such as young children or elderly subjects. When creating such priors, the disadvantage of applying more deformation must be weighed against the benefit of achieving a crisper image. We have previously suggested that statistically modeling demographic variables, instead of simply averaging images, is advantageous. Both aspects (more vs. less deformation and modeling vs. averaging) were explored here. We used imaging data from 1914 subjects, aged 13 months to 75 years, and employed multivariate adaptive regression splines to model the effects of age, field strength, gender, and data quality. Within the spm/cat12 framework, we compared an affine-only with a low- and a high-dimensional warping approach. As expected, more deformation on the individual level results in lower group dissimilarity. Consequently, effects of age in particular are less apparent in the resulting tissue maps when using a more extensive deformation scheme. Using statistically-described parameters, high-quality tissue probability maps could be generated for the whole age range; they are consistently closer to a gold standard than conventionally-generated priors based on 25, 50, or 100 subjects. Distinct effects of field strength, gender, and data quality were seen. We conclude that an extensive matching for generating tissue priors may model much of the variability inherent in the dataset which is then not contained in the resulting priors. Further, the statistical description of relevant parameters (using regression splines) allows for the generation of high-quality tissue probability maps while controlling for known confounds. The resulting CerebroMatic toolbox is available for download at http://irc.cchmc.org/software/cerebromatic.php.

  8. NeoAnalysis: a Python-based toolbox for quick electrophysiological data processing and analysis.

    Science.gov (United States)

    Zhang, Bo; Dai, Ji; Zhang, Tao

    2017-11-13

    In a typical electrophysiological experiment, especially one that includes studying animal behavior, the data collected normally contain spikes, local field potentials, behavioral responses and other associated data. In order to obtain informative results, the data must be analyzed simultaneously with the experimental settings. However, most open-source toolboxes currently available for data analysis were developed to handle only a portion of the data and did not take into account the sorting of experimental conditions. Additionally, these toolboxes require that the input data be in a specific format, which can be inconvenient to users. Therefore, the development of a highly integrated toolbox that can process multiple types of data regardless of input data format and perform basic analysis for general electrophysiological experiments is incredibly useful. Here, we report the development of a Python based open-source toolbox, referred to as NeoAnalysis, to be used for quick electrophysiological data processing and analysis. The toolbox can import data from different data acquisition systems regardless of their formats and automatically combine different types of data into a single file with a standardized format. In cases where additional spike sorting is needed, NeoAnalysis provides a module to perform efficient offline sorting with a user-friendly interface. Then, NeoAnalysis can perform regular analog signal processing, spike train, and local field potentials analysis, behavioral response (e.g. saccade) detection and extraction, with several options available for data plotting and statistics. Particularly, it can automatically generate sorted results without requiring users to manually sort data beforehand. In addition, NeoAnalysis can organize all of the relevant data into an informative table on a trial-by-trial basis for data visualization. Finally, NeoAnalysis supports analysis at the population level. With the multitude of general-purpose functions provided

  9. Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration.

    Science.gov (United States)

    Wanichthanarak, Kwanjeera; Fan, Sili; Grapov, Dmitry; Barupal, Dinesh Kumar; Fiehn, Oliver

    2017-01-01

    Similar to genomic and proteomic platforms, metabolomic data acquisition and analysis is becoming a routine approach for investigating biological systems. However, computational approaches for metabolomic data analysis and integration are still maturing. Metabox is a bioinformatics toolbox for deep phenotyping analytics that combines data processing, statistical analysis, functional analysis and integrative exploration of metabolomic data within proteomic and transcriptomic contexts. With the number of options provided in each analysis module, it also supports data analysis of other 'omic' families. The toolbox is an R-based web application, and it is freely available at http://kwanjeeraw.github.io/metabox/ under the GPL-3 license.

  10. Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning

    OpenAIRE

    Lemaitre, Guillaume; Nogueira, Fernando; Aridas, Christos K.

    2016-01-01

    International audience; imbalanced-learn is an open-source python toolbox aiming at providing a wide range of methods to cope with the problem of imbalanced dataset frequently encountered in machine learning and pattern recognition. The implemented state-of-the-art methods can be categorized into 4 groups: (i) under-sampling, (ii) over-sampling, (iii) combination of over-and under-sampling, and (iv) ensemble learning methods. The proposed toolbox depends only on numpy, scipy, and scikit-learn...

  11. MLP: a MATLAB toolbox for rapid and reliable auditory threshold estimation.

    Science.gov (United States)

    Grassi, Massimo; Soranzo, Alessandro

    2009-02-01

    In this article, we present MLP, a MATLAB toolbox enabling auditory thresholds estimation via the adaptive maximum likelihood procedure proposed by David Green (1990, 1993). This adaptive procedure is particularly appealing for those psychologists who need to estimate thresholds with a good degree of accuracy and in a short time. Together with a description of the toolbox, the present text provides an introduction to the threshold estimation theory and a theoretical explanation of the maximum likelihood adaptive procedure. MLP comes with a graphical interface, and it is provided with several built-in, classic psychoacoustics experiments ready to use at a mouse click.

  12. ElectroMagnetoEncephalography Software: Overview and Integration with Other EEG/MEG Toolboxes

    Directory of Open Access Journals (Sweden)

    Peter Peyk

    2011-01-01

    Full Text Available EMEGS (electromagnetic encephalography software is a MATLAB toolbox designed to provide novice as well as expert users in the field of neuroscience with a variety of functions to perform analysis of EEG and MEG data. The software consists of a set of graphical interfaces devoted to preprocessing, analysis, and visualization of electromagnetic data. Moreover, it can be extended using a plug-in interface. Here, an overview of the capabilities of the toolbox is provided, together with a simple tutorial for both a standard ERP analysis and a time-frequency analysis. Latest features and future directions of the software development are presented in the final section.

  13. From Images to 3D Models Made Easy

    NARCIS (Netherlands)

    Esteban, I.; Dijk, J.; Groen, F.

    2011-01-01

    FIT3D is a Toolbox built for Matlab that aims at unifying and distributing a set of tools that will allow the researcher to obtain a complete 3D model from a set of calibrated images. In this paper we motivate and present the structure of the toolbox in a tutorial and example based approach. Given

  14. Toolbox for Urban Mobility Simulation: High Resolution Population Dynamics for Global Cities

    Science.gov (United States)

    Bhaduri, B. L.; Lu, W.; Liu, C.; Thakur, G.; Karthik, R.

    2015-12-01

    In this rapidly urbanizing world, unprecedented rate of population growth is not only mirrored by increasing demand for energy, food, water, and other natural resources, but has detrimental impacts on environmental and human security. Transportation simulations are frequently used for mobility assessment in urban planning, traffic operation, and emergency management. Previous research, involving purely analytical techniques to simulations capturing behavior, has investigated questions and scenarios regarding the relationships among energy, emissions, air quality, and transportation. Primary limitations of past attempts have been availability of input data, useful "energy and behavior focused" models, validation data, and adequate computational capability that allows adequate understanding of the interdependencies of our transportation system. With increasing availability and quality of traditional and crowdsourced data, we have utilized the OpenStreetMap roads network, and has integrated high resolution population data with traffic simulation to create a Toolbox for Urban Mobility Simulations (TUMS) at global scale. TUMS consists of three major components: data processing, traffic simulation models, and Internet-based visualizations. It integrates OpenStreetMap, LandScanTM population, and other open data (Census Transportation Planning Products, National household Travel Survey, etc.) to generate both normal traffic operation and emergency evacuation scenarios. TUMS integrates TRANSIMS and MITSIM as traffic simulation engines, which are open-source and widely-accepted for scalable traffic simulations. Consistent data and simulation platform allows quick adaption to various geographic areas that has been demonstrated for multiple cities across the world. We are combining the strengths of geospatial data sciences, high performance simulations, transportation planning, and emissions, vehicle and energy technology development to design and develop a simulation

  15. PEANO, a toolbox for real-time process signal validation and estimation

    International Nuclear Information System (INIS)

    Fantoni, Paolo F.; Figedy, Stefan; Racz, Attila

    1998-02-01

    PEANO (Process Evaluation and Analysis by Neural Operators), a toolbox for real time process signal validation and condition monitoring has been developed. This system analyses the signals, which are e.g. the readings of process monitoring sensors, computes their expected values and alerts if real values are deviated from the expected ones more than limits allow. The reliability level of the current analysis is also produced. The system is based on neuro-fuzzy techniques. Artificial Neural Networks and Fuzzy Logic models can be combined to exploit learning and generalisation capability of the first technique with the approximate reasoning embedded in the second approach. Real-time process signal validation is an application field where the use of this technique can improve the diagnosis of faulty sensors and the identification of outliers in a robust and reliable way. This study implements a fuzzy and possibilistic clustering algorithm to classify the operating region where the validation process has to be performed. The possibilistic approach (rather than probabilistic) allows a ''don't know'' classification that results in a fast detection of unforeseen plant conditions or outliers. Specialised Artificial Neural Networks are used for the validation process, one for each fuzzy cluster in which the operating map has been divided. There are two main advantages in using this technique: the accuracy and generalisation capability is increased compared to the case of a single network working in the entire operating region, and the ability to identify abnormal conditions, where the system is not capable to operate with a satisfactory accuracy, is improved. This model has been tested in a simulated environment on a French PWR, to monitor safety-related reactor variables over the entire power-flow operating map. (author)

  16. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information

    DEFF Research Database (Denmark)

    Hansen, Thomas Mejer; Cordua, Knud Skou; Caroline Looms, Majken

    2013-01-01

    on the solution. The combined states of information (i.e. the solution to the inverse problem) is a probability density function typically referred to as the a posteriori probability density function. We present a generic toolbox for Matlab and Gnu Octave called SIPPI that implements a number of methods...

  17. Building a simulator in the $ mu $ CRL toolbox : a case-study in modern software engineering

    NARCIS (Netherlands)

    H.P. Korver

    1996-01-01

    textabstractIn this paper we report on the current status of our development of a simulator tool in the $mu CRL$ Toolbox. The tool is built from (reusable) software components which are implemented in different languages like C, TCL/TK and ASF+SDF. The components communicate with each other via the

  18. ERPWAVELAB A toolbox for multi-channel analysis of time-frequency transformed event related potentials

    DEFF Research Database (Denmark)

    Mørup, Morten; Hansen, Lars Kai; Arnfred, Sidse M.

    2006-01-01

    decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. Furthermore, the toolbox enables tracking of phase locked activity from one...

  19. ERPWAVELAB a toolbox for multi-channel analysis of time-frequency transformed event related potentials.

    Science.gov (United States)

    Mørup, Morten; Hansen, Lars Kai; Arnfred, Sidse M

    2007-04-15

    The open source toolbox 'ERPWAVELAB' is developed for multi-channel time-frequency analysis of event related activity of EEG and MEG data. The toolbox provides tools for data analysis and visualization of the most commonly used measures of time-frequency transformed event related data as well as data decomposition through non-negative matrix and multi-way (tensor) factorization. The decompositions provided can accommodate additional dimensions like subjects, conditions or repeats and as such they are perfected for group analysis. Furthermore, the toolbox enables tracking of phase locked activity from one channel-time-frequency instance to another as well as tools for artifact rejection in the time-frequency domain. Several other features are highlighted. ERPWAVELAB can freely be downloaded from www.erpwavelab.org, requires EEGLAB [Delorme A, Makeig S. EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis. J Neurosci Meth 2004;134:9-21] and runs under MATLAB (The Mathworks, Inc.).

  20. Cross-species 3D virtual reality toolbox for visual and cognitive experiments.

    Science.gov (United States)

    Doucet, Guillaume; Gulli, Roberto A; Martinez-Trujillo, Julio C

    2016-06-15

    Although simplified visual stimuli, such as dots or gratings presented on homogeneous backgrounds, provide strict control over the stimulus parameters during visual experiments, they fail to approximate visual stimulation in natural conditions. Adoption of virtual reality (VR) in neuroscience research has been proposed to circumvent this problem, by combining strict control of experimental variables and behavioral monitoring within complex and realistic environments. We have created a VR toolbox that maximizes experimental flexibility while minimizing implementation costs. A free VR engine (Unreal 3) has been customized to interface with any control software via text commands, allowing seamless introduction into pre-existing laboratory data acquisition frameworks. Furthermore, control functions are provided for the two most common programming languages used in visual neuroscience: Matlab and Python. The toolbox offers milliseconds time resolution necessary for electrophysiological recordings and is flexible enough to support cross-species usage across a wide range of paradigms. Unlike previously proposed VR solutions whose implementation is complex and time-consuming, our toolbox requires minimal customization or technical expertise to interface with pre-existing data acquisition frameworks as it relies on already familiar programming environments. Moreover, as it is compatible with a variety of display and input devices, identical VR testing paradigms can be used across species, from rodents to humans. This toolbox facilitates the addition of VR capabilities to any laboratory without perturbing pre-existing data acquisition frameworks, or requiring any major hardware changes. Copyright © 2016 Z. All rights reserved.

  1. The Psychometric Toolbox: An Excel Package for Use in Measurement and Psychometrics Courses

    Science.gov (United States)

    Ferrando, Pere J.; Masip-Cabrera, Antoni; Navarro-González, David; Lorenzo-Seva, Urbano

    2017-01-01

    The Psychometric Toolbox (PT) is a user-friendly, non-commercial package mainly intended to be used for instructional purposes in introductory courses of educational and psychological measurement, psychometrics and statistics. The PT package is organized in six separate modules or sub-programs: Data preprocessor (descriptive analyses and data…

  2. An integrated GIS-MARKAL toolbox for designing a CO2 infrastructure network in the Netherlands

    NARCIS (Netherlands)

    van den Broek, M.A.; Brederode, E.; Ramirez, C.A.; Kramers, K.; van der Kuip, M.; Wildenborg, T.; Faaij, A.P.C.; Turkenburg, W.C.

    2009-01-01

    Large-scale implementation of carbon capture and storage needs a whole new infrastructure to transport and store CO2. Tools that can support planning and designing of such infrastructure require incorporation of both temporal and spatial aspects. Therefore, a toolbox that integrates ArcGIS, a

  3. The Electric MondrianTM Toolbox Concept - a Luminescent Solar Concentrator Design Study

    NARCIS (Netherlands)

    van Sark, W.G.J.H.M.; Moraitis, P.

    2016-01-01

    Based on the performance characteristics of luminescent solar concentrator elements of different color and size, a toolbox is developed, which could assist product developers in their design of an Electric Mondrian: an LSC window design that can harvest solar energy to power and charge mobile

  4. Turbulence statistics in a spectral element code: a toolbox for High-Fidelity Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Vinuesa, Ricardo [KTH Mechanics, Stockholm (Sweden); Swedish e-Science Research Center (SeRC), Stockholm (Sweden); Fick, Lambert [Argonne National Lab. (ANL), Argonne, IL (United States); Negi, Prabal [KTH Mechanics, Stockholm (Sweden); Swedish e-Science Research Center (SeRC), Stockholm (Sweden); Marin, Oana [Argonne National Lab. (ANL), Argonne, IL (United States); Merzari, Elia [Argonne National Lab. (ANL), Argonne, IL (United States); Schlatter, Phillip [KTH Mechanics, Stockholm (Sweden); Swedish e-Science Research Center (SeRC), Stockholm (Sweden)

    2017-02-01

    In the present document we describe a toolbox for the spectral-element code Nek5000, aimed at computing turbulence statistics. The toolbox is presented for a small test case, namely a square duct with Lx = 2h, Ly = 2h and Lz = 4h, where x, y and z are the horizontal, vertical and streamwise directions, respectively. The number of elements in the xy-plane is 16 X 16 = 256, and the number of elements in z is 4, leading to a total of 1,204 spectral elements. A polynomial order of N = 5 is chosen, and the mesh is generated using the Nek5000 tool genbox. The toolbox presented here allows to compute mean-velocity components, the Reynolds-stress tensor as well as turbulent kinetic energy (TKE) and Reynolds-stress budgets. Note that the present toolbox allows to compute turbulence statistics in turbulent flows with one homogeneous direction (where the statistics are based on time-averaging as well as averaging in the homogeneous direction), as well as in fully three-dimensional flows (with no periodic directions, where only time-averaging is considered).

  5. Process evaluation of a Toolbox-training program for construction foremen in Denmark

    DEFF Research Database (Denmark)

    Jeschke, Katharina Christiane; Kines, Pete; Rasmussen, Liselotte

    2017-01-01

    Daily dialogue between leaders and workers on traditional construction sites is primarily focused on production, quality and time issues, and rarely involves occupational safety and health (OSH) issues. A leadership training program entitled 'Toolbox-training' was developed to improve constructio...

  6. Improved platform vulnerability/lethality assessment using TNO's toolbox for IM-threat response calculations

    NARCIS (Netherlands)

    Scholtes, J.H.G.; Hooijmeijer, P.A.

    2015-01-01

    A former study was dedicated to relating basic Insensitive Munitions behaviour to an operational context. At TNO, a toolbox with a series of engineering tools has been developed, but improvements are added on a regular bases. These tools focus on the mechanisms that occur in munition articles

  7. Par@Graph - a parallel toolbox for the construction and analysis of large complex climate networks

    NARCIS (Netherlands)

    Tantet, A.J.J.

    2015-01-01

    In this paper, we present Par@Graph, a software toolbox to reconstruct and analyze complex climate networks having a large number of nodes (up to at least 106) and edges (up to at least 1012). The key innovation is an efficient set of parallel software tools designed to leverage the inherited hybrid

  8. ObsPy: A Python Toolbox for Seismology - Recent Developments and Applications

    Science.gov (United States)

    Megies, T.; Krischer, L.; Barsch, R.; Sales de Andrade, E.; Beyreuther, M.

    2014-12-01

    ObsPy (http://www.obspy.org) is a community-driven, open-source project dedicated to building a bridge for seismology into the scientific Python ecosystem. It offersa) read and write support for essentially all commonly used waveform, station, and event metadata file formats with a unified interface,b) a comprehensive signal processing toolbox tuned to the needs of seismologists,c) integrated access to all large data centers, web services and databases, andd) convenient wrappers to legacy codes like libtau and evalresp.Python, currently the most popular language for teaching introductory computer science courses at top-ranked U.S. departments, is a full-blown programming language with the flexibility of an interactive scripting language. Its extensive standard library and large variety of freely available high quality scientific modules cover most needs in developing scientific processing workflows. Together with packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy enables the construction of complete workflows in Python. These vary from reading locally stored data or requesting data from one or more different data centers through to signal analysis and data processing and on to visualizations in GUI and web applications, output of modified/derived data and the creation of publication-quality figures.ObsPy enjoys a large world-wide rate of adoption in the community. Applications successfully using it include time-dependent and rotational seismology, big data processing, event relocations, and synthetic studies about attenuation kernels and full-waveform inversions to name a few examples. All functionality is extensively documented and the ObsPy tutorial and gallery give a good impression of the wide range of possible use cases.We will present the basic features of ObsPy, new developments and applications, and a roadmap for the near future and discuss the sustainability of our open-source development model.

  9. EasyCloneYALI: CRISPR/Cas9-based synthetic toolbox for engineering of the yeast Yarrowia lipolytica

    DEFF Research Database (Denmark)

    Holkenbrink, Carina; Dam, Marie Inger; Kildegaard, Kanchana Rueksomtawin

    2018-01-01

    . Here, we present the EasyCloneYALI genetic toolbox, which allows streamlined strain construction with high genome editing efficiencies in Y. lipolytica via the CRISPR/Cas9 technology. The toolbox allows marker-free integration of gene expression vectors into characterized genome sites as well as marker......-free deletion of genes with the help of CRISPR/Cas9. Genome editing efficiencies above 80% were achieved with transformation protocols using non-replicating DNA repair fragments (such as DNA oligos). Furthermore, the toolbox includes a set of integrative gene expression vectors with prototrophic markers...

  10. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave

    OpenAIRE

    Silva, Ikaro; Moody, George B.

    2014-01-01

    The WaveForm DataBase (WFDB) Toolbox for MATLAB/Octave enables  integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox allows direct loading into MATLAB/Octave's workspace of over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by meta data such as medical annotations of clinical events: arrhythmias, sleep stages, ...

  11. An Open-source Toolbox for Analysing and Processing PhysioNet Databases in MATLAB and Octave

    Directory of Open Access Journals (Sweden)

    Ikaro Silva

    2014-09-01

    Full Text Available The WaveForm DataBase (WFDB Toolbox for MATLAB/Octave enables  integrated access to PhysioNet's software and databases. Using the WFDB Toolbox for MATLAB/Octave, users have access to over 50 physiological databases in PhysioNet. The toolbox allows direct loading into MATLAB/Octave's workspace of over 4 TB of biomedical signals including ECG, EEG, EMG, and PLETH. Additionally, most signals are accompanied by meta data such as medical annotations of clinical events: arrhythmias, sleep stages, seizures, hypotensive episodes, etc. Users of this toolbox should easily be able to reproduce, validate, and compare results published based on PhysioNet's software and databases.

  12. Antiprotozoal drug nitazoxanide enhances parasitemia, tissue lesions and mortality caused by Trypanosoma cruzi in murine model.

    Science.gov (United States)

    Valle-Reyes, Juan Salvador; Melnikov, Valery; Dobrovinskaya, Oxana; Rodriguez-Hernández, Alejandrina; Wookee-Zea, Cristina; Pimientel-Rodrigez, Víctor; Rueda-Valdovinos, Gabriela; Delgado-Enciso, Iván; López-Lemus, Uriel A; Espinoza-Gómez, Francisco

    2017-01-01

    Chagas' disease is caused by unicellular parasite Trypanosoma cruzi (T. cruzi). It is endemic throughout Latin America, but nowadays has become a global challenge due to tourism and migration. Non-treated infection may result in health-threatening complications and lead to death. Current medications for this infection are nifurtimox (NFT) and benznidazol. Both drugs may cause side effects and are ineffective in the chronic phase. Therefore, new antichagasic compounds are urgently required. Nitazoxanide (NTZ) is a broad spectrum antiparasitic drug, proposed recently as a potential candidate to be added to the list of essential medicines for integrated neglected tropical disease control and elimination. Although the effect of NTZ against T. cruzi epimastigotes in vitro was reported, the corresponding experiments in animal models of T. cruzi infection have never been undertaken. The present work was designed to fill this gap and evaluate the effect of NTZ on experimental murine trypanosomiasis, in comparison with classical antichagasic agent NFT. Highly sensitive to T. cruzi BALB/c mice were infected using Albarrada T. cruzi strain, recently isolated in Mexico. Experimental groups were either left untreated, or otherwise treated with NFT, NTZ (100 and 1000 mg/kg), or with both drugs simultaneously. The severity of the infection was estimated based on criteria such as parasitemia, lesions in target tissues (heart, muscles and lungs) and mortality. Despite the expected protective effect, NTZ drastically aggravates the course of T. cruzi infection. Namely, parasitemia, tissue lesions and mortality caused by T. cruzi infection were significantly higher in NTZ-treated mice groups, even in comparison with untreated infected animals. NTZ by itself no produced mortality o tissue damage, and NFT showed an expected protective effect. Our results indicate that NTZ cannot be considered for Chagas' disease treatment. Moreover, NTZ should be used with caution in patients

  13. Wind Turbine Blockset in Matlab/Simulink. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Hansen, A. D.; Soerensen, P.

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines? and it has been used as a general developer tool for other three simulation tools...

  14. Development of a Toolbox for the Implementation of Sustainability in the Product Development Processes at Grundfos Holding A/S

    OpenAIRE

    Pigosso, Daniela Cristina Antelmi; McAloone, Tim C.; Pattis, Anna

    2014-01-01

    Grundfos, one of the world’s leading pump manufacturers, has been actively engaged in sustainability integration into its business over the last decades. This paper presents the approach followed by the company to develop a toolbox that aims to systematically integrate sustainability into the processes for strategic planning, frontloading and product development, following a life cycle approach. The methodology for development, validation and implementation of the toolbox was based on an acti...

  15. Wind Turbine Blockset in Matlab/Simulink - General overview and description of the models

    Energy Technology Data Exchange (ETDEWEB)

    Iov, F.; Hansen, A.D.; Soerensen, P.; Blaabjerg, F.

    2004-03-01

    This report presents a new developed Matlab/Simulink Toolbox for wind turbine applications. This toolbox has been developed during the research project 'Simulation Platform to model, optimize and design wind turbines' and it has been used as a general developer tool for other three simulation tools: Saber, DIgSILENT, HAWC. The report provides first a quick overview over Matlab issues and then explains the structure of the developed toolbox. The attention in the report is mainly drawn to the description of the most important mathematical models, which have been developed in the Toolbox. Then, some simulation results using the developed models are shown. Finally, some general conclusions regarding this new developed Toolbox as well as some directions for future work are made. (au)

  16. Building a symbolic computer algebra toolbox to compute 2D Fourier transforms in polar coordinates.

    Science.gov (United States)

    Dovlo, Edem; Baddour, Natalie

    2015-01-01

    The development of a symbolic computer algebra toolbox for the computation of two dimensional (2D) Fourier transforms in polar coordinates is presented. Multidimensional Fourier transforms are widely used in image processing, tomographic reconstructions and in fact any application that requires a multidimensional convolution. By examining a function in the frequency domain, additional information and insights may be obtained. The advantages of our method include: •The implementation of the 2D Fourier transform in polar coordinates within the toolbox via the combination of two significantly simpler transforms.•The modular approach along with the idea of lookup tables implemented help avoid the issue of indeterminate results which may occur when attempting to directly evaluate the transform.•The concept also helps prevent unnecessary computation of already known transforms thereby saving memory and processing time.

  17. Synthetic biology toolbox for controlling gene expression in the cyanobacterium Synechococcus sp. strain PCC 7002.

    Science.gov (United States)

    Markley, Andrew L; Begemann, Matthew B; Clarke, Ryan E; Gordon, Gina C; Pfleger, Brian F

    2015-05-15

    The application of synthetic biology requires characterized tools to precisely control gene expression. This toolbox of genetic parts previously did not exist for the industrially promising cyanobacterium, Synechococcus sp. strain PCC 7002. To address this gap, two orthogonal constitutive promoter libraries, one based on a cyanobacterial promoter and the other ported from Escherichia coli, were built and tested in PCC 7002. The libraries demonstrated 3 and 2.5 log dynamic ranges, respectively, but correlated poorly with E. coli expression levels. These promoter libraries were then combined to create and optimize a series of IPTG inducible cassettes. The resultant induction system had a 48-fold dynamic range and was shown to out-perform Ptrc constructs. Finally, a RBS library was designed and tested in PCC 7002. The presented synthetic biology toolbox will enable accelerated engineering of PCC 7002.

  18. IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis.

    Science.gov (United States)

    Trevisan, Júlio; Angelov, Plamen P; Scott, Andrew D; Carmichael, Paul L; Martin, Francis L

    2013-04-15

    IRootLab is a free and open-source MATLAB toolbox for vibrational biospectroscopy (VBS) data analysis. It offers an object-oriented programming class library, graphical user interfaces (GUIs) and automatic MATLAB code generation. The class library contains a large number of methods, concepts and visualizations for VBS data analysis, some of which are introduced in the toolbox. The GUIs provide an interface to the class library, including a module to merge several spectral files into a dataset. Automatic code allows developers to quickly write VBS data analysis scripts and is a unique resource among tools for VBS. Documentation includes a manual, tutorials, Doxygen-generated reference and a demonstration showcase. IRootLab can handle some of the most popular file formats used in VBS. License: GNU-LGPL. Official website: http://irootlab.googlecode.com/. Supplementary data are available at Bioinformatics online.

  19. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Directory of Open Access Journals (Sweden)

    Lucian A B Purvis

    Full Text Available In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  20. OXSA: An open-source magnetic resonance spectroscopy analysis toolbox in MATLAB.

    Science.gov (United States)

    Purvis, Lucian A B; Clarke, William T; Biasiolli, Luca; Valkovič, Ladislav; Robson, Matthew D; Rodgers, Christopher T

    2017-01-01

    In vivo magnetic resonance spectroscopy provides insight into metabolism in the human body. New acquisition protocols are often proposed to improve the quality or efficiency of data collection. Processing pipelines must also be developed to use these data optimally. Current fitting software is either targeted at general spectroscopy fitting, or for specific protocols. We therefore introduce the MATLAB-based OXford Spectroscopy Analysis (OXSA) toolbox to allow researchers to rapidly develop their own customised processing pipelines. The toolbox aims to simplify development by: being easy to install and use; seamlessly importing Siemens Digital Imaging and Communications in Medicine (DICOM) standard data; allowing visualisation of spectroscopy data; offering a robust fitting routine; flexibly specifying prior knowledge when fitting; and allowing batch processing of spectra. This article demonstrates how each of these criteria have been fulfilled, and gives technical details about the implementation in MATLAB. The code is freely available to download from https://github.com/oxsatoolbox/oxsa.

  1. A toolbox and sample object perception data for equalization of natural images

    Directory of Open Access Journals (Sweden)

    Wilma A. Bainbridge

    2015-12-01

    Full Text Available For psychologists and neuroscientists, careful selection of their stimuli is essential, so that low-level visual features such as color or spatial frequency do not serve as confounds between conditions of interest. Here, we detail the Natural Image Statistical Toolbox, which allows scientists to measure, visualize, and control stimulus sets along a set of low-level visual properties. Additionally, we provide a set of object images varying along several perceptual object properties, including physical size and interaction envelope size (i.e., the space around an object transversed during an interaction, serving as a test-bed for the Natural Image Statistical Toolbox. This stimulus set is also a highly characterized set useful to psychology and neuroscience studies on object perception.

  2. Ecological Modeling for Military Land Use Decision Support: Interim Progress Report for Ecological Modeling (Project CS/758/4567)

    National Research Council Canada - National Science Library

    Dale, Virginia

    1996-01-01

    .... The ecological models implemented as part of this project are components of the Conservation Thrust's "DoD Land Management Toolbox" and are compatible with the Integrated Dynamic Landscape Analysis and Modeling System ÎDLAMS...

  3. Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum.

    Science.gov (United States)

    Liu, Jiao; Wang, Yu; Lu, Yujiao; Zheng, Ping; Sun, Jibin; Ma, Yanhe

    2017-11-16

    Corynebacterium glutamicum is an important industrial workhorse and advanced genetic engineering tools are urgently demanded. Recently, the clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) have revolutionized the field of genome engineering. The CRISPR/Cas9 system that utilizes NGG as protospacer adjacent motif (PAM) and has good targeting specificity can be developed into a powerful tool for efficient and precise genome editing of C. glutamicum. Herein, we developed a versatile CRISPR/Cas9 genome editing toolbox for C. glutamicum. Cas9 and gRNA expression cassettes were reconstituted to combat Cas9 toxicity and facilitate effective termination of gRNA transcription. Co-transformation of Cas9 and gRNA expression plasmids was exploited to overcome high-frequency mutation of cas9, allowing not only highly efficient gene deletion and insertion with plasmid-borne editing templates (efficiencies up to 60.0 and 62.5%, respectively) but also simple and time-saving operation. Furthermore, CRISPR/Cas9-mediated ssDNA recombineering was developed to precisely introduce small modifications and single-nucleotide changes into the genome of C. glutamicum with efficiencies over 80.0%. Notably, double-locus editing was also achieved in C. glutamicum. This toolbox works well in several C. glutamicum strains including the widely-used strains ATCC 13032 and ATCC 13869. In this study, we developed a CRISPR/Cas9 toolbox that could facilitate markerless gene deletion, gene insertion, precise base editing, and double-locus editing in C. glutamicum. The CRISPR/Cas9 toolbox holds promise for accelerating the engineering of C. glutamicum and advancing its application in the production of biochemicals and biofuels.

  4. Numerical solution of multi groups point kinetic equations by simulink toolbox of Matlab software

    International Nuclear Information System (INIS)

    Hadad, K.; Mohamadi, A.; Sabet, H.; Ayobian, N.; Khani, M.

    2004-01-01

    The simulink toolbox of Matlab Software was employed to solve the point kinetics equation with six group delayed neutrons. The method of Adams-Bash ford showed a good convergence in solving the system of simultaneous equations and the obtained results showed good agreements with other numerical schemes. The flexibility of the package in changing the system parameters and the user friendly interface makes this approach a reliable educational package in revealing the affects of reactivity changes on power incursions

  5. Methanol regulated yeast promoters: production vehicles and toolbox for synthetic biology.

    Science.gov (United States)

    Gasser, Brigitte; Steiger, Matthias G; Mattanovich, Diethard

    2015-12-02

    Promoters are indispensable elements of a standardized parts collection for synthetic biology. Regulated promoters of a wide variety of well-defined induction ratios and expression strengths are highly interesting for many applications. Exemplarily, we discuss the application of published genome scale transcriptomics data for the primary selection of methanol inducible promoters of the yeast Pichia pastoris (Komagataella sp.). Such a promoter collection can serve as an excellent toolbox for cell and metabolic engineering, and for gene expression to produce heterologous proteins.

  6. Orfeo Toolbox: A Free And Open Source Solution For Research And Operational Remote Sensing Projects

    Science.gov (United States)

    Savinaud, Mickael; OTB-CS Team

    2013-12-01

    The free and open source solution, Orfeo ToolBox (OTB), offers the possibility to deal with large data processing. This library designed by CNES in the frame of the ORFEO accompaniment program to promote use of Pleiades data and other VHR data offers now a larger number of applications designed to end users. Due to its modular design, OTB is now used in different context from R&D studies to operational chain.

  7. Poblano v1.0 : a Matlab toolbox for gradient-based optimization.

    Energy Technology Data Exchange (ETDEWEB)

    Dunlavy, Daniel M.; Acar, Evrim (Sandia National Laboratories, Livermore, CA); Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)

    2010-03-01

    We present Poblano v1.0, a Matlab toolbox for solving gradient-based unconstrained optimization problems. Poblano implements three optimization methods (nonlinear conjugate gradients, limited-memory BFGS, and truncated Newton) that require only first order derivative information. In this paper, we describe the Poblano methods, provide numerous examples on how to use Poblano, and present results of Poblano used in solving problems from a standard test collection of unconstrained optimization problems.

  8. Improved platform vulnerability/lethality assessment using TNO's toolbox for IM-threat response calculations

    OpenAIRE

    Scholtes, J.H.G.; Hooijmeijer, P.A.

    2015-01-01

    A former study was dedicated to relating basic Insensitive Munitions behaviour to an operational context. At TNO, a toolbox with a series of engineering tools has been developed, but improvements are added on a regular bases. These tools focus on the mechanisms that occur in munition articles exposed to a range of IM-related threats (bullet, fragment impact, cook-off ) and that transfer the effects from a reacting (donor) munition article to the neighbouring (acceptor) munition articles, focu...

  9. Visualizing flow fields using acoustic Doppler current profilers and the Velocity Mapping Toolbox

    Science.gov (United States)

    Jackson, P. Ryan

    2013-01-01

    The purpose of this fact sheet is to provide examples of how the U.S. Geological Survey is using acoustic Doppler current profilers for much more than routine discharge measurements. These instruments are capable of mapping complex three-dimensional flow fields within rivers, lakes, and estuaries. Using the Velocity Mapping Toolbox to process the ADCP data allows detailed visualization of the data, providing valuable information for a range of studies and applications.

  10. FALCON: A Toolbox for the Fast Contextualisation of Logical Networks.

    OpenAIRE

    De Landtsheer, Sébastien; Trairatphisan, Panuwat; Lucarelli, Philippe; Sauter, Thomas

    2017-01-01

    Motivation: Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results: We have developed a computational approach to contextualise logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions bet...

  11. IV. NIH Toolbox Cognition Battery (CB): measuring language (vocabulary comprehension and reading decoding).

    Science.gov (United States)

    Gershon, Richard C; Slotkin, Jerry; Manly, Jennifer J; Blitz, David L; Beaumont, Jennifer L; Schnipke, Deborah; Wallner-Allen, Kathleen; Golinkoff, Roberta Michnick; Gleason, Jean Berko; Hirsh-Pasek, Kathy; Adams, Marilyn Jager; Weintraub, Sandra

    2013-08-01

    Mastery of language skills is an important predictor of daily functioning and health. Vocabulary comprehension and reading decoding are relatively quick and easy to measure and correlate highly with overall cognitive functioning, as well as with success in school and work. New measures of vocabulary comprehension and reading decoding (in both English and Spanish) were developed for the NIH Toolbox Cognition Battery (CB). In the Toolbox Picture Vocabulary Test (TPVT), participants hear a spoken word while viewing four pictures, and then must choose the picture that best represents the word. This approach tests receptive vocabulary knowledge without the need to read or write, removing the literacy load for children who are developing literacy and for adults who struggle with reading and writing. In the Toolbox Oral Reading Recognition Test (TORRT), participants see a letter or word onscreen and must pronounce or identify it. The examiner determines whether it was pronounced correctly by comparing the response to the pronunciation guide on a separate computer screen. In this chapter, we discuss the importance of language during childhood and the relation of language and brain function. We also review the development of the TPVT and TORRT, including information about the item calibration process and results from a validation study. Finally, the strengths and weaknesses of the measures are discussed. © 2013 The Society for Research in Child Development, Inc.

  12. NIH Toolbox Cognitive Function Battery (CFB): Composite Scores of Crystallized, Fluid, and Overall Cognition

    Science.gov (United States)

    Akshoomoff, Natacha; Beaumont, Jennifer L.; Bauer, Patricia J.; Dikmen, Sureyya; Gershon, Richard; Mungas, Dan; Slotkin, Jerry; Tulsky, David; Weintraub, Sandra; Zelazzo, Philip; Heaton, Robert K.

    2014-01-01

    The NIH Toolbox Cognitive Function Battery (CFB) includes 7 tests covering 8 cognitive abilities considered to be important in adaptive functioning across the lifespan (from early childhood to late adulthood). Here we present data on psychometric characteristics in children (N = 208; ages 3–15 years) of a total summary score and composite scores reflecting two major types of cognitive abilities: “crystallized” (more dependent upon past learning experiences) and “fluid” (capacity for new learning and information processing in novel situations). Both types of cognition are considered important in everyday functioning, but are thought to be differently affected by brain health status throughout life, from early childhood through older adulthood. All three Toolbox composite scores showed excellent test-retest reliability, robust developmental effects across the childhood age range considered here, and strong correlations with established, “gold standard” measures of similar abilities. Additional preliminary evidence of validity includes significant associations between all three Toolbox composite scores and maternal reports of children’s health status and school performance. PMID:23952206

  13. Wind wave analysis in depth limited water using OCEANLYZ, A MATLAB toolbox

    Science.gov (United States)

    Karimpour, Arash; Chen, Qin

    2017-09-01

    There are a number of well established methods in the literature describing how to assess and analyze measured wind wave data. However, obtaining reliable results from these methods requires adequate knowledge on their behavior, strengths and weaknesses. A proper implementation of these methods requires a series of procedures including a pretreatment of the raw measurements, and adjustment and refinement of the processed data to provide quality assurance of the outcomes, otherwise it can lead to untrustworthy results. This paper discusses potential issues in these procedures, explains what parameters are influential for the outcomes and suggests practical solutions to avoid and minimize the errors in the wave results. The procedure of converting the water pressure data into the water surface elevation data, treating the high frequency data with a low signal-to-noise ratio, partitioning swell energy from wind sea, and estimating the peak wave frequency from the weighted integral of the wave power spectrum are described. Conversion and recovery of the data acquired by a pressure transducer, particularly in depth-limited water like estuaries and lakes, are explained in detail. To provide researchers with tools for a reliable estimation of wind wave parameters, the Ocean Wave Analyzing toolbox, OCEANLYZ, is introduced. The toolbox contains a number of MATLAB functions for estimation of the wave properties in time and frequency domains. The toolbox has been developed and examined during a number of the field study projects in Louisiana's estuaries.

  14. STATSLAB: An open-source EEG toolbox for computing single-subject effects using robust statistics.

    Science.gov (United States)

    Campopiano, Allan; van Noordt, Stefon J R; Segalowitz, Sidney J

    2018-03-21

    Research on robust statistics during the past half century provides concrete evidence that classical hypothesis tests that rely on the sample mean and variance are problematic. Even seemingly minor departures from normality are now known to create major problems in terms of increased error rates and decreased power. Fortunately, numerous robust estimation techniques have been developed that circumvent the need for strict assumptions of normality and equal variances, leading to increased power and accuracy when testing hypotheses. Two robust methods that have been shown to have practical value across a wide range of applied situations are the trimmed mean and percentile bootstrap test. To facilitate the uptake of robust methods into the behavioural sciences, especially when dealing with trial-based data such as EEG, we introduce STATSLAB: An open-source EEG toolbox for computing single-subject effects using robust statistics. With the STATSLAB toolbox users can apply the percentile bootstrap test, with trimmed means, to a variety of neural signals including voltages, global field amplitude, and spectral features for both scalp channels and independent components. The toolbox offers a range of analytical strategies and is packaged with a fully functional graphical user interface that includes documentation. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

    Science.gov (United States)

    Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

    2013-01-01

    The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

  16. A participatory approach to design a toolbox to support forest management planning at regional level

    Directory of Open Access Journals (Sweden)

    A.F. Marques

    2013-07-01

    Full Text Available Aim of the study: Forest management planning in a region typically involves multiple stakeholders. Decisions processes are idiosyncratic, driven by individual goals and supported by segmented forest-based information. Nevertheless, stakeholders’ decisions do impact one another leading to complex interaction networks where communication, cooperation and negotiation play a key role. This research addresses the need to develop decision tools to support these roles. Emphasis is on the integration of participatory planning tools and techniques in the architecture of a regional decision support toolbox.Area of the study: The proposed approach was applied in the Chamusca County in Central Portugal although it is easily extended to other regions.Material and methods: This research proposes an Enterprise Architecture methodological approach to design a toolbox that may address distinct stakeholders’ interests and decision processes, while enabling communication, cooperation, negotiation and information sharing among all those involved in the regional interactions network.Main results: the proposed approach was tested in a regional network involving decision processes and information shared by 22 entities clustered into 13 stakeholders groups, including industrial owners, and non-industrial private forestland owners (NIPF - acting individually or grouped into associations and federations -, national and regional offices of the forest authority, forest services providers, non-governmental organizations and research centers. Results suggest that the proposed approach may provide a toolbox that may effectively address stakeholders’ decision processes and goals and support the regional interaction network.Key-words: forest management; multiple stakeholders; decision support systems; enterprise architecture; participatory process.

  17. A participatory approach to design a toolbox to support forest management planning at regional level

    Energy Technology Data Exchange (ETDEWEB)

    Marques, A. F.; Borges, J. G.; Garcia-Gonzalo, J.; Lucas, B.; Melo, I.

    2013-09-01

    Aim of the study: Forest management planning in a region typically involves multiple stake holders. Decisions processes are idiosyncratic, driven by individual goals and supported by segmented forest-based information. Nevertheless, stake holders' decisions do impact one another leading to complex interaction networks where communication, cooperation and negotiation play a key role. This research addresses the need to develop decision tools to support these roles. Emphasis is on the integration of participatory planning tools and techniques in the architecture of a regional decision support toolbox. Area of the study: The proposed approach was applied in the Chamusca County in Central Portugal although it is easily extended to other regions. Material and methods: This research proposes an Enterprise Architecture methodological approach to design a toolbox that may address distinct stake holders' interests and decision processes, while enabling communication, cooperation, negotiation and information sharing among all those involved in the regional interactions network. Main results: the proposed approach was tested in a regional network involving decision processes and information shared by 22 entities clustered into 13 stake holders groups, including industrial owners, and non-industrial private forest land owners (NIPF) acting individually or grouped into associations and federations, national and regional offices of the forest authority, forest services providers, non-governmental organizations and research centers. Results suggest that the proposed approach may provide a toolbox that may effectively address stake holders decision processes and goals and support the regional interaction network. (Author)

  18. An optogenetic toolbox for unbiased discovery of functionally connected cells in neural circuits.

    Science.gov (United States)

    Förster, Dominique; Dal Maschio, Marco; Laurell, Eva; Baier, Herwig

    2017-07-24

    Optical imaging approaches have revolutionized our ability to monitor neural network dynamics, but by themselves are unable to link a neuron's activity to its functional connectivity. We present a versatile genetic toolbox, termed 'Optobow', for all-optical discovery of excitatory connections in vivo. By combining the Gal4-UAS system with Cre/lox recombination, we target the optogenetic actuator ChrimsonR and the sensor GCaMP6 to stochastically labeled, nonoverlapping and sparse subsets of neurons. Photostimulation of single cells using two-photon computer-generated holography evokes calcium responses in downstream neurons. Morphological reconstruction of neurite arbors, response latencies and localization of presynaptic markers suggest that some neuron pairs recorded here are directly connected, while others are two or more synapses apart from each other. With this toolbox, we discover wiring principles between specific cell types in the larval zebrafish tectum. Optobow should be useful for identification and manipulation of networks of interconnected neurons, even in dense neural tissues.Mechanisms of neural processing can only be understood by revealing patterns of connectivity among the cellular components of the circuit. Here the authors report a new genetic toolbox, 'Optobow', which enables simultaneous optogenetic activation of single neurons in zebrafish and measuring the activity of downstream neurons in the network.

  19. ERPLAB: An Open-Source Toolbox for the Analysis of Event-Related Potentials

    Directory of Open Access Journals (Sweden)

    Javier eLopez-Calderon

    2014-04-01

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

  20. The Cementitious Barriers Partnership (CBP) Software Toolbox Capabilities In Assessing The Degradation Of Cementitious Barriers

    Energy Technology Data Exchange (ETDEWEB)

    Flach, G. P. [Savannah River Site (SRS), Aiken, SC (United States); Burns, H. H. [Savannah River Site (SRS), Aiken, SC (United States); Langton, C. [Savannah River Site (SRS), Aiken, SC (United States); Smith, F. G. III [Savannah River Site (SRS), Aiken, SC (United States); Brown, K. G. [Vanderbilt University, Nashville, TN (United States); Kosson, D. S. [Vanderbilt University, Nashville, TN (United States); Garrabrants, A. C. [Vanderbilt University, Nashville, TN (United States); Sarkar, S. [Vanderbilt University, Nashville, TN (United States); van der Sloot, H. [Hans van der Sloot Consultancy (The Netherlands); Meeussen, J. C.L. [Nuclear Research and Consultancy Group, Petten (The Netherlands); Samson, E. [SIMCO Technologies Inc. , 1400, boul. du Parc - Technologique , Suite 203, Quebec (Canada); Mallick, P. [United States Department of Energy, 1000 Independence Ave. SW , Washington, DC (United States); Suttora, L. [United States Department of Energy, 1000 Independence Ave. SW , Washington, DC (United States); Esh, D. W. [U .S. Nuclear Regulatory Commission , Washington, DC (United States); Fuhrmann, M. J. [U .S. Nuclear Regulatory Commission , Washington, DC (United States); Philip, J. [U .S. Nuclear Regulatory Commission , Washington, DC (United States)

    2013-01-11

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy (US DOE) Office of Tank Waste and Nuclear Materials Management. The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that help improve understanding and predictions of the long-term structural, hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program have been used to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance up to 100 years and longer for operating facilities and longer than 1000 years for waste disposal. The CBP Software Toolbox has produced tangible benefits to the DOE Performance Assessment (PA) community. A review of prior DOE PAs has provided a list of potential opportunities for improving cementitious barrier performance predictions through the use of the CBP software tools. These opportunities include: 1) impact of atmospheric exposure to concrete and grout before closure, such as accelerated slag and Tc-99 oxidation, 2) prediction of changes in Kd/mobility as a function of time that result from changing pH and redox conditions, 3) concrete degradation from rebar corrosion due to carbonation, 4) early age cracking from drying and/or thermal shrinkage and 5) degradation due to sulfate attack. The CBP has already had opportunity to provide near-term, tangible support to ongoing DOE-EM PAs such as the Savannah River Saltstone Disposal Facility (SDF) by providing a sulfate attack analysis that predicts the extent and damage that sulfate ingress will have on the concrete vaults over extended time (i.e., > 1000 years). This analysis is one of the many technical opportunities in cementitious barrier performance that can be addressed by the DOE-EM sponsored CBP software

  1. A Python Software Toolbox for the Analysis of SO2 Camera Data. Implications in Geosciences

    Directory of Open Access Journals (Sweden)

    Jonas Gliß

    2017-12-01

    Full Text Available Ultraviolet (UV SO2 cameras have become a common tool to measure and monitor SO2 emission rates, mostly from volcanoes but also from anthropogenic sources (e.g., power plants or ships. Over the past decade, the analysis of UV SO2 camera data has seen many improvements. As a result, for many of the required analysis steps, several alternatives exist today (e.g., cell vs. DOAS based camera calibration; optical flow vs. cross-correlation based gas-velocity retrieval. This inspired the development of Pyplis (Python plume imaging software, an open-source software toolbox written in Python 2.7, which unifies the most prevalent methods from literature within a single, cross-platform analysis framework. Pyplis comprises a vast collection of algorithms relevant for the analysis of UV SO2 camera data. These include several routines to retrieve plume background radiances as well as routines for cell and DOAS based camera calibration. The latter includes two independent methods to identify the DOAS field-of-view (FOV within the camera images (based on (1 Pearson correlation and (2 IFR inversion method. Plume velocities can be retrieved using an optical flow algorithm as well as signal cross-correlation. Furthermore, Pyplis includes a routine to perform a first order correction of the signal dilution effect (also referred to as light dilution. All required geometrical calculations are performed within a 3D model environment allowing for distance retrievals to plume and local terrain features on a pixel basis. SO2 emission rates can be retrieved simultaneously for an arbitrary number of plume intersections. Hence, Pyplis provides a state-of-the-art framework for more efficient and flexible analyses of UV SO2 camera data and, therefore, marks an important step forward towards more transparency, reliability and inter-comparability of the results. Pyplis has been extensively and successfully tested using data from several field campaigns. Here, the main features

  2. GCE Data Toolbox for MATLAB - a software framework for automating environmental data processing, quality control and documentation

    Science.gov (United States)

    Sheldon, W.; Chamblee, J.; Cary, R. H.

    2013-12-01

    developing automated workflows for unattended processing. Finalized data and structured metadata can be exported in a wide variety of text and MATLAB formats or uploaded to a relational database for long-term archiving and distribution. The GCE Data Toolbox can be used as a complete, light-weight solution for environmental data and metadata management, but it can also be used in conjunction with other cyber infrastructure to provide a more comprehensive solution. For example, newly acquired data can be retrieved from a Data Turbine or Campbell LoggerNet Database server for quality control and processing, then transformed to CUAHSI Observations Data Model format and uploaded to a HydroServer for distribution through the CUAHSI Hydrologic Information System. The GCE Data Toolbox can also be leveraged in analytical workflows developed using Kepler or other systems that support MATLAB integration or tool chaining. This software can therefore be leveraged in many ways to help researchers manage, analyze and distribute the data they collect.

  3. Characterisation of Shigella Spa33 and Thermotoga FliM/N reveals a new model for C-ring assembly in T3SS.

    Science.gov (United States)

    McDowell, Melanie A; Marcoux, Julien; McVicker, Gareth; Johnson, Steven; Fong, Yu Hang; Stevens, Rebecca; Bowman, Lesley A H; Degiacomi, Matteo T; Yan, Jun; Wise, Adam; Friede, Miriam E; Benesch, Justin L P; Deane, Janet E; Tang, Christoph M; Robinson, Carol V; Lea, Susan M

    2016-02-01

    Flagellar type III secretion systems (T3SS) contain an essential cytoplasmic-ring (C-ring) largely composed of two proteins FliM and FliN, whereas an analogous substructure for the closely related non-flagellar (NF) T3SS has not been observed in situ. We show that the spa33 gene encoding the putative NF-T3SS C-ring component in Shigella flexneri is alternatively translated to produce both full-length (Spa33-FL) and a short variant (Spa33-C), with both required for secretion. They associate in a 1:2 complex (Spa33-FL/C2) that further oligomerises into elongated arrays in vitro. The structure of Spa33-C2 and identification of an unexpected intramolecular pseudodimer in Spa33-FL reveal a molecular model for their higher order assembly within NF-T3SS. Spa33-FL and Spa33-C are identified as functional counterparts of a FliM-FliN fusion and free FliN respectively. Furthermore, we show that Thermotoga maritima FliM and FliN form a 1:3 complex structurally equivalent to Spa33-FL/C2 , allowing us to propose a unified model for C-ring assembly by NF-T3SS and flagellar-T3SS. © 2015 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

  4. A Monte Carlo-type simulation toolbox for Solar System small body dynamics: Application to the October Draconids

    Science.gov (United States)

    Kastinen, D.; Kero, J.

    2017-09-01

    We present the current status and first results from a Monte Carlo-type simulation toolbox for Solar System small body dynamics. We also present fundamental methods for evaluating the results of this type of simulations using convergence criteria. The calculations consider a body in the Solar System with a mass loss mechanism that generates smaller particles. In our application the body, or parent body, is a comet and the mass loss mechanism is a sublimation process. In order to study mass propagation from parent bodies to Earth, we use the toolbox to sample the uncertainty distributions of relevant comet parameters and to find the resulting Earth influx distributions. The initial distributions considered represent orbital elements, sublimation distance, cometary and meteoroid densities, comet and meteoroid sizes and cometary surface activity. Simulations include perturbations from all major planets, radiation pressure and the Poynting-Robertson effect. In this paper we present the results of an initial software validation performed by producing synthetic versions of the 1933, 1946, 2011 and 2012 October Draconids meteor outbursts and comparing them with observational data and previous models. The synthetic meteor showers were generated by ejecting and propagating material from the recognized parent body of the October Draconids; the comet 21P/Giacobini-Zinner. Material was ejected during 17 perihelion passages between 1866 and 1972. Each perihelion passage was sampled with 50 clones of the parent body, all producing meteoroid streams. The clones were drawn from a multidimensional Gaussian distribution on the orbital elements, with distribution variances proportional to observational uncertainties. In the simulations, each clone ejected 8000 particles. Each particle was assigned an individual weight proportional to the mass loss it represented. This generated a total of 6.7 million test particles, out of which 43 thousand entered the Earth's Hill sphere during 1900

  5. Rat traps: filling the toolbox for manipulating the rat genome

    NARCIS (Netherlands)

    van Boxtel, R.; Cuppen, E.

    2010-01-01

    The laboratory rat is rapidly gaining momentum as a mammalian genetic model organism. Although traditional forward genetic approaches are well established, recent technological developments have enabled efficient gene targeting and mutant generation. Here we outline the current status, possibilities

  6. Construction and evaluation of a Toolbox for the formulation of the Hydrologic component of the Basin Management Plans in Colombia

    Science.gov (United States)

    Garzón, Victor H.; Garzón, Ricardo; Avellaneda, Pedro M.; Rodríguez, Erasmo A.; Alfonso, Leonardo

    2016-10-01

    The Colombian Ministry of Environment, Housing and Territorial Development issued the Policy for Integrated Water Resources Management in 2010, with the formulation of Basin Management Plans (POMCA) as a key component. The main purpose of these plans is to support land use planning and sustainable management of renewable natural resources. Since the announcement of the policy; however, advances in the formulation of POMCAs have been limited, due to the need of generating knowledge and the necessary information to formulate such plans. To contribute to the generation of such knowledge, we developed HidroCHEP: a Toolbox to support the formulation and hydrologic characterization of Colombian basins. In this paper, we report the design, architecture, implementation and use of the toolbox, to understand the climatic variability of the country and to improve predictions in ungauged basins. The use of the toolbox is illustrated and evaluated through its application in three pilot river basins (Pamplonita, Gualí and Ceibas) each with different level of available hydrologic and climatic data. This paper focuses on the use of the toolbox for the development of one of the products required by the technical guide for the formulation of POMCA, in the Pamplonita river basin. Main advantages and disadvantages of its application are evaluated. It is demonstrated that the toolbox has the potential to support the formulation of POMCAs in the country and to contribute to integrated national water resources management.

  7. Construction and evaluation of a Toolbox for the formulation of the Hydrologic component of the Basin Management Plans in Colombia

    Directory of Open Access Journals (Sweden)

    V. H. Garzón

    2016-10-01

    Full Text Available The Colombian Ministry of Environment, Housing and Territorial Development issued the Policy for Integrated Water Resources Management in 2010, with the formulation of Basin Management Plans (POMCA as a key component. The main purpose of these plans is to support land use planning and sustainable management of renewable natural resources. Since the announcement of the policy; however, advances in the formulation of POMCAs have been limited, due to the need of generating knowledge and the necessary information to formulate such plans. To contribute to the generation of such knowledge, we developed HidroCHEP: a Toolbox to support the formulation and hydrologic characterization of Colombian basins. In this paper, we report the design, architecture, implementation and use of the toolbox, to understand the climatic variability of the country and to improve predictions in ungauged basins. The use of the toolbox is illustrated and evaluated through its application in three pilot river basins (Pamplonita, Gualí and Ceibas each with different level of available hydrologic and climatic data. This paper focuses on the use of the toolbox for the development of one of the products required by the technical guide for the formulation of POMCA, in the Pamplonita river basin. Main advantages and disadvantages of its application are evaluated. It is demonstrated that the toolbox has the potential to support the formulation of POMCAs in the country and to contribute to integrated national water resources management.

  8. Toolbox for Research, or how to facilitate a central data management in small-scale research projects.

    Science.gov (United States)

    Bialke, Martin; Rau, Henriette; Thamm, Oliver C; Schuldt, Ronny; Penndorf, Peter; Blumentritt, Arne; Gött, Robert; Piegsa, Jens; Bahls, Thomas; Hoffmann, Wolfgang

    2018-01-25

    In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture systems are too expensive. Consequently, these projects use simple local approaches (e.g. Excel) for data capture instead of a central data management including web-based data capture and proper research databases. This leads to manual processes to merge, analyze and, if possible, pseudonymize research data of different study sites. To support multi-site data capture, storage and analyses in small-scall research projects, corresponding requirements were analyzed within the MOSAIC project. Based on the identified requirements, the Toolbox for Research was developed as a flexible software solution for various research scenarios. Additionally, the Toolbox facilitates data integration of research data as well as metadata by performing necessary procedures automatically. Also, Toolbox modules allow the integration of device data. Moreover, separation of personally identifiable information and medical data by using only pseudonyms for storing medical data ensures the compliance to data protection regulations. This pseudonymized data can then be exported in SPSS format in order to enable scientists to prepare reports and analyses. The Toolbox for Research was successfully piloted in the German Burn Registry in 2016 facilitating the documentation of 4350 burn cases at 54 study sites. The Toolbox for Research can be downloaded free of charge from the project website and automatically installed due to the use of Docker technology.

  9. The Self-Powered Detector Simulation `MATiSSe' Toolbox applied to SPNDs for severe accident monitoring in PWRs

    Science.gov (United States)

    Barbot, Loïc; Villard, Jean-François; Fourrez, Stéphane; Pichon, Laurent; Makil, Hamid

    2018-01-01

    In the framework of the French National Research Agency program on nuclear safety and radioprotection, the `DIstributed Sensing for COrium Monitoring and Safety' project aims at developing innovative instrumentation for corium monitoring in case of severe accident in a Pressurized Water nuclear Reactor. Among others, a new under-vessel instrumentation based on Self-Powered Neutron Detectors is developed using a numerical simulation toolbox, named `MATiSSe'. The CEA Instrumentation Sensors and Dosimetry Lab developed MATiSSe since 2010 for Self-Powered Neutron Detectors material selection and geometry design, as well as for their respective partial neutron and gamma sensitivity calculations. MATiSSe is based on a comprehensive model of neutron and gamma interactions which take place in Selfpowered neutron detector components using the MCNP6 Monte Carlo code. As member of the project consortium, the THERMOCOAX SAS Company is currently manufacturing some instrumented pole prototypes to be tested in 2017. The full severe accident monitoring equipment, including the standalone low current acquisition system, will be tested during a joined CEA-THERMOCOAX experimental campaign in some realistic irradiation conditions, in the Slovenian TRIGA Mark II research reactor.

  10. An educational model for ensemble streamflow simulation and uncertainty analysis

    Directory of Open Access Journals (Sweden)

    A. AghaKouchak

    2013-02-01

    Full Text Available This paper presents the hands-on modeling toolbox, HBV-Ensemble, designed as a complement to theoretical hydrology lectures, to teach hydrological processes and their uncertainties. The HBV-Ensemble can be used for in-class lab practices and homework assignments, and assessment of students' understanding of hydrological processes. Using this modeling toolbox, students can gain more insights into how hydrological processes (e.g., precipitation, snowmelt and snow accumulation, soil moisture, evapotranspiration and runoff generation are interconnected. The educational toolbox includes a MATLAB Graphical User Interface (GUI and an ensemble simulation scheme that can be used for teaching uncertainty analysis, parameter estimation, ensemble simulation and model sensitivity. HBV-Ensemble was administered in a class for both in-class instruction and a final project, and students submitted their feedback about the toolbox. The results indicate that this educational software had a positive impact on students understanding and knowledge of uncertainty in hydrological modeling.

  11. climwin: An R Toolbox for Climate Window Analysis

    Science.gov (United States)

    van de Pol, Martijn

    2016-01-01

    When studying the impacts of climate change, there is a tendency to select climate data from a small set of arbitrary time periods or climate windows (e.g., spring temperature). However, these arbitrary windows may not encompass the strongest periods of climatic sensitivity and may lead to erroneous biological interpretations. Therefore, there is a need to consider a wider range of climate windows to better predict the impacts of future climate change. We introduce the R package climwin that provides a number of methods to test the effect of different climate windows on a chosen response variable and compare these windows to identify potential climate signals. climwin extracts the relevant data for each possible climate window and uses this data to fit a statistical model, the structure of which is chosen by the user. Models are then compared using an information criteria approach. This allows users to determine how well each window explains variation in the response variable and compare model support between windows. climwin also contains methods to detect type I and II errors, which are often a problem with this type of exploratory analysis. This article presents the statistical framework and technical details behind the climwin package and demonstrates the applicability of the method with a number of worked examples. PMID:27973534

  12. MagPy: A Python toolbox for controlling Magstim transcranial magnetic stimulators.

    Science.gov (United States)

    McNair, Nicolas A

    2017-01-30

    To date, transcranial magnetic stimulation (TMS) studies manipulating stimulation parameters have largely used blocked paradigms. However, altering these parameters on a trial-by-trial basis in Magstim stimulators is complicated by the need to send regular (1Hz) commands to the stimulator. Additionally, effecting such control interferes with the ability to send TMS pulses or simultaneously present stimuli with high-temporal precision. This manuscript presents the MagPy toolbox, a Python software package that provides full control over Magstim stimulators via the serial port. It is able to maintain this control with no impact on concurrent processing, such as stimulus delivery. In addition, a specially-designed "QuickFire" serial cable is specified that allows MagPy to trigger TMS pulses with very low-latency. In a series of experimental simulations, MagPy was able to maintain uninterrupted remote control over the connected Magstim stimulator across all testing sessions. In addition, having MagPy enabled had no effect on stimulus timing - all stimuli were presented for precisely the duration specified. Finally, using the QuickFire cable, MagPy was able to elicit TMS pulses with sub-millisecond latencies. The MagPy toolbox allows for experiments that require manipulating stimulation parameters from trial to trial. Furthermore, it can achieve this in contexts that require tight control over timing, such as those seeking to combine TMS with fMRI or EEG. Together, the MagPy toolbox and QuickFire serial cable provide an effective means for controlling Magstim stimulators during experiments while ensuring high-precision timing. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. HERMES: towards an integrated toolbox to characterize functional and effective brain connectivity.

    Science.gov (United States)

    Niso, Guiomar; Bruña, Ricardo; Pereda, Ernesto; Gutiérrez, Ricardo; Bajo, Ricardo; Maestú, Fernando; del-Pozo, Francisco

    2013-10-01

    The analysis of the interdependence between time series has become an important field of research in the last years, mainly as a result of advances in the characterization of dynamical systems from the signals they produce, the introduction of concepts such as generalized and phase synchronization and the application of information theory to time series analysis. In neurophysiology, different analytical tools stemming from these concepts have added to the 'traditional' set of linear methods, which includes the cross-correlation and the coherency function in the time and frequency domain, respectively, or more elaborated tools such as Granger Causality.This increase in the number of approaches to tackle the existence of functional (FC) or effective connectivity (EC) between two (or among many) neural networks, along with the mathematical complexity of the corresponding time series analysis tools, makes it desirable to arrange them into a unified-easy-to-use software package. The goal is to allow neuroscientists, neurophysiologists and researchers from related fields to easily access and make use of these analysis methods from a single integrated toolbox.Here we present HERMES ( http://hermes.ctb.upm.es ), a toolbox for the Matlab® environment (The Mathworks, Inc), which is designed to study functional and effective brain connectivity from neurophysiological data such as multivariate EEG and/or MEG records. It includes also visualization tools and statistical methods to address the problem of multiple comparisons. We believe that this toolbox will be very helpful to all the researchers working in the emerging field of brain connectivity analysis.

  14. The FermiFab toolbox for fermionic many-particle quantum systems

    Science.gov (United States)

    Mendl, Christian B.

    2011-06-01

    This paper introduces the FermiFab toolbox for many-particle quantum systems. It is mainly concerned with the representation of (symbolic) fermionic wavefunctions and the calculation of corresponding reduced density matrices (RDMs). The toolbox transparently handles the inherent antisymmetrization of wavefunctions and incorporates the creation/annihilation formalism. Thus, it aims at providing a solid base for a broad audience to use fermionic wavefunctions with the same ease as matrices in Matlab, say. Leveraging symbolic computation, the toolbox can greatly simply tedious pen-and-paper calculations for concrete quantum mechanical systems, and serves as "sandbox" for theoretical hypothesis testing. FermiFab (including full source code) is freely available as a plugin for both Matlab and Mathematica. Program summaryProgram title:FermiFab Catalogue identifier: AEIN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEIN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Special license provided by the author No. of lines in distributed program, including test data, etc.: 1 165 461 No. of bytes in distributed program, including test data, etc.: 15 557 308 Distribution format: tar.gz Programming language: MATLAB 7.9, Mathematica 7.0, C Computer: PCs, Sun Solaris workstation Operating system: Any platform supporting MATLAB or Mathematica; tested with Windows (32 and 64 bit) and Sun Solaris. RAM: Case dependent Classification: 4.15 Nature of problem: Representation of fermionic wavefunctions, computation of RDMs (reduced density matrices) and handing of the creation/annihilation operator formalism. Solution method: Mapping of Slater determinants to bitfields, implementation of the creation/annihilation and RDM formalism by bit operations. Running time: Depends on the problem size; several seconds for the provided demonstration files.

  15. MICA-A toolbox for masked independent component analysis of fMRI data.

    Science.gov (United States)

    Moher Alsady, Tawfik; Blessing, Esther M; Beissner, Florian

    2016-10-01

    Independent component analysis (ICA) is a widely used technique for investigating functional connectivity (fc) in functional magnetic resonance imaging data. Masked independent component analysis (mICA), that is, ICA restricted to a defined region of interest, has been shown to detect local fc networks in particular brain regions, including the cerebellum, brainstem, posterior cingulate cortex, operculo-insular cortex, hippocampus, and spinal cord. Here, we present the mICA toolbox, an open-source GUI toolbox based on FSL command line tools that performs mICA and related analyses in an integrated way. Functions include automated mask generation from atlases, essential preprocessing, mICA-based parcellation, back-reconstruction of whole-brain fc networks from local ones, and reproducibility analysis. Automated slice-wise calculation and cropping are additional functions that reduce computational time and memory requirements for large analyses. To validate our toolbox, we tested these different functions on the cerebellum, hippocampus, and brainstem, using resting-state and task-based data from the Human Connectome Project. In the cerebellum, mICA detected six local networks together with their whole-brain counterparts, closely replicating previous results. MICA-based parcellation of the hippocampus showed a longitudinally discrete configuration with greater heterogeneity in the anterior hippocampus, consistent with animal and human literature. Finally, brainstem mICA detected motor and sensory nuclei involved in the motor task of tongue movement, thereby replicating and extending earlier results. Hum Brain Mapp 37:3544-3556, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  16. Recent advances of molecular toolbox construction expand Pichia pastoris in synthetic biology applications.

    Science.gov (United States)

    Kang, Zhen; Huang, Hao; Zhang, Yunfeng; Du, Guocheng; Chen, Jian

    2017-01-01

    Pichia pastoris: (reclassified as Komagataella phaffii), a methylotrophic yeast strain has been widely used for heterologous protein production because of its unique advantages, such as readily achievable high-density fermentation, tractable genetic modifications and typical eukaryotic post-translational modifications. More recently, P. pastoris as a metabolic pathway engineering platform has also gained much attention. In this mini-review, we addressed recent advances of molecular toolboxes, including synthetic promoters, signal peptides, and genome engineering tools that established for P. pastoris. Furthermore, the applications of P. pastoris towards synthetic biology were also discussed and prospected especially in the context of genome-scale metabolic pathway analysis.

  17. Cognitive functioning in socially anxious adults: Insights from the NIH Toolbox Cognition Battery

    Directory of Open Access Journals (Sweden)

    Sonya Violet Troller-Renfree

    2015-06-01

    Full Text Available Theory suggests that individuals with social anxiety manifest unique patterns of cognition with less efficient fluid cognition and unperturbed crystallized cognition; however, empirical support for these ideas remains inconclusive. The heterogeneity of past findings may reflect unreliability in cognitive assessments or the influence of confounding variables. The present study examined the relations among social anxiety and performance on the reliable, newly established NIH Toolbox Cognition Battery. Results indicate that high socially anxious adults performed as well as low anxious participants on all measures of fluid cognition. However, highly socially anxious adults demonstrated enhanced crystallized cognitive abilities relative to a low socially anxious comparison group.

  18. ACCEPT: Introduction of the Adverse Condition and Critical Event Prediction Toolbox

    Science.gov (United States)

    Martin, Rodney A.; Santanu, Das; Janakiraman, Vijay Manikandan; Hosein, Stefan

    2015-01-01

    The prediction of anomalies or adverse events is a challenging task, and there are a variety of methods which can be used to address the problem. In this paper, we introduce a generic framework developed in MATLAB (sup registered mark) called ACCEPT (Adverse Condition and Critical Event Prediction Toolbox). ACCEPT is an architectural framework designed to compare and contrast the performance of a variety of machine learning and early warning algorithms, and tests the capability of these algorithms to robustly predict the onset of adverse events in any time-series data generating systems or processes.

  19. Wind Turbine Blockset in Saber. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Timbus, Adrian Vasile; Hansen, A. D.

    This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines?. The report provides a quick overview of the Saber and then explains the structure...... of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed...

  20. Assessing the health status of managed honeybee colonies (HEALTHY-B): a toolbox to facilitate harmonised data collection

    DEFF Research Database (Denmark)

    Nielsen, Søren Saxmose

    2016-01-01

    . Integrating multiple attributes of honeybee health, for instance, via a Health Status Index, is required to support a holistic assessment. Examples are provided on how the toolbox could be used by different stakeholders. Continued interaction between the Member State organisations, the EU Reference Laboratory......Tools are provided to assess the health status of managed honeybee colonies by facilitating further harmonisation of data collection and reporting, design of field surveys across the European Union (EU) and analysis of data on bee health. The toolbox is based on characteristics of a healthy managed...

  1. Development of a Toolbox for the Implementation of Sustainability in the Product Development Processes at Grundfos Holding A/S

    DEFF Research Database (Denmark)

    Pigosso, Daniela Cristina Antelmi; McAloone, Tim C.; Pattis, Anna

    2014-01-01

    and internal processes. The main elements and tools of the SPS toolbox and key learnings within its development are presented in this paper, which can inspire companies in the approach to be followed when developing, customizing and developing new tools for integrating sustainability in their business......Grundfos, one of the world’s leading pump manufacturers, has been actively engaged in sustainability integration into its business over the last decades. This paper presents the approach followed by the company to develop a toolbox that aims to systematically integrate sustainability...

  2. Yeast synthetic biology toolbox and applications for biofuel production.

    Science.gov (United States)

    Tsai, Ching-Sung; Kwak, Suryang; Turner, Timothy L; Jin, Yong-Su

    2015-02-01

    Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

  3. A Toolbox for Optophysiological Experiments in Freely Moving Rats

    Directory of Open Access Journals (Sweden)

    Stefanie Hardung

    2017-05-01

    Full Text Available Simultaneous recordings and manipulations of neural circuits that control the behavior of animals is one of the key techniques in modern neuroscience. Rapid advances in optogenetics have led to a variety of probes combining multichannel readout and optogenetic write in. Given the complexity of the brain, it comes as no surprise that the choice of the device is constrained by several factors such as the animal model, the structure and location of the brain area of interest, as well as the behavioral read out. Here we provide an overview of available devices for chronic simultaneous neural recordings and optogenetic manipulation in awake behaving rats. We focus on two fixed arrays and two moveable drives. For both options, we present data from one custom-made (in house and one commercially available device. Here we provide evidence that simultaneous neural recordings and optogenetic manipulations are feasible with all four tested devices. Further we give detailed information about the recording quality, and also contrast the different features of the probes. As we provide detailed information about equipment and building procedures for combined chronic multichannel readout and optogenetic control with maximum performance at minimized costs, this overview might help especially researchers who want to enter the field of in vivo optophysiology.

  4. PreSurgMapp: a MATLAB Toolbox for Presurgical Mapping of Eloquent Functional Areas Based on Task-Related and Resting-State Functional MRI.

    Science.gov (United States)

    Huang, Huiyuan; Ding, Zhongxiang; Mao, Dewang; Yuan, Jianhua; Zhu, Fangmei; Chen, Shuda; Xu, Yan; Lou, Lin; Feng, Xiaoyan; Qi, Le; Qiu, Wusi; Zhang, Han; Zang, Yu-Feng

    2016-10-01

    The main goal of brain tumor surgery is to maximize tumor resection while minimizing the risk of irreversible postoperative functional sequelae. Eloquent functional areas should be delineated preoperatively, particularly for patients with tumors near eloquent areas. Functional magnetic resonance imaging (fMRI) is a noninvasive technique that demonstrates great promise for presurgical planning. However, specialized data processing toolkits for presurgical planning remain lacking. Based on several functions in open-source software such as Statistical Parametric Mapping (SPM), Resting-State fMRI Data Analysis Toolkit (REST), Data Processing Assistant for Resting-State fMRI (DPARSF) and Multiple Independent Component Analysis (MICA), here, we introduce an open-source MATLAB toolbox named PreSurgMapp. This toolbox can reveal eloquent areas using comprehensive methods and various complementary fMRI modalities. For example, PreSurgMapp supports both model-based (general linear model, GLM, and seed correlation) and data-driven (independent component analysis, ICA) methods and processes both task-based and resting-state fMRI data. PreSurgMapp is designed for highly automatic and individualized functional mapping with a user-friendly graphical user interface (GUI) for time-saving pipeline processing. For example, sensorimotor and language-related components can be automatically identified without human input interference using an effective, accurate component identification algorithm using discriminability index. All the results generated can be further evaluated and compared by neuro-radiologists or neurosurgeons. This software has substantial value for clinical neuro-radiology and neuro-oncology, including application to patients with low- and high-grade brain tumors and those with epilepsy foci in the dominant language hemisphere who are planning to undergo a temporal lobectomy.

  5. SPP Toolbox: Supporting Sustainable Public Procurement in the Context of Socio-Technical Transitions

    Directory of Open Access Journals (Sweden)

    Paula Cayolla Trindade

    2017-12-01

    Full Text Available Public procurement can shape production and consumption trends and represents a stimulus for both innovation and diversification in products and services, through a direct increase in demand. In recent years, the interest in demand-side policies has grown and several approaches have emerged, such as Green Public Procurement (GPP, Sustainable Public Procurement (SPP and Public Procurement of Innovation (PPI, representing strategic goals to be achieved through public procurement. In this context, there is a need to guide and support public organizations in the uptake of GPP, SPP and PPI practices. To respond to the challenges raised by the operationalization of such strategies, this paper proposes a new tool—the SPP Toolbox—for guiding public organizations as they re-think the procurement process, raising their ambitions and broadening their vision, thus changing the organizational approach towards culture, strategies, structures and practices. This toolbox integrates insights from GPP, SPP and PPI objectives and practices, in the context of the emergence of socio-technical transitions. The toolbox coherently links GPP, SPP and PPI, allowing flexibility in terms of goals, yet promoting an increasing complexity of institutionalized practices and skills—from GPP to SPP and then from SPP to PPI, organized in a framework fully integrated into the organizational strategy.

  6. NeAT: a toolbox for the analysis of biological networks, clusters, classes and pathways

    Science.gov (United States)

    Brohée, Sylvain; Faust, Karoline; Lima-Mendez, Gipsi; Sand, Olivier; Janky, Rekin's; Vanderstocken, Gilles; Deville, Yves; van Helden, Jacques

    2008-01-01

    The network analysis tools (NeAT) (http://rsat.ulb.ac.be/neat/) provide a user-friendly web access to a collection of modular tools for the analysis of networks (graphs) and clusters (e.g. microarray clusters, functional classes, etc.). A first set of tools supports basic operations on graphs (comparison between two graphs, neighborhood of a set of input nodes, path finding and graph randomization). Another set of programs makes the connection between networks and clusters (graph-based clustering, cliques discovery and mapping of clusters onto a network). The toolbox also includes programs for detecting significant intersections between clusters/classes (e.g. clusters of co-expression versus functional classes of genes). NeAT are designed to cope with large datasets and provide a flexible toolbox for analyzing biological networks stored in various databases (protein interactions, regulation and metabolism) or obtained from high-throughput experiments (two-hybrid, mass-spectrometry and microarrays). The web interface interconnects the programs in predefined analysis flows, enabling to address a series of questions about networks of interest. Each tool can also be used separately by entering custom data for a specific analysis. NeAT can also be used as web services (SOAP/WSDL interface), in order to design programmatic workflows and integrate them with other available resources. PMID:18524799

  7. The Hordeum Toolbox: The Barley Coordinated Agricultural Project Genotype and Phenotype Resource

    Directory of Open Access Journals (Sweden)

    Victoria C. Blake

    2012-07-01

    Full Text Available The use of DNA markers in public sector plant breeding is now the norm. Such markers are common across breeding programs and this commonality enables and enhances collaboration. Therefore, large collaborative research projects that measure several phenotypes across multiple environments coupled with the expanding amount of genotype data attainable with current marker technologies are on the rise and these projects demand efficient data delivery. However, development of computational tools for advanced data integration, visualization, and analysis is still a bottleneck, even though these resources have the greatest potential impact for users who are extracting and developing hypothesis-based solutions. The Hordeum Toolbox (THT was developed as a data resource for the Barley Coordinated Agricultural Project (CAP with the novel capability of constructing user-defined downloadable sets of phenotype and/or genotype data for downstream analysis. Internal tools in THT enable users to create clusters of a selected group of lines based on genotype data, parse pedigrees, and select germplasm based on haplotype, phenotype, and agronomic properties. The Hordeum Toolbox can be adapted to breeding programs or collaborations to assist researchers in germplasm selection, genotype data visualization, and the integration of complex data sets for statistical analysis.

  8. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Science.gov (United States)

    Römer, Michael; Eichner, Johannes; Dräger, Andreas; Wrzodek, Clemens; Wrzodek, Finja; Zell, Andreas

    2016-01-01

    Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT) Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  9. KNIME4NGS: a comprehensive toolbox for Next Generation Sequencing analysis.

    Science.gov (United States)

    Hastreiter, Maximilian; Jeske, Tim; Hoser, Jonathan; Kluge, Michael; Ahomaa, Kaarin; Friedl, Marie-Sophie; Kopetzky, Sebastian J; Quell, Jan-Dominik; Werner Mewes, H-; Küffner, Robert

    2017-01-09

    Analysis of Next Generation Sequencing (NGS) data requires the processing of large datasets by chaining various tools with complex input and output formats. In order to automate data analysis, we propose to standardize NGS tasks into modular workflows. This simplifies reliable handling and processing of NGS data, and corresponding solutions become substantially more reproducible and easier to maintain. Here, we present a documented, linux-based, toolbox of 42 processing modules that are combined to construct workflows facilitating a variety of tasks such as DNAseq and RNAseq analysis. We also describe important technical extensions. The high throughput executor (HTE) helps to increase the reliability and to reduce manual interventions when processing complex datasets. We also provide a dedicated binary manager that assists users in obtaining the modules' executables and keeping them up to date. As basis for this actively developed toolbox we use the workflow management software KNIME. See http://ibisngs.github.io/knime4ngs for nodes and user manual (GPLv3 license) CONTACT: robert.kueffner@helmholtz-muenchen.de. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  10. ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

    Directory of Open Access Journals (Sweden)

    Michael Römer

    Full Text Available Bioinformatics analysis has become an integral part of research in biology. However, installation and use of scientific software can be difficult and often requires technical expert knowledge. Reasons are dependencies on certain operating systems or required third-party libraries, missing graphical user interfaces and documentation, or nonstandard input and output formats. In order to make bioinformatics software easily accessible to researchers, we here present a web-based platform. The Center for Bioinformatics Tuebingen (ZBIT Bioinformatics Toolbox provides web-based access to a collection of bioinformatics tools developed for systems biology, protein sequence annotation, and expression data analysis. Currently, the collection encompasses software for conversion and processing of community standards SBML and BioPAX, transcription factor analysis, and analysis of microarray data from transcriptomics and proteomics studies. All tools are hosted on a customized Galaxy instance and run on a dedicated computation cluster. Users only need a web browser and an active internet connection in order to benefit from this service. The web platform is designed to facilitate the usage of the bioinformatics tools for researchers without advanced technical background. Users can combine tools for complex analyses or use predefined, customizable workflows. All results are stored persistently and reproducible. For each tool, we provide documentation, tutorials, and example data to maximize usability. The ZBIT Bioinformatics Toolbox is freely available at https://webservices.cs.uni-tuebingen.de/.

  11. An open-source toolbox for standardized use of PhysioNet Sleep EDF Expanded Database.

    Science.gov (United States)

    Imtiaz, Syed Anas; Rodriguez-Villegas, Esther

    2015-01-01

    PhysioNet Sleep EDF database has been the most popular source of data used for developing and testing many automatic sleep staging algorithms. However, the recordings from this database has been used in an inconsistent fashion. For example, arbitrary selection of start and end times from long term recordings, data-hypnogram mismatches, different performance metrics and hypnogram conversion from R&K to AASM. All these differences result in different data sections and performance metrics being used by researchers thereby making any direct comparison between algorithms very difficult. Recently, a superset of this database has been made available on PhysioNet, known as the Sleep EDF Expanded Database which includes 61 recordings. This provides an opportunity to standardize the way in which signals from this database should be used. With this goal in mind, we present in this paper a toolbox for automatically downloading and extracting recordings from the Sleep EDF Expanded database and converting them to a suitable format for use in MATLAB. This toolbox contains functions for selecting appropriate data for sleep analysis (based on our previous recommendations for sleep staging), hypnogram conversion and computation of performance metrics. Its use makes it simpler to start using the new sleep database and also provides a foundation for much-needed standardization in this research field.

  12. BOLDSync: a MATLAB-based toolbox for synchronized stimulus presentation in functional MRI.

    Science.gov (United States)

    Joshi, Jitesh; Saharan, Sumiti; Mandal, Pravat K

    2014-02-15

    Precise and synchronized presentation of paradigm stimuli in functional magnetic resonance imaging (fMRI) is central to obtaining accurate information about brain regions involved in a specific task. In this manuscript, we present a new MATLAB-based toolbox, BOLDSync, for synchronized stimulus presentation in fMRI. BOLDSync provides a user friendly platform for design and presentation of visual, audio, as well as multimodal audio-visual (AV) stimuli in functional imaging experiments. We present simulation experiments that demonstrate the millisecond synchronization accuracy of BOLDSync, and also illustrate the functionalities of BOLDSync through application to an AV fMRI study. BOLDSync gains an advantage over other available proprietary and open-source toolboxes by offering a user friendly and accessible interface that affords both precision in stimulus presentation and versatility across various types of stimulus designs and system setups. BOLDSync is a reliable, efficient, and versatile solution for synchronized stimulus presentation in fMRI study. Copyright © 2013 Elsevier B.V. All rights reserved.

  13. Robust correlation analyses: false positive and power validation using a new open source matlab toolbox.

    Science.gov (United States)

    Pernet, Cyril R; Wilcox, Rand; Rousselet, Guillaume A

    2012-01-01

    Pearson's correlation measures the strength of the association between two variables. The technique is, however, restricted to linear associations and is overly sensitive to outliers. Indeed, a single outlier can result in a highly inaccurate summary of the data. Yet, it remains the most commonly used measure of association in psychology research. Here we describe a free Matlab((R)) based toolbox (http://sourceforge.net/projects/robustcorrtool/) that computes robust measures of association between two or more random variables: the percentage-bend correlation and skipped-correlations. After illustrating how to use the toolbox, we show that robust methods, where outliers are down weighted or removed and accounted for in significance testing, provide better estimates of the true association with accurate false positive control and without loss of power. The different correlation methods were tested with normal data and normal data contaminated with marginal or bivariate outliers. We report estimates of effect size, false positive rate and power, and advise on which technique to use depending on the data at hand.

  14. Computational testing for automated preprocessing: a Matlab toolbox to enable large scale electroencephalography data processing

    Directory of Open Access Journals (Sweden)

    Benjamin U. Cowley

    2017-03-01

    Full Text Available Electroencephalography (EEG is a rich source of information regarding brain function. However, the preprocessing of EEG data can be quite complicated, due to several factors. For example, the distinction between true neural sources and noise is indeterminate; EEG data can also be very large. The various factors create a large number of subjective decisions with consequent risk of compound error. Existing tools present the experimenter with a large choice of analysis methods. Yet it remains a challenge for the researcher to integrate methods for batch-processing of the average large datasets, and compare methods to choose an optimal approach across the many possible parameter configurations. Additionally, many tools still require a high degree of manual decision making for, e.g. the classification of artefacts in channels, epochs or segments. This introduces extra subjectivity, is slow and is not reproducible. Batching and well-designed automation can help to regularise EEG preprocessing, and thus reduce human effort, subjectivity and consequent error. We present the computational testing for automated preprocessing (CTAP toolbox, to facilitate: (i batch-processing that is easy for experts and novices alike; (ii testing and manual comparison of preprocessing methods. CTAP extends the existing data structure and functions from the well-known EEGLAB toolbox, based on Matlab and produces extensive quality control outputs. CTAP is available under MIT licence from https://github.com/bwrc/ctap.

  15. Sentinel-3 SAR Altimetry Toolbox - Scientific Exploitation of Operational Missions (SEOM) Program Element

    Science.gov (United States)

    Benveniste, Jérôme; Lucas, Bruno; Dinardo, Salvatore

    2014-05-01

    The prime objective of the SEOM (Scientific Exploitation of Operational Missions) element is to federate, support and expand the large international research community that the ERS, ENVISAT and the Envelope programmes have build up over the last 20 years for the future European operational Earth Observation missions, the Sentinels. Sentinel-3 builds directly on a proven heritage pioneered by ERS-1, ERS-2, Envisat and CryoSat-2, with a dual-frequency (Ku and C band) advanced Synthetic Aperture Radar Altimeter (SRAL) that provides measurements at a resolution of ~300m in SAR mode along track. Sentinel-3 will provide exact measurements of sea-surface height along with accurate topography measurements over sea ice, ice sheets, rivers and lakes. The first of the Sentinel-3 series is planned for launch in early 2015. The current universal altimetry toolbox is BRAT (Basic Radar Altimetry Toolbox) which can read all previous and current altimetry mission's data, but it does not have the capabilities to read the upcoming Sentinel-3 L1 and L2 products. ESA will endeavour to develop and supply this capability to support the users of the future Sentinel-3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales, the French Space Agency), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats, the BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with Matlab/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as net

  16. Wind turbine blockset in Saber. General overview and description of the models

    DEFF Research Database (Denmark)

    Iov, Florin; Timbus, Adrian Vasile; Hansen, Anca Daniela

    This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project “Simulation Platform to model, optimize and design wind turbines”. The report provides a quick overview of the Saber and then explains the structure...... of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed...... blocks. Since the developed models are based on Saber built-in blocks, a description of the libraries from Saber is given. Then some simulation results using the developed models are shown. Finally some general conclusions regarding this new developed Toolbox as well as some directions for future work...

  17. Wind Turbine Blockset in Saber. General Overview and Description of the Model

    DEFF Research Database (Denmark)

    Iov, Florin; Timbus, Adrian Vasile; Hansen, A. D.

    This report presents a new developed Saber Toolbox for wind turbine applications. This toolbox has been developed during the research project ?Simulation Platform to model, optimize and design wind turbines?. The report provides a quick overview of the Saber and then explains the structure...... of this simulation package, which is different than other tools e.g. Matlab/Simulink. Then the structure of the toolbox is shown as well as the description of the developed models. The main focus here is to underline the special structure of the models, which are a mixture of Saber built-in blocks and new developed...... blocks. Since the developed models are based on Saber built-in blocks, a description of the libraries from Saber is given. Then some simulation results using the developed models are shown. Finally some general conclusions regarding this new developed Toolbox as well as some directions for future work...

  18. A molecular toolbox for rapid generation of viral vectors to up- or down-regulate in vivo neuronal gene expression

    Directory of Open Access Journals (Sweden)

    Melanie D. White

    2011-07-01

    Full Text Available We introduce a molecular toolbox for manipulation of neuronal gene expression in vivo. The toolbox includes promoters, ion channels, optogenetic tools, fluorescent proteins and intronic artificial microRNAs. The components are easily assembled into adeno-associated virus (AAV or lentivirus vectors using recombination cloning. We demonstrate assembly of toolbox components into lentivirus and AAV vectors and use these vectors for in vivo expression of inwardly rectifying potassium channels (Kir2.1, Kir3.1 and Kir3.2 and an artificial microRNA targeted against the ion channel HCN1 (HCN1 miR. We show that AAV assembled to express HCN1 miR produces efficacious and specific in vivo knockdown of HCN1 channels. Comparison of in vivo viral transduction using HCN1 miR with mice containing a germ line deletion of HCN1 reveals similar physiological phenotypes in cerebellar Purkinje cells. The easy assembly and re-usability of the toolbox components, together with the ability to up- or down-regulate neuronal gene expression in vivo, may be useful for applications in many areas of neuroscience.

  19. SAINTS toolbox

    DEFF Research Database (Denmark)

    Petersen, Anders

    2000-01-01

    En virtuel redskabskasse der bl.a. indeholder materiale om forretningsmodeller, analysemodeller, cases, WebQuests mm.......En virtuel redskabskasse der bl.a. indeholder materiale om forretningsmodeller, analysemodeller, cases, WebQuests mm....

  20. Cementitious Barriers Partnership (CBP): Using the CBP Software Toolbox to Simulate Sulfate Attack and Carbonation of Concrete Structures - 13481

    International Nuclear Information System (INIS)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S.; Flach, G.; Langton, C.; Smith, F.G.III; Burns, H.; Van der Sloot, H.; Meeussen, J.C.L.; Seignette, P.F.A.B.; Samson, E.; Mallick, P.; Suttora, L.; Esh, D.; Fuhrmann, M.; Philip, J.

    2013-01-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy Office of Tank Waste Management. The CBP project has developed a set of integrated modeling tools and leaching test methods to help improve understanding and prediction of the long-term hydraulic and chemical performance of cementitious materials used in nuclear applications. State-of-the-art modeling tools, including LeachXS TM /ORCHESTRA and STADIUM R , were selected for their demonstrated abilities to simulate reactive transport and degradation in cementitious materials. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF), now adopted as part of the SW-846 RCRA methods, have been used to help make the link between modeling and experiment. Although each of the CBP tools has demonstrated utility as a standalone product, coupling the models over relevant spatial and temporal solution domains can provide more accurate predictions of cementitious materials behavior over relevant periods of performance. The LeachXS TM /ORCHESTRA and STADIUM R models were first linked to the GoldSim Monte Carlo simulator to better and more easily characterize model uncertainties and as a means to coupling the models allowing linking to broader performance assessment evaluations that use CBP results for a source term. Two important degradation scenarios were selected for initial demonstration: sulfate ingress / attack and carbonation of cementitious materials. When sufficient sulfate is present in the pore solution external to a concrete barrier, sulfate can diffuse into the concrete, react with the concrete solid phases, and cause cracking that significantly changes the transport and structural properties of the concrete. The penetration of gaseous carbon dioxide within partially saturated concrete usually initiates a series of carbonation reactions with

  1. Cementitious Barriers Partnership (CBP): Using the CBP Software Toolbox to Simulate Sulfate Attack and Carbonation of Concrete Structures - 13481

    Energy Technology Data Exchange (ETDEWEB)

    Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.; Sarkar, S. [Vanderbilt University, School of Engineering, CRESP, Nashville, TN 37235 (United States); Flach, G.; Langton, C.; Smith, F.G.III; Burns, H. [Savannah River National Laboratory, Aiken, SC 29808 (United States); Van der Sloot, H. [Hans Van der Sloot Consultancy, Dorpsstraat 216, 1721BV Langedijk (Netherlands); Meeussen, J.C.L. [Nuclear Research and Consultancy Group, Westerduinweg 3, Petten (Netherlands); Seignette, P.F.A.B. [Energy Research Center of The Netherlands, Petten (Netherlands); Samson, E. [SIMCO Technologies, Inc., Quebec (Canada); Mallick, P.; Suttora, L. [U.S. Department of Energy, Washington, DC (United States); Esh, D.; Fuhrmann, M.; Philip, J. [U.S. Nuclear Regulatory Commission, Washington, DC (United States)

    2013-07-01

    The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the U.S. Department of Energy Office of Tank Waste Management. The CBP project has developed a set of integrated modeling tools and leaching test methods to help improve understanding and prediction of the long-term hydraulic and chemical performance of cementitious materials used in nuclear applications. State-of-the-art modeling tools, including LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R}, were selected for their demonstrated abilities to simulate reactive transport and degradation in cementitious materials. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF), now adopted as part of the SW-846 RCRA methods, have been used to help make the link between modeling and experiment. Although each of the CBP tools has demonstrated utility as a standalone product, coupling the models over relevant spatial and temporal solution domains can provide more accurate predictions of cementitious materials behavior over relevant periods of performance. The LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} models were first linked to the GoldSim Monte Carlo simulator to better and more easily characterize model uncertainties and as a means to coupling the models allowing linking to broader performance assessment evaluations that use CBP results for a source term. Two important degradation scenarios were selected for initial demonstration: sulfate ingress / attack and carbonation of cementitious materials. When sufficient sulfate is present in the pore solution external to a concrete barrier, sulfate can diffuse into the concrete, react with the concrete solid phases, and cause cracking that significantly changes the transport and structural properties of the concrete. The penetration of gaseous carbon dioxide within partially saturated concrete usually initiates a series of carbonation

  2. The GridCAT: A Toolbox for Automated Analysis of Human Grid Cell Codes in fMRI

    Directory of Open Access Journals (Sweden)

    Matthias Stangl

    2017-07-01

    Full Text Available Human functional magnetic resonance imaging (fMRI studies examining the putative firing of grid cells (i.e., the grid code suggest that this cellular mechanism supports not only spatial navigation, but also more abstract cognitive processes. Despite increased interest in this research, there remain relatively few human grid code studies, perhaps due to the complex analysis methods, which are not included in standard fMRI analysis packages. To overcome this, we have developed the Matlab-based open-source Grid Code Analysis Toolbox (GridCAT, which performs all analyses, from the estimation and fitting of the grid code in the general linear model (GLM, to the generation of grid code metrics and plots. The GridCAT, therefore, opens up this cutting-edge research area by allowing users to analyze data by means of a simple and user-friendly graphical user interface (GUI. Researchers confident with programming can edit the open-source code and use example scripts accompanying the GridCAT to implement their own analysis pipelines. Here, we review the current literature in the field of fMRI grid code research with particular focus on the different analysis options that have been implemented, which we describe in detail. Key features of the GridCAT are demonstrated via analysis of an example dataset, which is also provided online together with a detailed manual, so that users can replicate the results presented here, and explore the GridCAT’s functionality. By making the GridCAT available to the wider neuroscience community, we believe that it will prove invaluable in elucidating the role of grid codes in higher-order cognitive processes.

  3. PREVIEW Behavior Modification Intervention Toolbox (PREMIT): A Study Protocol for a Psychological Element of a Multicenter Project.

    Science.gov (United States)

    Kahlert, Daniela; Unyi-Reicherz, Annelie; Stratton, Gareth; Meinert Larsen, Thomas; Fogelholm, Mikael; Raben, Anne; Schlicht, Wolfgang

    2016-01-01

    Losing excess body weight and preventing weight regain by changing lifestyle is a challenging but promising task to prevent the incidence of type-2 diabetes. To be successful, it is necessary to use evidence-based and theory-driven interventions, which also contribute to the science of behavior modification by providing a deeper understanding of successful intervention components. To develop a physical activity and dietary behavior modification intervention toolbox (PREMIT) that fulfills current requirements of being theory-driven and evidence-based, comprehensively described and feasible to evaluate. PREMIT is part of an intervention trial, which aims to prevent the onset of type-2 diabetes in pre-diabetics in eight clinical centers across the world by guiding them in changing their physical activity and dietary behavior through a group counseling approach. The program development took five progressive steps, in line with the Public Health Action Cycle: (1) Summing-up the intervention goal(s), target group and the setting, (2) uncovering the generative psychological mechanisms, (3) identifying behavior change techniques and tools, (4) preparing for evaluation and (5) implementing the intervention and assuring quality. PREMIT is based on a trans-theoretical approach referring to valid behavior modification theories, models and approaches. A major "product" of PREMIT is a matrix, constructed for use by onsite-instructors. The matrix includes objectives, tasks and activities ordered by periods. PREMIT is constructed to help instructors guide participants' behavior change. To ensure high fidelity and adherence of program-implementation across the eight intervention centers standardized operational procedures were defined and "train-the-trainer" workshops were held. In summary PREMIT is a theory-driven, evidence-based program carefully developed to change physical activity and dietary behaviors in pre-diabetic people.

  4. PREVIEW behavior modification intervention toolbox (PREMIT: a study protocol for a psychological element of a multicenter project

    Directory of Open Access Journals (Sweden)

    Daniela Kahlert

    2016-08-01

    Full Text Available Background: Losing excess body weight and preventing weight regain by changing lifestyle is a challenging but promising task to prevent the incidence of type-2 diabetes. To be successful, it is necessary to use evidence-based and theory-driven interventions, which also contribute to the science of behavior modification by providing a deeper understanding of successful intervention components. Objective: To develop a physical activity and dietary behavior modification intervention toolbox (PREMIT that fulfills current requirements of being theory-driven and evidence-based, comprehensively described and feasible to evaluate. PREMIT is part of an intervention trial, which aims to prevent the onset of type-2 diabetes in pre-diabetics in eight clinical centers across the world by guiding them in changing their physical activity and dietary behavior through a group counselling approach. Methods: The program development took five progressive steps, in line with the Public Health Action Cycle: (1 Summing-up the intervention goal(s, target group and the setting, (2 uncovering the generative psychological mechanisms, (3 identifying behavior change techniques and tools, (4 preparing for evaluation and (5 implementing the intervention and assuring quality. Results: PREMIT is based on a trans-theoretical approach referring to valid behavior modification theories, models and approaches. A major ‘product’ of PREMIT is a matrix, constructed for use by onsite-instructors. The matrix includes objectives, tasks and activities ordered by periods. PREMIT is constructed to help instructors guide participant’s behavior change. To ensure high fidelity and adherence of program-implementation across the eight intervention centers standardized operational procedures were defined and train-the-trainer workshops were held. In summary PREMIT is a theory-driven, evidence-based program carefully developed to change physical activity and dietary behaviors in pre

  5. A Rapid Aeroelastic/Aeroservoelastic Modeling, Analysis and Optimization System for Advanced Flight Vehicles, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Stirling Dynamics Inc and the University of Washington propose to develop a MATLAB toolbox for rapid aeroelastic (AE) and aeroservoelastic (ASE) modeling, analysis...

  6. Mobile Context Toolbox - an extensible context framework for S60 mobile phones

    DEFF Research Database (Denmark)

    Larsen, Jakob Eg; Jensen, Kristian

    2009-01-01

    We describe an open framework utilizing sensors and application data on S60 mobile phones enabling rapid prototyping of context-aware mobile applications. The framework has an extensible layered architecture allowing new sensors and features to be added to the context framework as they become...... available on mobile phone platforms. The framework provides access to multiple sensors to derive user context, and we present results from experiments with two prototype applications built using the toolbox. Initial experiments have been carried out to validate the data obtained by the tool....... In the experiments 14 participants have been continuously using a Nokia N95 mobile phone with a context logger application for an average of 48 days per user and covering 70% of the time. The study has provided valuable insights into the performance issues of the system in real-life usage situations, including...

  7. Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology.

    Science.gov (United States)

    Liu, Gang; Puri, Apurv; Neelamegham, Sriram

    2013-02-01

    Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported. The software package including source code, help documentation and demonstrations are available at http://sourceforge.net/projects/gnatmatlab/files/.

  8. Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology

    Science.gov (United States)

    Liu, Gang; Neelamegham, Sriram

    2013-01-01

    Summary: Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported. Availability: The software package including source code, help documentation and demonstrations are available at http://sourceforge.net/projects/gnatmatlab/files/. Contact: neel@buffalo.edu or gangliu@buffalo.edu PMID:23230149

  9. Sonification and visualization of predecisional information search: Identifying toolboxes in children.

    Science.gov (United States)

    Betsch, Tilmann; Wünsche, Kirsten; Großkopf, Armin; Schröder, Klara; Stenmans, Rachel

    2018-03-01

    Prior evidence has suggested that preschoolers and elementary schoolers search information largely with no systematic plan when making decisions in probabilistic environments. However, this finding might be due to the insensitivity of standard classification methods that assume a lack of variance in decision strategies for tasks of the same kind. Using a novel approach, we explore strategy variability in existing data that documented unsystematic searches in children (Betsch, Lehmann, Lindow, Lang, & Schoemann, 2016). By means of sonification and visualizations, we identified combinations of search patterns that children employed systematically. In contrast to adult controls, there was no dominating strategy in children. Rather, they used a limited number of strategies (toolboxes) and switched between them over a series of trials belonging to the same type of decision task. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  10. NIH Toolbox Cognition Battery (NIHTB-CB): list sorting test to measure working memory.

    Science.gov (United States)

    Tulsky, David S; Carlozzi, Noelle; Chiaravalloti, Nancy D; Beaumont, Jennifer L; Kisala, Pamela A; Mungas, Dan; Conway, Kevin; Gershon, Richard

    2014-07-01

    The List Sorting Working Memory Test was designed to assess working memory (WM) as part of the NIH Toolbox Cognition Battery. List Sorting is a sequencing task requiring children and adults to sort and sequence stimuli that are presented visually and auditorily. Validation data are presented for 268 participants ages 20 to 85 years. A subset of participants (N=89) was retested 7 to 21 days later. As expected, the List Sorting Test had moderately high correlations with other measures of working memory and executive functioning (convergent validity) but a low correlation with a test of receptive vocabulary (discriminant validity). Furthermore, List Sorting demonstrates expected changes over the age span and has excellent test-retest reliability. Collectively, these results provide initial support for the construct validity of the List Sorting Working Memory Measure as a measure of working memory. However, the relationship between the List Sorting Test and general executive function has yet to be determined.

  11. aBEAT: A Toolbox for Consistent Analysis of Longitudinal Adult Brain MRI

    Science.gov (United States)

    Dai, Yakang; Wang, Yaping; Wang, Li; Wu, Guorong; Shi, Feng; Shen, Dinggang

    2013-01-01

    Longitudinal brain image analysis is critical for revealing subtle but complex structural and functional changes of brain during aging or in neurodevelopmental disease. However, even with the rapid increase of clinical research and trials, a software toolbox dedicated for longitudinal image analysis is still lacking publicly. To cater for this increasing need, we have developed a dedicated 4D Adult Brain Extraction and Analysis Toolbox (aBEAT) to provide robust and accurate analysis of the longitudinal adult brain MR images. Specially, a group of image processing tools were integrated into aBEAT, including 4D brain extraction, 4D tissue segmentation, and 4D brain labeling. First, a 4D deformable-surface-based brain extraction algorithm, which can deform serial brain surfaces simultaneously under temporal smoothness constraint, was developed for consistent brain extraction. Second, a level-sets-based 4D tissue segmentation algorithm that incorporates local intensity distribution, spatial cortical-thickness constraint, and temporal cortical-thickness consistency was also included in aBEAT for consistent brain tissue segmentation. Third, a longitudinal groupwise image registration framework was further integrated into aBEAT for consistent ROI labeling by simultaneously warping a pre-labeled brain atlas to the longitudinal brain images. The performance of aBEAT has been extensively evaluated on a large number of longitudinal MR T1 images which include normal and dementia subjects, achieving very promising results. A Linux-based standalone package of aBEAT is now freely available at http://www.nitrc.org/projects/abeat. PMID:23577105

  12. aBEAT: a toolbox for consistent analysis of longitudinal adult brain MRI.

    Directory of Open Access Journals (Sweden)

    Yakang Dai

    Full Text Available Longitudinal brain image analysis is critical for revealing subtle but complex structural and functional changes of brain during aging or in neurodevelopmental disease. However, even with the rapid increase of clinical research and trials, a software toolbox dedicated for longitudinal image analysis is still lacking publicly. To cater for this increasing need, we have developed a dedicated 4D Adult Brain Extraction and Analysis Toolbox (aBEAT to provide robust and accurate analysis of the longitudinal adult brain MR images. Specially, a group of image processing tools were integrated into aBEAT, including 4D brain extraction, 4D tissue segmentation, and 4D brain labeling. First, a 4D deformable-surface-based brain extraction algorithm, which can deform serial brain surfaces simultaneously under temporal smoothness constraint, was developed for consistent brain extraction. Second, a level-sets-based 4D tissue segmentation algorithm that incorporates local intensity distribution, spatial cortical-thickness constraint, and temporal cortical-thickness consistency was also included in aBEAT for consistent brain tissue segmentation. Third, a longitudinal groupwise image registration framework was further integrated into aBEAT for consistent ROI labeling by simultaneously warping a pre-labeled brain atlas to the longitudinal brain images. The performance of aBEAT has been extensively evaluated on a large number of longitudinal MR T1 images which include normal and dementia subjects, achieving very promising results. A Linux-based standalone package of aBEAT is now freely available at http://www.nitrc.org/projects/abeat.

  13. EEGVIS: A MATLAB toolbox for browsing, exploring, and viewing large datasets

    Directory of Open Access Journals (Sweden)

    Kay A Robbins

    2012-05-01

    Full Text Available Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/ eegvis.

  14. EEGVIS: A MATLAB Toolbox for Browsing, Exploring, and Viewing Large Datasets.

    Science.gov (United States)

    Robbins, Kay A

    2012-01-01

    Recent advances in data monitoring and sensor technology have accelerated the acquisition of very large data sets. Streaming data sets from instrumentation such as multi-channel EEG recording usually must undergo substantial pre-processing and artifact removal. Even when using automated procedures, most scientists engage in laborious manual examination and processing to assure high quality data and to indentify interesting or problematic data segments. Researchers also do not have a convenient method of method of visually assessing the effects of applying any stage in a processing pipeline. EEGVIS is a MATLAB toolbox that allows users to quickly explore multi-channel EEG and other large array-based data sets using multi-scale drill-down techniques. Customizable summary views reveal potentially interesting sections of data, which users can explore further by clicking to examine using detailed viewing components. The viewer and a companion browser are built on our MoBBED framework, which has a library of modular viewing components that can be mixed and matched to best reveal structure. Users can easily create new viewers for their specific data without any programming during the exploration process. These viewers automatically support pan, zoom, resizing of individual components, and cursor exploration. The toolbox can be used directly in MATLAB at any stage in a processing pipeline, as a plug-in for EEGLAB, or as a standalone precompiled application without MATLAB running. EEGVIS and its supporting packages are freely available under the GNU general public license at http://visual.cs.utsa.edu/eegvis.

  15. BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases.

    Science.gov (United States)

    Jamialahmadi, Oveis; Motamedian, Ehsan; Hashemi-Najafabadi, Sameereh

    2016-10-18

    Development of an interface tool between the Biochemical, Genetic and Genomic (BiGG) and KEGG databases is necessary for simultaneous access to the features of both databases. For this purpose, we present the BiKEGG toolbox, an open source COBRA toolbox extension providing a set of functions to infer the reaction correspondences between the KEGG reaction identifiers and those in the BiGG knowledgebase using a combination of manual verification and computational methods. Inferred reaction correspondences using this approach are supported by evidence from the literature, which provides a higher number of reconciled reactions between these two databases compared to the MetaNetX and MetRxn databases. This set of equivalent reactions is then used to automatically superimpose the predicted fluxes using COBRA methods on classical KEGG pathway maps or to create a customized metabolic map based on the KEGG global metabolic pathway, and to find the corresponding reactions in BiGG based on the genome annotation of an organism in the KEGG database. Customized metabolic maps can be created for a set of pathways of interest, for the whole KEGG global map or exclusively for all pathways for which there exists at least one flux carrying reaction. This flexibility in visualization enables BiKEGG to indicate reaction directionality as well as to visualize the reaction fluxes for different static or dynamic conditions in an animated manner. BiKEGG allows the user to export (1) the output visualized metabolic maps to various standard image formats or save them as a video or animated GIF file, and (2) the equivalent reactions for an organism as an Excel spreadsheet.

  16. RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO DRINKING WATER CONTAMINATION THREATS AND INCIDENTS. MODULE 1: WATER UTILITIES PLANNING GUIDE - INTERIM FINAL - DECEMBER 2003

    Science.gov (United States)

    The interim final Response Protocol Toolbox: Planning for and Responding to Contamination Threats to Drinking Water Systems is designed to help the water sector effectively and appropriately respond to intentional contamination threats and incidents. It was produced by EPA, buil...

  17. UAS-NAS Live Virtual Constructive Distributed Environment (LVC): LVC Gateway, Gateway Toolbox, Gateway Data Logger (GDL), SaaProc Software Design Description

    Science.gov (United States)

    Jovic, Srboljub

    2015-01-01

    This document provides the software design description for the two core software components, the LVC Gateway, the LVC Gateway Toolbox, and two participants, the LVC Gateway Data Logger and the SAA Processor (SaaProc).

  18. Load forecasting using different architectures of neural networks with the assistance of the MATLAB toolboxes; Previsao de cargas eletricas utilizando diferentes arquiteturas de redes neurais artificiais com o auxilio das toolboxes do MATLAB

    Energy Technology Data Exchange (ETDEWEB)

    Nose Filho, Kenji; Araujo, Klayton A.M.; Maeda, Jorge L.Y.; Lotufo, Anna Diva P. [Universidade Estadual Paulista Julio de Mesquita Filho (UNESP), Ilha Solteira, SP (Brazil)], Emails: kenjinose@yahoo.com.br, klayton_ama@hotmail.com, jorge-maeda@hotmail.com, annadiva@dee.feis.unesp.br

    2009-07-01

    This paper presents a development and implementation of a program to electrical load forecasting with data from a Brazilian electrical company, using four different architectures of neural networks of the MATLAB toolboxes: multilayer backpropagation gradient descendent with momentum, multilayer backpropagation Levenberg-Marquardt, adaptive network based fuzzy inference system and general regression neural network. The program presented a satisfactory performance, guaranteeing very good results. (author)

  19. From black box to toolbox: Outlining device functionality, engagement activities, and the pervasive information architecture of mHealth interventions

    Directory of Open Access Journals (Sweden)

    Brian G. Danaher

    2015-03-01

    Full Text Available mHealth interventions that deliver content via mobile phones represent a burgeoning area of health behavior change. The current paper examines two themes that can inform the underlying design of mHealth interventions: (1 mobile device functionality, which represents the technological toolbox available to intervention developers; and (2 the pervasive information architecture of mHealth interventions, which determines how intervention content can be delivered concurrently using mobile phones, personal computers, and other devices. We posit that developers of mHealth interventions will be able to better achieve the promise of this burgeoning arena by leveraging the toolbox and functionality of mobile devices in order to engage participants and encourage meaningful behavior change within the context of a carefully designed pervasive information architecture.

  20. A Multi-Point, Boundary-Value Problem, Collocation Toolbox for the Continuation of sets of Constrained Orbit Segments

    DEFF Research Database (Denmark)

    Dankowicz, Harry; Schilder, Frank

    This paper presents a collocation toolbox for multi-point, boundary-value problems. This toolbox has been recently developed by the authors to support general-purpose parameter continuation of sets of constrained orbit segments, such as i) segmented trajectories in hybrid dynamical systems......, for example, mechanical systems with impacts, friction, and switching control, ii) homoclinic orbits represented by an equilibrium point and a finite-time trajectory that starts and ends near this equilibrium point, and iii) collections of trajectories that represent quasi-periodic invariant tori...... the continuation of families of periodic orbits in a hybrid dynamical system with impacts and friction as well as detection and constrained continuation of selected degeneracies characteristic of such systems, such as grazing and switching-sliding bifurcations....

  1. Multirate Flutter Suppression System Design for the Benchmark Active Controls Technology Wing. Part 2; Methodology Application Software Toolbox

    Science.gov (United States)

    Mason, Gregory S.; Berg, Martin C.; Mukhopadhyay, Vivek

    2002-01-01

    To study the effectiveness of various control system design methodologies, the NASA Langley Research Center initiated the Benchmark Active Controls Project. In this project, the various methodologies were applied to design a flutter suppression system for the Benchmark Active Controls Technology (BACT) Wing. This report describes the user's manual and software toolbox developed at the University of Washington to design a multirate flutter suppression control law for the BACT wing.

  2. Demonstration of a Fractured Rock Geophysical Toolbox (FRGT) for Characterization and Monitoring of DNAPL Biodegradation in Fractured Rock Aquifers

    Science.gov (United States)

    2016-01-01

    USER’S GUIDE Demonstration of a Fractured Rock Geophysical Toolbox (FRGT) for Characterization and Monitoring of DNAPL Biodegradation in...Fractured Rock Aquifers ESTCP Project ER-201118 JANUARY 2016 F.D. Day-Lewis C.D. Johnson U. S. Geological Survey, Office of Groundwater...RESPONSIBLE PERSON 19b. TELEPHONE NUMBER (Include area code) 01/01/2016 Guidance July 2011 - January 2016 Demonstration of a Fractured Rock Geophysical

  3. The Clinician's Toolbox: Assessing the Sexual Impacts of Cancer on Adolescents and Young Adults with Cancer (AYAC

    Directory of Open Access Journals (Sweden)

    Sylvie Aubin, PhD

    2015-09-01

    Conclusion: Cancer can have a significant impact on numerous domains of AYAC sexuality. The assessment of and attention to the impact of sexuality on AYAC is crucial in order to provide effective and comprehensive quality patient cancer care. Aubin S and Perez S. The clinician's toolbox: assessing the sexual impacts of cancer on adolescents and young adults with cancer (AYAC. Sex Med 2015;3:198–212.

  4. Using GPI-2 for distributed memory paralleliziation of the caffe toolbox to speed up deep neural network training

    OpenAIRE

    Kühn, Martin; Keuper, Janis; Pfreundt, Franz-Josef

    2017-01-01

    Deep Neural Network (DNN) are currently of great inter- est in research and application. The training of these net- works is a compute intensive and time consuming task. To reduce training times to a bearable amount at reasonable cost we extend the popular Caffe toolbox for DNN with an efficient distributed memory communication pattern. To achieve good scalability we emphasize the overlap of computation and communication and prefer fine granu- lar synchronization patterns over global barriers...

  5. Image processing and pattern recognition with CVIPtools MATLAB toolbox: automatic creation of masks for veterinary thermographic images

    Science.gov (United States)

    Mishra, Deependra K.; Umbaugh, Scott E.; Lama, Norsang; Dahal, Rohini; Marino, Dominic J.; Sackman, Joseph

    2016-09-01

    CVIPtools is a software package for the exploration of computer vision and image processing developed in the Computer Vision and Image Processing Laboratory at Southern Illinois University Edwardsville. CVIPtools is available in three variants - a) CVIPtools Graphical User Interface, b) CVIPtools C library and c) CVIPtools MATLAB toolbox, which makes it accessible to a variety of different users. It offers students, faculty, researchers and any user a free and easy way to explore computer vision and image processing techniques. Many functions have been implemented and are updated on a regular basis, the library has reached a level of sophistication that makes it suitable for both educational and research purposes. In this paper, the detail list of the functions available in the CVIPtools MATLAB toolbox are presented and how these functions can be used in image analysis and computer vision applications. The CVIPtools MATLAB toolbox allows the user to gain practical experience to better understand underlying theoretical problems in image processing and pattern recognition. As an example application, the algorithm for the automatic creation of masks for veterinary thermographic images is presented.

  6. TopoToolbox: Using Sensor Topography to Calculate Psychologically Meaningful Measures from Event-Related EEG/MEG

    Directory of Open Access Journals (Sweden)

    Xing Tian

    2011-01-01

    Full Text Available The open-source toolbox “TopoToolbox” is a suite of functions that use sensor topography to calculate psychologically meaningful measures (similarity, magnitude, and timing from multisensor event-related EEG and MEG data. Using a GUI and data visualization, TopoToolbox can be used to calculate and test the topographic similarity between different conditions (Tian and Huber, 2008. This topographic similarity indicates whether different conditions involve a different distribution of underlying neural sources. Furthermore, this similarity calculation can be applied at different time points to discover when a response pattern emerges (Tian and Poeppel, 2010. Because the topographic patterns are obtained separately for each individual, these patterns are used to produce reliable measures of response magnitude that can be compared across individuals using conventional statistics (Davelaar et al. Submitted and Huber et al., 2008. TopoToolbox can be freely downloaded. It runs under MATLAB (The MathWorks, Inc. and supports user-defined data structure as well as standard EEG/MEG data import using EEGLAB (Delorme and Makeig, 2004.

  7. Development of a broad-host synthetic biology toolbox for Ralstonia eutropha and its application to engineering hydrocarbon biofuel production.

    Science.gov (United States)

    Bi, Changhao; Su, Peter; Müller, Jana; Yeh, Yi-Chun; Chhabra, Swapnil R; Beller, Harry R; Singer, Steven W; Hillson, Nathan J

    2013-11-13

    The chemoautotrophic bacterium Ralstonia eutropha can utilize H2/CO2 for growth under aerobic conditions. While this microbial host has great potential to be engineered to produce desired compounds (beyond polyhydroxybutyrate) directly from CO2, little work has been done to develop genetic part libraries to enable such endeavors. We report the development of a toolbox for the metabolic engineering of Ralstonia eutropha H16. We have constructed a set of broad-host-range plasmids bearing a variety of origins of replication, promoters, 5' mRNA stem-loop structures, and ribosomal binding sites. Specifically, we analyzed the origins of replication pCM62 (IncP), pBBR1, pKT (IncQ), and their variants. We tested the promoters P(BAD), T7, P(xyls/PM), P(lacUV5), and variants thereof for inducible expression. We also evaluated a T7 mRNA stem-loop structure sequence and compared a set of ribosomal binding site (RBS) sequences derived from Escherichia coli, R. eutropha, and a computational RBS design tool. Finally, we employed the toolbox to optimize hydrocarbon production in R. eutropha and demonstrated a 6-fold titer improvement using the appropriate combination of parts. We constructed and evaluated a versatile synthetic biology toolbox for Ralstonia eutropha metabolic engineering that could apply to other microbial hosts as well.

  8. PLDAPS: A Hardware Architecture and Software Toolbox for Neurophysiology Requiring Complex Visual Stimuli and Online Behavioral Control.

    Science.gov (United States)

    Eastman, Kyler M; Huk, Alexander C

    2012-01-01

    Neurophysiological studies in awake, behaving primates (both human and non-human) have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed a MATLAB toolbox that integrates several modern pieces of equipment, but still grants experimenters the flexibility of a high-level programming language. Our toolbox takes advantage of three popular and powerful technologies: the Plexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas, TX, USA), a Datapixx peripheral (Vpixx Technologies, Saint-Bruno, QC, Canada) for control of analog, digital, and video input-output signals, and the Psychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997; Pelli, 1997; Kleiner et al., 2007). The PLDAPS ("Platypus") system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  9. Development of a versatile Cas9-driven subpopulation-selection toolbox inLactococcus lactis.

    Science.gov (United States)

    van der Els, Simon; James, Jennelle K; Kleerebezem, Michiel; Bron, Peter A

    2018-02-16

    CRISPR-Cas9 technology has been exploited for the removal or replacement of genetic elements in a wide range of prokaryotes and eukaryotes. Here we describe the extension of the Cas9 application toolbox to the industrially important dairy species Lactococcus lactis The Cas9 expression vector pLABTarget was constructed, encoding the Streptocccus pyogenes Cas9 under control of a constitutive promoter, and allowing plug and play introduction of sgRNA sequences to target specific genetic loci. Introduction of a pepN -targeting derivative of pLABTarget into L. lactis MG1363 led to a strong reduction in the number of transformants obtained, which did not occur in a pepN deletion derivative of the same strain, demonstrating the specificity and lethality of the Cas9 mediated double strand breaks in the lactococcal chromosome. Moreover, the same pLABTarget derivative allowed the selection of a pepN deletion subpopulation from its corresponding single crossover plasmid integrant precursor, accelerating the construction and selection of gene-specific deletion derivatives in L. lactis Finally, pLABTarget containing sgRNAs designed to target mobile genetic elements, allowed the effective curing of plasmids, prophages and integrative conjugative elements (ICE). These results establish that pLABTarget enables the effective exploitation of Cas9 targeting in L. lactis , while the broad host range vector used suggests that this toolbox could be readily expanded to other Gram-positive bacteria. Significance statement Mobile genetic elements in Lactococcus lactis and other lactic acid bacteria play an important role in dairy fermentation, having both positive and detrimental effects during the production of fermented dairy products. The pLABTarget vector offers an efficient cloning platform for Cas9 application in lactic acid bacteria. Targeting Cas9 towards mobile genetic elements enabled their effective curing, which is of particular interest in the context of potentially

  10. An Educational Model for Hands-On Hydrology Education

    Science.gov (United States)

    AghaKouchak, A.; Nakhjiri, N.; Habib, E. H.

    2014-12-01

    This presentation provides an overview of a hands-on modeling tool developed for students in civil engineering and earth science disciplines to help them learn the fundamentals of hydrologic processes, model calibration, sensitivity analysis, uncertainty assessment, and practice conceptual thinking in solving engineering problems. The toolbox includes two simplified hydrologic models, namely HBV-EDU and HBV-Ensemble, designed as a complement to theoretical hydrology lectures. The models provide an interdisciplinary application-oriented learning environment that introduces the hydrologic phenomena through the use of a simplified conceptual hydrologic model. The toolbox can be used for in-class lab practices and homework assignments, and assessment of students' understanding of hydrological processes. Using this modeling toolbox, students can gain more insights into how hydrological processes (e.g., precipitation, snowmelt and snow accumulation, soil moisture, evapotranspiration and runoff generation) are interconnected. The educational toolbox includes a MATLAB Graphical User Interface (GUI) and an ensemble simulation scheme that can be used for teaching more advanced topics including uncertainty analysis, and ensemble simulation. Both models have been administered in a class for both in-class instruction and a final project, and students submitted their feedback about the toolbox. The results indicate that this educational software had a positive impact on students understanding and knowledge of hydrology.

  11. Pt based PEMFC catalysts prepared from colloidal particle suspensions--a toolbox for model studies.

    Science.gov (United States)

    Speder, Jozsef; Altmann, Lena; Roefzaad, Melanie; Bäumer, Marcus; Kirkensgaard, Jacob J K; Mortensen, Kell; Arenz, Matthias

    2013-03-14

    A colloidal synthesis approach is presented that allows systematic studies of the properties of supported proton exchange membrane fuel cell (PEMFC) catalysts. The applied synthesis route is based on the preparation of monodisperse nanoparticles in the absence of strong binding organic stabilizing agents. No temperature post-treatment of the catalyst is required rendering the synthesis route ideally suitable for comparative studies. We report work concerning a series of catalysts based on the same colloidal Pt nanoparticle (NP) suspension, but with different high surface area (HSA) carbon supports. It is shown that for the prepared catalysts the carbon support has no catalytic co-function, but carbon pre-treatment leads to enhanced sticking of the Pt NPs on the support. An unwanted side effect, however, is NP agglomeration during synthesis. By contrast, enhanced NP sticking without agglomeration can be accomplished by the addition of an ionomer to the NP suspension. The catalytic activity of the prepared catalysts for the oxygen reduction reaction is comparable to industrial catalysts and no influence of the particle size is found in the range of 2-5 nm.

  12. C++ Toolbox for Object-Oriented Modeling and Dynamic Simulation of Physical Systems

    DEFF Research Database (Denmark)

    Wagner, Falko Jens; Poulsen, Mikael Zebbelin

    1999-01-01

    This paper presents the efforts made in an ongoing project that exploits the advantages of using object-oriented methodologies for describing and simulating dynamical systems. The background for this work is a search for new and better ways to simulate physical systems....

  13. ObspyDMT: a Python toolbox for retrieving and processing large seismological data sets

    Directory of Open Access Journals (Sweden)

    K. Hosseini

    2017-10-01

    Full Text Available We present obspyDMT, a free, open-source software toolbox for the query, retrieval, processing and management of seismological data sets, including very large, heterogeneous and/or dynamically growing ones. ObspyDMT simplifies and speeds up user interaction with data centers, in more versatile ways than existing tools. The user is shielded from the complexities of interacting with different data centers and data exchange protocols and is provided with powerful diagnostic and plotting tools to check the retrieved data and metadata. While primarily a productivity tool for research seismologists and observatories, easy-to-use syntax and plotting functionality also make obspyDMT an effective teaching aid. Written in the Python programming language, it can be used as a stand-alone command-line tool (requiring no knowledge of Python or can be integrated as a module with other Python codes. It facilitates data archiving, preprocessing, instrument correction and quality control – routine but nontrivial tasks that can consume much user time. We describe obspyDMT's functionality, design and technical implementation, accompanied by an overview of its use cases. As an example of a typical problem encountered in seismogram preprocessing, we show how to check for inconsistencies in response files of two example stations. We also demonstrate the fully automated request, remote computation and retrieval of synthetic seismograms from the Synthetics Engine (Syngine web service of the Data Management Center (DMC at the Incorporated Research Institutions for Seismology (IRIS.

  14. ANÁLISIS DE SISTEMAS DINÁMICOS CON pplane8.m (MATLAB® toolbox

    Directory of Open Access Journals (Sweden)

    Alejandro Regalado-Méndez

    2013-01-01

    Full Text Available En este trabajo se analizaron cuatro sistemas dinámicos (físico, químico, ecológico y económico, los cuales son representados por sistemas autónomos de dos ecuaciones diferenciales ordinarias. El objetivo principal es demostrar que pplane8.m es una herramienta computacional adecuada y eficiente. El análisis de los sistemas autónomos se llevó a cabo con base en la caracterización de sus puntos críticos de acuerdo a lo citado por Coughanowr & LeBlanc (2009 y con ayuda de pplane8.m (MATLAB® toolbox. Los principales resultados de este trabajo son que, pplane8.m (Polking, 2009 dibuja rápida y precisamente las trayectorias de todos los planos de fases, calcula con facilidad todos los puntos críticos y caracteriza correctamente cada uno de los puntos de equilibrio de los sistemas autónomos estudiados. Finalmente se puede decir que pplane8.m es una herramienta poderosa para ayudar en el proceso de enseñanza aprendizaje para estudiantes de un programa de ingeniería.

  15. Measuring Episodic Memory Across the Lifespan: NIH Toolbox Picture Sequence Memory Test

    Science.gov (United States)

    Dikmen, Sureyya S.; Bauer, Patricia J.; Weintraub, Sandra; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L.; Gershon, Richard; Temkin, Nancy R.; Heaton, Robert K.

    2014-01-01

    Episodic memory is one of the most important cognitive domains that involves acquiring, storing and recalling new information. In this article, we describe a new measure developed for the NIH Toolbox, called the Picture Sequence Memory Test (PSMT) that is the first to examine episodic memory across the age range from 3 to 85. We describe the development of the measure and present validation data for ages 20 to 85. The PSMT involves presentation of sequences of pictured objects and activities in a fixed order on a computer screen and simultaneously verbally described, that the participant must remember and then reproduce over three learning trials. The results indicate good test–retest reliability and construct validity. Performance is strongly related to well-established “gold standard” measures of episodic memory and, as expected, much less well correlated with those of a measure of vocabulary. It shows clear decline with aging in parallel with a gold standard summary measure and relates to several other demographic factors and to self-reported general health status. The PSMT appears to be a reliable and valid test of episodic memory for adults, a finding similar to those found for the same measure with children. PMID:24960230

  16. The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding

    Directory of Open Access Journals (Sweden)

    Victoria C. Blake

    2016-07-01

    Full Text Available The Triticeae Toolbox (; T3 is the database schema enabling plant breeders and researchers to combine, visualize, and interrogate the wealth of phenotype and genotype data generated by the Triticeae Coordinated Agricultural Project (TCAP. T3 enables users to define specific data sets for download in formats compatible with the external tools TASSEL, Flapjack, and R; or to use by software residing on the T3 server for operations such as Genome Wide Association and Genomic Prediction. New T3 tools to assist plant breeders include a Selection Index Generator, analytical tools to compare phenotype trials using common or user-defined indices, and a histogram generator for nursery reports, with applications using the Android OS, and a Field Plot Layout Designer in development. Researchers using T3 will soon enjoy the ability to design training sets, define core germplasm sets, and perform multivariate analysis. An increased collaboration with GrainGenes and integration with the small grains reference sequence resources will place T3 in a pivotal role for on-the-fly data analysis, with instant access to the knowledge databases for wheat and barley. T3 software is available under the GNU General Public License and is freely downloadable.

  17. Measuring episodic memory across the lifespan: NIH Toolbox Picture Sequence Memory Test.

    Science.gov (United States)

    Dikmen, Sureyya S; Bauer, Patricia J; Weintraub, Sandra; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L; Gershon, Richard; Temkin, Nancy R; Heaton, Robert K

    2014-07-01

    Episodic memory is one of the most important cognitive domains that involves acquiring, storing and recalling new information. In this article, we describe a new measure developed for the NIH Toolbox, called the Picture Sequence Memory Test (PSMT) that is the first to examine episodic memory across the age range from 3 to 85. We describe the development of the measure and present validation data for ages 20 to 85. The PSMT involves presentation of sequences of pictured objects and activities in a fixed order on a computer screen and simultaneously verbally described, that the participant must remember and then reproduce over three learning trials. The results indicate good test-retest reliability and construct validity. Performance is strongly related to well-established "gold standard" measures of episodic memory and, as expected, much less well correlated with those of a measure of vocabulary. It shows clear decline with aging in parallel with a gold standard summary measure and relates to several other demographic factors and to self-reported general health status. The PSMT appears to be a reliable and valid test of episodic memory for adults, a finding similar to those found for the same measure with children.

  18. Evolutionary process development towards next generation crystalline silicon solar cells : a semiconductor process toolbox application

    Directory of Open Access Journals (Sweden)

    Tous L.

    2012-08-01

    Full Text Available Bulk crystalline Silicon solar cells are covering more than 85% of the world’s roof top module installation in 2010. With a growth rate of over 30% in the last 10 years this technology remains the working horse of solar cell industry. The full Aluminum back-side field (Al BSF technology has been developed in the 90’s and provides a production learning curve on module price of constant 20% in average. The main reason for the decrease of module prices with increasing production capacity is due to the effect of up scaling industrial production. For further decreasing of the price per wattpeak silicon consumption has to be reduced and efficiency has to be improved. In this paper we describe a successive efficiency improving process development starting from the existing full Al BSF cell concept. We propose an evolutionary development includes all parts of the solar cell process: optical enhancement (texturing, polishing, anti-reflection coating, junction formation and contacting. Novel processes are benchmarked on industrial like baseline flows using high-efficiency cell concepts like i-PERC (Passivated Emitter and Rear Cell. While the full Al BSF crystalline silicon solar cell technology provides efficiencies of up to 18% (on cz-Si in production, we are achieving up to 19.4% conversion efficiency for industrial fabricated, large area solar cells with copper based front side metallization and local Al BSF applying the semiconductor toolbox.

  19. PyMVPA: A python toolbox for multivariate pattern analysis of fMRI data.

    Science.gov (United States)

    Hanke, Michael; Halchenko, Yaroslav O; Sederberg, Per B; Hanson, Stephen José; Haxby, James V; Pollmann, Stefan

    2009-01-01

    Decoding patterns of neural activity onto cognitive states is one of the central goals of functional brain imaging. Standard univariate fMRI analysis methods, which correlate cognitive and perceptual function with the blood oxygenation-level dependent (BOLD) signal, have proven successful in identifying anatomical regions based on signal increases during cognitive and perceptual tasks. Recently, researchers have begun to explore new multivariate techniques that have proven to be more flexible, more reliable, and more sensitive than standard univariate analysis. Drawing on the field of statistical learning theory, these new classifier-based analysis techniques possess explanatory power that could provide new insights into the functional properties of the brain. However, unlike the wealth of software packages for univariate analyses, there are few packages that facilitate multivariate pattern classification analyses of fMRI data. Here we introduce a Python-based, cross-platform, and open-source software toolbox, called PyMVPA, for the application of classifier-based analysis techniques to fMRI datasets. PyMVPA makes use of Python's ability to access libraries written in a large variety of programming languages and computing environments to interface with the wealth of existing machine learning packages. We present the framework in this paper and provide illustrative examples on its usage, features, and programmability.

  20. Evaluating educators using a novel toolbox: applying rigorous criteria flexibly across institutions.

    Science.gov (United States)

    Gusic, Maryellen E; Baldwin, Constance D; Chandran, Latha; Rose, Suzanne; Simpson, Deborah; Strobel, Henry W; Timm, Craig; Fincher, Ruth Marie E

    2014-07-01

    Valuing faculty as educators is essential for medical schools to fulfill their unique mission of educating physicians. The 2006 Consensus Conference on Educational Scholarship, sponsored by the Association of American Medical Colleges (AAMC) Group on Educational Affairs, provided educators seeking academic promotion with a portfolio-based format for documenting activities in five domains, using evidence of quantity, quality, a scholarly approach, and educational scholarship. Yet, the lack of a rigorous, widely accepted system to assess educator portfolio submissions during the promotion and tenure process continues to impede the ability to fully value educators and educational scholars.The AAMC Task Force on Educator Evaluation was formed in 2010 to establish consensus guidelines for use by those responsible for the rigorous evaluation of the educational contributions of faculty. The task force delineated the educational contributions currently valued by institutions and then fulfilled its charge by creating the Toolbox for Evaluating Educators, a resource which contains explicit evidence-based criteria to evaluate faculty in each of the five domains of educator activity. Adoption of such criteria is now the rate-limiting step in using a fair process to recognize educators through academic promotion. To inform institutional review and implementation of these criteria, this article describes the iterative, evidence- and stakeholder-based process to establish the criteria. The authors advocate institutional adoption of these criteria so that faculty seeking academic promotion as educators, like their researcher colleagues, can be judged and valued using established standards for the assessment of their work.

  1. A modular cloning toolbox for the generation of chloroplast transformation vectors.

    Directory of Open Access Journals (Sweden)

    Yavar Vafaee

    Full Text Available Plastid transformation is a powerful tool for basic research, but also for the generation of stable genetically engineered plants producing recombinant proteins at high levels or for metabolic engineering purposes. However, due to the genetic makeup of plastids and the distinct features of the transformation process, vector design, and the use of specific genetic elements, a large set of basic transformation vectors is required, making cloning a tedious and time-consuming effort. Here, we describe the adoption of standardized modular cloning (GoldenBraid to the design and assembly of the full spectrum of plastid transformation vectors. The modular design of genetic elements allows straightforward and time-efficient build-up of transcriptional units as well as construction of vectors targeting any homologous recombination site of choice. In a three-level assembly process, we established a vector fostering gene expression and formation of griffithsin, a potential viral entry inhibitor and HIV prophylactic, in the plastids of tobacco. Successful transformation as well as transcript and protein production could be shown. In concert with the aforesaid endeavor, a set of modules facilitating plastid transformation was generated, thus augmenting the GoldenBraid toolbox. In short, the work presented in this study enables efficient application of synthetic biology methods to plastid transformation in plants.

  2. What’s new in the toolbox for constipation and faecal incontinence?

    Directory of Open Access Journals (Sweden)

    Yeong Yeh eLee

    2014-03-01

    Full Text Available Constipation and faecal incontinence are common complaints predominantly affecting the elderly and women. They are associated with significant morbidity and high healthcare costs. The causes are often multifactorial and overlapping. With the advent of new technologies, we have a better understanding of their underlying pathophysiology which may involve disruption at any levels along the gut-brain-microbiota axis. Initial approach to management should always be the exclusion of secondary causes. Mild symptoms can be approached with conservative measures that may include dietary modifications, exercise and medications. New prokinetics (e.g. prucalopride and secretagogues (e.g. lubiprostone and linaclotide are effective and safe in constipation. Biofeedback is the treatment of choice for dyssynergic defecation. Refractory constipation may respond to neuromodulation therapy with colectomy as the last resort especially for slow-transit constipation of neuropathic origin. Likewise, in refractory FI, less invasive approach can be tried first before progressing to more invasive surgical approach. Injectable bulking agents, sacral nerve stimulation and SECCA procedure have modest efficacy but safe and less invasive. Surgery has equivocal efficacy but there are promising new techniques including dynamic graciloplasty, artificial bowel sphincter and magnetic anal sphincter. Despite being challenging, there are no short of alternatives in our toolbox for the management of constipation and FI.

  3. Educating for resilience in the North: building a toolbox for teachers

    Directory of Open Access Journals (Sweden)

    Katie V. Spellman

    2015-03-01

    Full Text Available Communities at far northern latitudes must respond rapidly to the many complex problems that are arising from changing climate. An emerging body of theoretical and empirical work has explored the role that education plays in enhancing the resilience and adaptability of social-ecological systems. To foster effective, local, and timely responses of high-latitude communities to climate-driven social-ecological change, educators need access to successful and efficient teaching tools to foster resilience-promoting feedbacks. The potential for existing teaching practices to address this need, however, must be investigated and communicated to teachers. Here, I review the education and sustainability science literature for attributes of resilience to which formal education can contribute, and I investigate teaching strategies that help to enhance these attributes. Using examples from Alaska, I examine the potential for systems thinking, metacognition, scenarios thinking, citizen science, and stewardship learning to promote resilience in social-ecological systems. I begin to develop a toolbox of teaching strategies for resilience education and suggest that policy for formal schools incorporates these tools into everyday teaching practice.

  4. SWToolbox: A surface-water tool-box for statistical analysis of streamflow time series

    Science.gov (United States)

    Kiang, Julie E.; Flynn, Kate; Zhai, Tong; Hummel, Paul; Granato, Gregory

    2018-03-07

    This report is a user guide for the low-flow analysis methods provided with version 1.0 of the Surface Water Toolbox (SWToolbox) computer program. The software combines functionality from two software programs—U.S. Geological Survey (USGS) SWSTAT and U.S. Environmental Protection Agency (EPA) DFLOW. Both of these programs have been used primarily for computation of critical low-flow statistics. The main analysis methods are the computation of hydrologic frequency statistics such as the 7-day minimum flow that occurs on average only once every 10 years (7Q10), computation of design flows including biologically based flows, and computation of flow-duration curves and duration hydrographs. Other annual, monthly, and seasonal statistics can also be computed. The interface facilitates retrieval of streamflow discharge data from the USGS National Water Information System and outputs text reports for a record of the analysis. Tools for graphing data and screening tests are available to assist the analyst in conducting the analysis.

  5. ObspyDMT: a Python toolbox for retrieving and processing large seismological data sets

    Science.gov (United States)

    Hosseini, Kasra; Sigloch, Karin

    2017-10-01

    We present obspyDMT, a free, open-source software toolbox for the query, retrieval, processing and management of seismological data sets, including very large, heterogeneous and/or dynamically growing ones. ObspyDMT simplifies and speeds up user interaction with data centers, in more versatile ways than existing tools. The user is shielded from the complexities of interacting with different data centers and data exchange protocols and is provided with powerful diagnostic and plotting tools to check the retrieved data and metadata. While primarily a productivity tool for research seismologists and observatories, easy-to-use syntax and plotting functionality also make obspyDMT an effective teaching aid. Written in the Python programming language, it can be used as a stand-alone command-line tool (requiring no knowledge of Python) or can be integrated as a module with other Python codes. It facilitates data archiving, preprocessing, instrument correction and quality control - routine but nontrivial tasks that can consume much user time. We describe obspyDMT's functionality, design and technical implementation, accompanied by an overview of its use cases. As an example of a typical problem encountered in seismogram preprocessing, we show how to check for inconsistencies in response files of two example stations. We also demonstrate the fully automated request, remote computation and retrieval of synthetic seismograms from the Synthetics Engine (Syngine) web service of the Data Management Center (DMC) at the Incorporated Research Institutions for Seismology (IRIS).

  6. MiToBo - A Toolbox for Image Processing and Analysis

    Directory of Open Access Journals (Sweden)

    Birgit Möller

    2016-04-01

    Full Text Available MiToBo is a toolbox and Java library for solving basic as well as advanced image processing and analysis tasks. It features a rich collection of fundamental, intermediate and high-level image processing operators and algorithms as well as a couple of sophisticated tools for specific biological and biomedical applications. These tools include operators for elucidating cellular morphology and locomotion as well as operators for the characterization of certain intracellular particles and structures. MiToBo builds upon and integrates into the widely-used image analysis software packages ImageJ and Fiji [11, 10], and all of its operators can easily be run in ImageJ and Fiji via a generic operator runner plugin. Alternatively MiToBo operators can directly be run from command line, and using its functionality as a library for developing own applications is also supported. Thanks to the Alida library [8] forming the base of MiToBo all operators share unified APIs fostering reusability, and graphical as well as command line user interfaces for operators are automatically generated. MiToBo is available from its website http://www.informatik.uni-halle.de/mitobo, on Github, via an Apache Archiva Maven repository server, and it can easily be activated in Fiji via its own update site.

  7. The emerging molecular biology toolbox for the study of long noncoding RNA biology.

    Science.gov (United States)

    Fok, Ezio T; Scholefield, Janine; Fanucchi, Stephanie; Mhlanga, Musa M

    2017-10-01

    Long noncoding RNAs (lncRNAs) have been implicated in many biological processes. However, due to the unique nature of lncRNAs and the consequential difficulties associated with their characterization, there is a growing disparity between the rate at which lncRNAs are being discovered and the assignment of biological function to these transcripts. Here we present a molecular biology toolbox equipped to help dissect aspects of lncRNA biology and reveal functionality. We outline an approach that begins with a broad survey of genome-wide, high-throughput datasets to identify potential lncRNA candidates and then narrow the focus on specific methods that are well suited to interrogate the transcripts of interest more closely. This involves the use of imaging-based strategies to validate these candidates and observe the behaviors of these transcripts at single molecule resolution in individual cells. We also describe the use of gene editing tools and interactome capture techniques to interrogate functionality and infer mechanism, respectively. With the emergence of lncRNAs as important molecules in healthy and diseased cellular function, it remains crucial to deepen our understanding of their biology.

  8. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 1: Line Segment Detection and Extraction

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-06-01

    Full Text Available Geological structures, such as faults and fractures, appear as image discontinuities or lineaments in remote sensing data. Geologic lineament mapping is a very important issue in geo-engineering, especially for construction site selection, seismic, and risk assessment, mineral exploration and hydrogeological research. Classical methods of lineaments extraction are based on semi-automated (or visual interpretation of optical data and digital elevation models. We developed a freely available Matlab based toolbox TecLines (Tectonic Lineament Analysis for locating and quantifying lineament patterns using satellite data and digital elevation models. TecLines consists of a set of functions including frequency filtering, spatial filtering, tensor voting, Hough transformation, and polynomial fitting. Due to differences in the mathematical background of the edge detection and edge linking procedure as well as the breadth of the methods, we introduce the approach in two-parts. In this first study, we present the steps that lead to edge detection. We introduce the data pre-processing using selected filters in spatial and frequency domains. We then describe the application of the tensor-voting framework to improve position and length accuracies of the detected lineaments. We demonstrate the robustness of the approach in a complex area in the northeast of Afghanistan using a panchromatic QUICKBIRD-2 image with 1-meter resolution. Finally, we compare the results of TecLines with manual lineament extraction, and other lineament extraction algorithms, as well as a published fault map of the study area.

  9. The Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT): An Open-source Tool for Efficient Fitting of Astrometric and Radial Velocity Data

    Science.gov (United States)

    Mede, Kyle; Brandt, Timothy D.

    2017-03-01

    We present the Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT), a new, open-source suite to fit the orbital elements of planetary or stellar-mass companions to any combination of radial velocity and astrometric data. To explore the parameter space of Keplerian models, ExoSOFT may be operated with its own multistage sampling approach or interfaced with third-party tools such as emcee. In addition, ExoSOFT is packaged with a collection of post-processing tools to analyze and summarize the results. Although only a few systems have been observed with both radial velocity and direct imaging techniques, this number will increase, thanks to upcoming spacecraft and ground-based surveys. Providing both forms of data enables simultaneous fitting that can help break degeneracies in the orbital elements that arise when only one data type is available. The dynamical mass estimates this approach can produce are important when investigating the formation mechanisms and subsequent evolution of substellar companions. ExoSOFT was verified through fitting to artificial data and was implemented using the Python and Cython programming languages; it is available for public download at https://github.com/kylemede/ExoSOFT under GNU General Public License v3.

  10. Systematic identification of crystallization kinetics within a generic modelling framework

    DEFF Research Database (Denmark)

    Abdul Samad, Noor Asma Fazli Bin; Meisler, Kresten Troelstrup; Gernaey, Krist

    2012-01-01

    A systematic development of constitutive models within a generic modelling framework has been developed for use in design, analysis and simulation of crystallization operations. The framework contains a tool for model identification connected with a generic crystallizer modelling tool-box, a tool...

  11. SCT: Spinal Cord Toolbox, an open-source software for processing spinal cord MRI data.

    Science.gov (United States)

    De Leener, Benjamin; Lévy, Simon; Dupont, Sara M; Fonov, Vladimir S; Stikov, Nikola; Louis Collins, D; Callot, Virginie; Cohen-Adad, Julien

    2017-01-15

    For the past 25 years, the field of neuroimaging has witnessed the development of several software packages for processing multi-parametric magnetic resonance imaging (mpMRI) to study the brain. These software packages are now routinely used by researchers and clinicians, and have contributed to important breakthroughs for the understanding of brain anatomy and function. However, no software package exists to process mpMRI data of the spinal cord. Despite the numerous clinical needs for such advanced mpMRI protocols (multiple sclerosis, spinal cord injury, cervical spondylotic myelopathy, etc.), researchers have been developing specific tools that, while necessary, do not provide an integrative framework that is compatible with most usages and that is capable of reaching the community at large. This hinders cross-validation and the possibility to perform multi-center studies. In this study we introduce the Spinal Cord Toolbox (SCT), a comprehensive software dedicated to the processing of spinal cord MRI data. SCT builds on previously-validated methods and includes state-of-the-art MRI templates and atlases of the spinal cord, algorithms to segment and register new data to the templates, and motion correction methods for diffusion and functional time series. SCT is tailored towards standardization and automation of the processing pipeline, versatility, modularity, and it follows guidelines of software development and distribution. Preliminary applications of SCT cover a variety of studies, from cross-sectional area measures in large databases of patients, to the precise quantification of mpMRI metrics in specific spinal pathways. We anticipate that SCT will bring together the spinal cord neuroimaging community by establishing standard templates and analysis procedures. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

    Science.gov (United States)

    Hodneland, Erlend; Kögel, Tanja; Frei, Dominik Michael; Gerdes, Hans-Hermann; Lundervold, Arvid

    2013-08-09

    : The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening.

  13. CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation

    Science.gov (United States)

    2013-01-01

    The application of fluorescence microscopy in cell biology often generates a huge amount of imaging data. Automated whole cell segmentation of such data enables the detection and analysis of individual cells, where a manual delineation is often time consuming, or practically not feasible. Furthermore, compared to manual analysis, automation normally has a higher degree of reproducibility. CellSegm, the software presented in this work, is a Matlab based command line software toolbox providing an automated whole cell segmentation of images showing surface stained cells, acquired by fluorescence microscopy. It has options for both fully automated and semi-automated cell segmentation. Major algorithmic steps are: (i) smoothing, (ii) Hessian-based ridge enhancement, (iii) marker-controlled watershed segmentation, and (iv) feature-based classfication of cell candidates. Using a wide selection of image recordings and code snippets, we demonstrate that CellSegm has the ability to detect various types of surface stained cells in 3D. After detection and outlining of individual cells, the cell candidates can be subject to software based analysis, specified and programmed by the end-user, or they can be analyzed by other software tools. A segmentation of tissue samples with appropriate characteristics is also shown to be resolvable in CellSegm. The command-line interface of CellSegm facilitates scripting of the separate tools, all implemented in Matlab, offering a high degree of flexibility and tailored workflows for the end-user. The modularity and scripting capabilities of CellSegm enable automated workflows and quantitative analysis of microscopic data, suited for high-throughput image based screening. PMID:23938087

  14. iELVis: An open source MATLAB toolbox for localizing and visualizing human intracranial electrode data.

    Science.gov (United States)

    Groppe, David M; Bickel, Stephan; Dykstra, Andrew R; Wang, Xiuyuan; Mégevand, Pierre; Mercier, Manuel R; Lado, Fred A; Mehta, Ashesh D; Honey, Christopher J

    2017-04-01

    Intracranial electrical recordings (iEEG) and brain stimulation (iEBS) are invaluable human neuroscience methodologies. However, the value of such data is often unrealized as many laboratories lack tools for localizing electrodes relative to anatomy. To remedy this, we have developed a MATLAB toolbox for intracranial electrode localization and visualization, iELVis. NEW METHOD: iELVis uses existing tools (BioImage Suite, FSL, and FreeSurfer) for preimplant magnetic resonance imaging (MRI) segmentation, neuroimaging coregistration, and manual identification of electrodes in postimplant neuroimaging. Subsequently, iELVis implements methods for correcting electrode locations for postimplant brain shift with millimeter-scale accuracy and provides interactive visualization on 3D surfaces or in 2D slices with optional functional neuroimaging overlays. iELVis also localizes electrodes relative to FreeSurfer-based atlases and can combine data across subjects via the FreeSurfer average brain. It takes 30-60min of user time and 12-24h of computer time to localize and visualize electrodes from one brain. We demonstrate iELVis's functionality by showing that three methods for mapping primary hand somatosensory cortex (iEEG, iEBS, and functional MRI) provide highly concordant results. COMPARISON WITH EXISTING METHODS: iELVis is the first public software for electrode localization that corrects for brain shift, maps electrodes to an average brain, and supports neuroimaging overlays. Moreover, its interactive visualizations are powerful and its tutorial material is extensive. iELVis promises to speed the progress and enhance the robustness of intracranial electrode research. The software and extensive tutorial materials are freely available as part of the EpiSurg software project: https://github.com/episurg/episurg. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The oceanographic toolbox for the collection of sinking and suspended marine particles

    Science.gov (United States)

    McDonnell, Andrew M. P.; Lam, Phoebe J.; Lamborg, Carl H.; Buesseler, Ken O.; Sanders, Richard; Riley, Jennifer S.; Marsay, Chris; Smith, Helen E. K.; Sargent, Elizabeth C.; Lampitt, Richard S.; Bishop, James K. B.

    2015-04-01

    Marine particles play a central role in controlling the transport, cycling, and inventories of many major elements and trace elements and isotopes throughout the oceans. Studies seeking to elucidate the biogeochemical roles of marine particles often require reliable ways to collect them from the ocean. Here, we review the oceanographic toolbox of techniques and instrumentation that are employed to collect both suspended and sinking particles. With these tools, it is possible to determine both the concentrations and vertical fluxes of important elements and individual particle types. We describe the various methods for quantifying the concentrations of particulate matter with in situ pumps, towed sampling devices, bottle collectors, and large volume capture devices. The uses of various types of flux collection platforms are discussed including surface tethered, neutrally buoyant, and bottom moored devices. We address the issues of sediment trap collection biases and the apparent inconsistencies that can arise due to differences in the temporal and spatial scales sampled by the various methodologies. Special attention is given to collection considerations made for the analysis of trace metals and isotopes, as these methodologies are of high importance to the ongoing GEOTRACES program which seeks to identify the processes and quantify fluxes that control the distributions of key trace elements and isotopes in the ocean. With the emergence of new particle collection methodologies and the continued reliance on traditional collection methods, it is imperative that we combine these multiple approaches in ways that will help improve their accuracy and precision while enhancing their utility in advancing understanding of the biogeochemical and ecological roles of marine particles.

  16. Despeckle filtering software toolbox for ultrasound imaging of the common carotid artery.

    Science.gov (United States)

    Loizou, Christos P; Theofanous, Charoula; Pantziaris, Marios; Kasparis, Takis

    2014-04-01

    Ultrasound imaging of the common carotid artery (CCA) is a non-invasive tool used in medicine to assess the severity of atherosclerosis and monitor its progression through time. It is also used in border detection and texture characterization of the atherosclerotic carotid plaque in the CCA, the identification and measurement of the intima-media thickness (IMT) and the lumen diameter that all are very important in the assessment of cardiovascular disease (CVD). Visual perception, however, is hindered by speckle, a multiplicative noise, that degrades the quality of ultrasound B-mode imaging. Noise reduction is therefore essential for improving the visual observation quality or as a pre-processing step for further automated analysis, such as image segmentation of the IMT and the atherosclerotic carotid plaque in ultrasound images. In order to facilitate this preprocessing step, we have developed in MATLAB(®) a unified toolbox that integrates image despeckle filtering (IDF), texture analysis and image quality evaluation techniques to automate the pre-processing and complement the disease evaluation in ultrasound CCA images. The proposed software, is based on a graphical user interface (GUI) and incorporates image normalization, 10 different despeckle filtering techniques (DsFlsmv, DsFwiener, DsFlsminsc, DsFkuwahara, DsFgf, DsFmedian, DsFhmedian, DsFad, DsFnldif, DsFsrad), image intensity normalization, 65 texture features, 15 quantitative image quality metrics and objective image quality evaluation. The software is publicly available in an executable form, which can be downloaded from http://www.cs.ucy.ac.cy/medinfo/. It was validated on 100 ultrasound images of the CCA, by comparing its results with quantitative visual analysis performed by a medical expert. It was observed that the despeckle filters DsFlsmv, and DsFhmedian improved image quality perception (based on the expert's assessment and the image texture and quality metrics). It is anticipated that the

  17. A MATLAB toolbox for classification and visualization of heterogenous multi-scale human data using the Disease State Fingerprint method.

    Science.gov (United States)

    Cluitmans, Luc; Mattila, Jussi; Runtti, Hilkka; van Gils, Mark; Lötjönen, Jyrki

    2013-01-01

    As the amount of data acquired from humans is constantly increasing, efficient tools are needed for extracting relevant information from this data. This paper presents a Matlab implementation of a method to classify and visually explore (highly) multi-variate patient data. The method uses the so-called Disease State Index (DSI) which measures the fit of a test subject's data to two classes present in the data (e.g. 'controls' and 'positives'). DSI values of the different variables measured from a patient can be combined and visualized in a tree-like form using the Disease State Fingerprint (DSF) method. This allows a researcher to explore and understand the relevance of the different variables in classification problems. Moreover, the method is robust with respect to missing data. After giving an introduction to the DSF and DSI methods, the paper describes the steps required to use the methods and presents a MATLAB toolbox to perform these steps. To demonstrate the methods' versatility, the paper illustrates the usage of the toolbox in a few different contexts in which personal health data is to be classified. With this implementation, a powerful and flexible tool is made available to the biomedical research community.

  18. Expanding the toolbox for studying the biological responses of individual fish to hydropower infrastructure and operating strategies

    International Nuclear Information System (INIS)

    Hasler, C.T.; Cooke, S.J.; Patterson, D.A.

    2009-01-01

    Hydropower infrastructure and the operational strategies used by power utilities have the potential to change local aquatic environments. However, few studies have evaluated sub-organismal responses such as physiological consequences of individual fish to fluctuating flows or hydropower infrastructure such as fishways or turbines. Rather than review the impacts of hydropower on fish, this paper detailed the behavioural, energetic, genomic, molecular, forensic, isotopic, and physiological tools available for studying sub-organismal responses of fish to hydropower infrastructure and operating procedures with a critical assessment of their benefits and limitations. A brief summary of the current state of knowledge regarding the 12 types of tools was provided along with their usefulness in fisheries science and environmental management. The benefits and limitations of using these techniques for evaluating hydropower impacts on fish and fish habitat were discussed. Two case studies were presented to demonstrate how the inclusion of individual-based information into hydropower research has helped to improve the understanding of complex fish and hydropower issues. Practitioners can use the expanded toolbox to assess fishway performance, migration delays, and fish responses to fluctuating flows through a mechanistic approach. These tools are also relevant for evaluating other anthropogenic impacts such as water withdrawal for irrigation or drinking water, habitat alteration, and fisheries interactions. The expanded toolbox can contribute to a more sustainable hydropower industry by providing regulators with tools for making informed decisions and evaluating compliance issues. 150 refs., 1 tab., 4 figs

  19. EALab (Eye Activity Lab): a MATLAB Toolbox for Variable Extraction, Multivariate Analysis and Classification of Eye-Movement Data.

    Science.gov (United States)

    Andreu-Perez, Javier; Solnais, Celine; Sriskandarajah, Kumuthan

    2016-01-01

    Recent advances in the reliability of the eye-tracking methodology as well as the increasing availability of affordable non-intrusive technology have opened the door to new research opportunities in a variety of areas and applications. This has raised increasing interest within disciplines such as medicine, business and education for analysing human perceptual and psychological processes based on eye-tracking data. However, most of the currently available software requires programming skills and focuses on the analysis of a limited set of eye-movement measures (e.g., saccades and fixations), thus excluding other measures of interest to the classification of a determined state or condition. This paper describes 'EALab', a MATLAB toolbox aimed at easing the extraction, multivariate analysis and classification stages of eye-activity data collected from commercial and independent eye trackers. The processing implemented in this toolbox enables to evaluate variables extracted from a wide range of measures including saccades, fixations, blinks, pupil diameter and glissades. Using EALab does not require any programming and the analysis can be performed through a user-friendly graphical user interface (GUI) consisting of three processing modules: 1) eye-activity measure extraction interface, 2) variable selection and analysis interface, and 3) classification interface.

  20. PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eye-tracking experiments

    NARCIS (Netherlands)

    Dalmaijer, E.S.; Mathôt, S.; van der Stigchel, S.|info:eu-repo/dai/nl/29880977X

    2014-01-01

    he PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and

  1. System-Events Toolbox--Activating Urban Places for Social Cohesion through Designing a System of Events That Relies on Local Resources

    Science.gov (United States)

    Fassi, Davide; Motter, Roberta

    2014-01-01

    This paper is a reflection on the use of public spaces in towns and the development of a system-events toolbox to activate them towards social cohesion. It is the result of a 1 year action research developed together with POLIMI DESIS Lab of the Department of Design to develop design solutions to open up the public spaces of the campus to the…

  2. Development of a harmonized risk mitigation toolbox dedicated to environmental risks of pesticides in farmland in Europe: outcome of the MAgPIE workshop

    Directory of Open Access Journals (Sweden)

    Alix, A.

    2015-11-01

    Full Text Available Risk mitigation measures are a key component in designing conditions of use of pesticides in crop protection. A 2-step workshop was organized under the auspices of SETAC and the European Commission and gathered risk assessors and risk managers of 21 European countries, industry, academia and agronomical advisors/extension services, in order to provide European regulatory authorities with a toolbox of risk mitigation measures designed to reduce environmental risks of pesticides used in agriculture, and thus contribute to a better harmonization within Europe in the area. The workshop gathered an inventory of the risk mitigation tools for pesticides being implemented or in development in European countries. The inventory was discussed in order to identify the most promising tools for a harmonized toolbox in the European area. The discussions concerned the level of confidence in the technical data on which the tools identified rely, possible regulatory hurdles, expectations as regards the implementation of these tools by farmers and links with risk assessment. Finally, this workshop was a first step towards a network gathering all stakeholders, i.e. experts from national authorities, research sector, industry and farmers, to share information and further develop this toolbox. This paper presents an outline of the content of the toolbox with an emphasis on spray drift reducing techniques, in line with the discussions ongoing in the SPISE workshop.

  3. OPTESIM, a versatile toolbox for numerical simulation of electron spin echo envelope modulation (ESEEM) that features hybrid optimization and statistical assessment of parameters

    Science.gov (United States)

    Sun, Li; Hernandez-Guzman, Jessica; Warncke, Kurt

    2009-09-01

    Electron spin echo envelope modulation (ESEEM) is a technique of pulsed-electron paramagnetic resonance (EPR) spectroscopy. The analyis of ESEEM data to extract information about the nuclear and electronic structure of a disordered (powder) paramagnetic system requires accurate and efficient numerical simulations. A single coupled nucleus of known nuclear g value (gN) and spin I = 1 can have up to eight adjustable parameters in the nuclear part of the spin Hamiltonian. We have developed OPTESIM, an ESEEM simulation toolbox, for automated numerical simulation of powder two- and three-pulse one-dimensional ESEEM for arbitrary number (N) and type (I, gN) of coupled nuclei, and arbitrary mutual orientations of the hyperfine tensor principal axis systems for N > 1. OPTESIM is based in the Matlab environment, and includes the following features: (1) a fast algorithm for translation of the spin Hamiltonian into simulated ESEEM, (2) different optimization methods that can be hybridized to achieve an efficient coarse-to-fine grained search of the parameter space and convergence to a global minimum, (3) statistical analysis of the simulation parameters, which allows the identification of simultaneous confidence regions at specific confidence levels. OPTESIM also includes a geometry-preserving spherical averaging algorithm as default for N > 1, and global optimization over multiple experimental conditions, such as the dephasing time (τ) for three-pulse ESEEM, and external magnetic field values. Application examples for simulation of 14N coupling (N = 1, N = 2) in biological and chemical model paramagnets are included. Automated, optimized simulations by using OPTESIM lead to a convergence on dramatically shorter time scales, relative to manual simulations.

  4. Modeling and controller design on ARX model of Electro-Hydrolic ...

    African Journals Online (AJOL)

    This paper studies the performance of Fuzzy PID controller on ARX model parameters of vertical position of electro-hydraulic actuator. The system transfer function is obtained via system identification technique using MATLAB Toolbox. The performance of the controller is analyzed through simulation by using step and ...

  5. TecDEM: A MATLAB based toolbox for tectonic geomorphology, Part 2: Surface dynamics and basin analysis

    Science.gov (United States)

    Shahzad, Faisal; Gloaguen, Richard

    2011-02-01

    We present the analytical capability of TecDEM, a MATLAB toolbox used in conjunction with Global DEMs for the extraction of tectonic geomorphologic information. TecDEM includes a suite of algorithms to analyze topography, extracted drainage networks and sub-basins. The aim of part 2 of this paper series is the generation of morphometric maps for surface dynamics and basin analysis. TecDEM therefore allows the extraction of parameters such as isobase, incision, drainage density and surface roughness maps. We also provide tools for basin asymmetry and hypsometric analysis. These are efficient graphical user interfaces (GUIs) for mapping drainage deviation from basin mid-line and basin hypsometry. A morphotectonic interpretation of the Kaghan Valley (Northern Pakistan) is performed with TecDEM and the findings indicate a high correlation between surface dynamics and basin analysis parameters with neotectonic features in the study area.

  6. PyGaze: an open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments.

    Science.gov (United States)

    Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

    2014-12-01

    The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

  7. Development of a Web-Based Quality Dashboard Including a Toolbox to Improve Pain Management in Dutch Intensive Care.

    Science.gov (United States)

    Roos-Blom, Marie-José; Gude, Wouter T; de Jonge, Evert; Spijkstra, Jan Jaap; van der Veer, Sabine N; Dongelmans, Dave A; de Keizer, Nicolette F

    2017-01-01

    Audit and feedback (A&F) is a common strategy to improve quality of care. Meta-analyses have indicated that A&F may be more effective in realizing desired change when baseline performance is low, it is delivered by a supervisor or colleague, it is provided frequently and in a timely manner, it is delivered in both verbal and written formats, and it includes specific targets and an action plan. However, there is little information to guide operationalization of these factors. Researchers have consequently called for A&F interventions featuring well-described and carefully justified components, with their theoretical rationale made explicit. This paper describes the rationale and development of a quality dashboard including an improvement toolbox for four previous developed pain indicators, guided by Control Theory.

  8. PyTRiP - a toolbox and GUI for the proton/ion therapy planning system TRiP

    Science.gov (United States)

    Toftegaard, J.; Petersen, J. B.; Bassler, N.

    2014-03-01

    Purpose: Only very few treatment planning systems (TPS) are capable of handling heavy ions. Commercial heavy ion TPS are costly and normally restrict the possibility to implement new functionalities. PyTRiP provides Python bindings and a platform-independent graphical user interface (GUI) for the heavy ion treatment program TRiP, and adds seamless support of DICOM files. We aim to provide a front-end for TRiP which does not require any special computer skills. Methods: PyTRiP is written in Python combined with C for fast computing. Routines for DICOM file import/export to TRiPs native file format are implemented. The GUI comes as an executable with all its dependencies including PyTRiP making it easy to install on Windows, Mac and Linux. Results: PyTRiP is a comprehensive toolbox for handling TRiP. Treatment plans are handled using an object oriented structure. Bindings to TRiP (which only runs on Linux, either locally or on a remote server) are performed through a single function call. GUI users can intuitively create treatment plans without much knowledge about the TRiP user interface. Advanced users still have full access to all TRiP functionality. The user interface comes with a comprehensive plotting tool, which can visualize 2D contours, volume histograms, as well as dose- and linear energy transfer (LET) distributions. Conclusion: We developed a powerful toolbox for ion therapy research using TRiP as backend. The corresponding GUI allows to easily and intuitively create, calculate and visualize treatment plans. TRiP is thereby more accessible and simpler to use.

  9. Modelling of queuing process at airport check-in system: a case ...

    African Journals Online (AJOL)

    This study built a Simulation Model (SM) using SimEvents toolbox in MATLAB for implementing Analytical Models (AM) of queuing process at airport check - in system. Air travel demand data for Manchester and Leeds - Bradford airports in 2014 were adopted for validation of the model. There was no statistical differenc e ...

  10. Development and validation of a modular simulation model for commercial vehicles

    NARCIS (Netherlands)

    Evers, W.J.; Besselink, I.J.M.; Nijmeijer, H.; Knaap, A.C.M. van der

    2009-01-01

    In this paper a modular truck semi-trailer model is developed in the multi-body toolbox SimMechanics, which is part of MATLAB/Simulink. It can be used to analyse a wide range of active control solutions (anywhere in the model), as well as the influence of passive vehicle modifications. As the model

  11. Three-dimensional mapping of mechanical activation patterns, contractile dyssynchrony and dyscoordination by two-dimensional strain echocardiography: Rationale and design of a novel software toolbox

    Directory of Open Access Journals (Sweden)

    Cramer Maarten J

    2008-05-01

    Full Text Available Abstract Background Dyssynchrony of myocardial deformation is usually described in terms of variability only (e.g. standard deviations SD's. A description in terms of the spatio-temporal distribution pattern (vector-analysis of dyssynchrony or by indices estimating its impact by expressing dyscoordination of shortening in relation to the global ventricular shortening may be preferential. Strain echocardiography by speckle tracking is a new non-invasive, albeit 2-D imaging modality to study myocardial deformation. Methods A post-processing toolbox was designed to incorporate local, speckle tracking-derived deformation data into a 36 segment 3-D model of the left ventricle. Global left ventricular shortening, standard deviations and vectors of timing of shortening were calculated. The impact of dyssynchrony was estimated by comparing the end-systolic values with either early peak values only (early shortening reserve ESR or with all peak values (virtual shortening reserve VSR, and by the internal strain fraction (ISF expressing dyscoordination as the fraction of deformation lost internally due to simultaneous shortening and stretching. These dyssynchrony parameters were compared in 8 volunteers (NL, 8 patients with Wolff-Parkinson-White syndrome (WPW, and 7 patients before (LBBB and after cardiac resynchronization therapy (CRT. Results Dyssynchrony indices merely based on variability failed to detect differences between WPW and NL and failed to demonstrate the effect of CRT. Only the 3-D vector of onset of shortening could distinguish WPW from NL, while at peak shortening and by VSR, ESR and ISF no differences were found. All tested dyssynchrony parameters yielded higher values in LBBB compared to both NL and WPW. CRT reduced the spatial divergence of shortening (both vector magnitude and direction, and improved global ventricular shortening along with reductions in ESR and dyscoordination of shortening expressed by ISF. Conclusion Incorporation

  12. Hybrid Electric Vehicle Simulink Toolbox User's Guide, Technical Notes and PATHS Validation

    National Research Council Canada - National Science Library

    Nedungadi, Ashok

    1999-01-01

    ...) was developed using Matlab(registered) and Simulink(registered). PATHS is a forward looking model organized into a suite of libraries, each containing modular computer models of typical HEV components...

  13. TLM.open: a SystemC/TLM Frontend for the CADP Verification Toolbox

    Directory of Open Access Journals (Sweden)

    Claude Helmstetter

    2014-04-01

    Full Text Available SystemC/TLM models, which are C++ programs, allow the simulation of embedded software before hardware low-level descriptions are available and are used as golden models for hardware verification. The verification of the SystemC/TLM models is an important issue since an error in the model can mislead the system designers or reveal an error in the specifications. An open-source simulator for SystemC/TLM is provided but there are no tools for formal verification.In order to apply model checking to a SystemC/TLM model, a semantics for standard C++ code and for specific SystemC/TLM features must be provided. The usual approach relies on the translation of the SystemC/TLM code into a formal language for which a model checker is available.We propose another approach that suppresses the error-prone translation effort. Given a SystemC/TLM program, the transitions are obtained by executing the original code using g++ and an extended SystemC library, and we ask the user to provide additional functions to store the current model state. These additional functions generally represent less than 20% of the size of the original model, and allow it to apply all CADP verification tools to the SystemC/TLM model itself.

  14. The EnMAP-Box—A Toolbox and Application Programming Interface for EnMAP Data Processing

    Directory of Open Access Journals (Sweden)

    Sebastian van der Linden

    2015-09-01

    Full Text Available The EnMAP-Box is a toolbox that is developed for the processing and analysis of data acquired by the German spaceborne imaging spectrometer EnMAP (Environmental Mapping and Analysis Program. It is developed with two aims in mind in order to guarantee full usage of future EnMAP data, i.e., (1 extending the EnMAP user community and (2 providing access to recent approaches for imaging spectroscopy data processing. The software is freely available and offers a range of tools and applications for the processing of spectral imagery, including classical processing tools for imaging spectroscopy data as well as powerful machine learning approaches or interfaces for the integration of methods available in scripting languages. A special developer version includes the full open source code, an application programming interface and an application wizard for easy integration and documentation of new developments. This paper gives an overview of the EnMAP-Box for users and developers, explains typical workflows along an application example and exemplifies the concept for making it a frequently used and constantly extended platform for imaging spectroscopy applications.

  15. Reprocessing Close Range Terrestrial and Uav Photogrammetric Projects with the Dbat Toolbox for Independent Verification and Quality Control

    Science.gov (United States)

    Murtiyoso, A.; Grussenmeyer, P.; Börlin, N.

    2017-11-01

    Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles), close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT) developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  16. DAFNE: A Matlab toolbox for Bayesian multi-source remote sensing and ancillary data fusion, with application to flood mapping

    Science.gov (United States)

    D'Addabbo, Annarita; Refice, Alberto; Lovergine, Francesco P.; Pasquariello, Guido

    2018-03-01

    High-resolution, remotely sensed images of the Earth surface have been proven to be of help in producing detailed flood maps, thanks to their synoptic overview of the flooded area and frequent revisits. However, flood scenarios can be complex situations, requiring the integration of different data in order to provide accurate and robust flood information. Several processing approaches have been recently proposed to efficiently combine and integrate heterogeneous information sources. In this paper, we introduce DAFNE, a Matlab®-based, open source toolbox, conceived to produce flood maps from remotely sensed and other ancillary information, through a data fusion approach. DAFNE is based on Bayesian Networks, and is composed of several independent modules, each one performing a different task. Multi-temporal and multi-sensor data can be easily handled, with the possibility of following the evolution of an event through multi-temporal output flood maps. Each DAFNE module can be easily modified or upgraded to meet different user needs. The DAFNE suite is presented together with an example of its application.

  17. PL-DA-PS: A hardware architecture and software toolbox for neurophysiology requiring complex visual stimuli and online behavioral control

    Directory of Open Access Journals (Sweden)

    Kyler M. Eastman

    2012-01-01

    Full Text Available Neurophysiological studies in awake, behaving primates (both human and nonhuman primates have focused with increasing scrutiny on the temporal relationship between neural signals and behaviors. Consequently, laboratories are often faced with the problem of developing experimental equipment that can support data recording with high temporal precision and also be flexible enough to accommodate a wide variety of experimental paradigms. To this end, we have developed an architecture that integrates several modern pieces of equipment, but still grants experimenters a high degree of flexibility. Our hardware architecture and software tools take advantage of three popular and powerful technologies: the PLexon apparatus for neurophysiological recordings (Plexon, Inc., Dallas TX, a DAtapixx box (Vpixx Technologies, Saint-Bruno, QC, Canada for analog, digital, and video signal input-output control, and the PSychtoolbox MATLAB toolbox for stimulus generation (Brainard, 1997. The PL-DA-PS (Platypus system is designed to support the study of the visual systems of awake, behaving primates during multi-electrode neurophysiological recordings, but can be easily applied to other related domains. Despite its wide range of capabilities and support for cutting-edge video displays and neural recording systems, the PLDAPS system is simple enough for someone with basic MATLAB programming skills to design their own experiments.

  18. A House Full of Trap Doors. Identifying barriers to resilient drylands in the toolbox of pastoral development

    Science.gov (United States)

    Krätli, Saverio; Kaufmann, Brigitte; Roba, Hassan; Hiernaux, Pierre; Li, Wenjun; Easdale, Marcos H.; Huelsebusch, Christian

    2016-04-01

    The theoretical understanding of drylands and pastoral systems has long undergone a U-turn from the initial perspective rooted in classical ecology. The shift has hinged on the way to represent asymmetric variability, from a disturbance in an ecosystem that naturally tends towards uniformity and stability, to a constitutive part of a dynamic ecosystem. Operationalising the new reversed perspective, including the need to update the methodological infrastructure to plan around drylands and pastoral development, remains a challenge. Underlying assumptions about stability and uniformity, that are a legacy of equilibrium thinking, remain embedded in the toolbox of pastoral development, starting from the technical language to talk about the subject. This effectively gets in the way of operationalizing state of the art understanding of pastoral systems and the drylands. Unless these barriers are identified, unpacked and managed, even the present calls for increasing the rigour and intensity of data collection - for example as part of the ongoing global process to revise and improve agricultural data - cannot deliver a realistic representation of pastoral systems in statistics and policy making. This contribution presents the case for understanding variability as an asset, and provides a range of examples of methodological barriers, including classifications of livestock systems, scale of observation, key parameters in animal production, indicators in the measurement of ecological efficiency, concepts of ecological fragility, natural resources, and pastoral risk. The need to update this legacy is a pressing challenge for policy makers concerned with both modernisation and resilience in the drylands.

  19. Fecal pollution source tracking toolbox for identification, evaluation and characterization of fecal contamination in receiving urban surface waters and groundwater.

    Science.gov (United States)

    Tran, Ngoc Han; Gin, Karina Yew-Hoong; Ngo, Huu Hao

    2015-12-15

    The quality of surface waters/groundwater of a geographical region can be affected by anthropogenic activities, land use patterns and fecal pollution sources from humans and animals. Therefore, the development of an efficient fecal pollution source tracking toolbox for identifying the origin of the fecal pollution sources in surface waters/groundwater is especially helpful for improving management efforts and remediation actions of water resources in a more cost-effective and efficient manner. This review summarizes the updated knowledge on the use of fecal pollution source tracking markers for detecting, evaluating and characterizing fecal pollution sources in receiving surface waters and groundwater. The suitability of using chemical markers (i.e. fecal sterols, fluorescent whitening agents, pharmaceuticals and personal care products, and artificial sweeteners) and/or microbial markers (e.g. F+RNA coliphages, enteric viruses, and host-specific anaerobic bacterial 16S rDNA genetic markers) for tracking fecal pollution sources in receiving water bodies is discussed. In addition, this review also provides a comprehensive approach, which is based on the detection ratios (DR), detection frequencies (DF), and fate of potential microbial and chemical markers. DR and DF are considered as the key criteria for selecting appropriate markers for identifying and evaluating the impacts of fecal contamination in surface waters/groundwater. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. REPROCESSING CLOSE RANGE TERRESTRIAL AND UAV PHOTOGRAMMETRIC PROJECTS WITH THE DBAT TOOLBOX FOR INDEPENDENT VERIFICATION AND QUALITY CONTROL

    Directory of Open Access Journals (Sweden)

    A. Murtiyoso

    2017-11-01

    Full Text Available Photogrammetry has recently seen a rapid increase in many applications, thanks to developments in computing power and algorithms. Furthermore with the democratisation of UAVs (Unmanned Aerial Vehicles, close range photogrammetry has seen more and more use due to the easier capability to acquire aerial close range images. In terms of photogrammetric processing, many commercial software solutions exist in the market that offer results from user-friendly environments. However, in most commercial solutions, a black-box approach to photogrammetric calculations is often used. This is understandable in light of the proprietary nature of the algorithms, but it may pose a problem if the results need to be validated in an independent manner. In this paper, the Damped Bundle Adjustment Toolbox (DBAT developed for Matlab was used to reprocess some photogrammetric projects that were processed using the commercial software Agisoft Photoscan. Several scenarios were experimented on in order to see the performance of DBAT in reprocessing terrestrial and UAV close range photogrammetric projects in several configurations of self-calibration setting. Results show that DBAT managed to reprocess PS projects and generate metrics which can be useful for project verification.

  1. iSpectra: An Open Source Toolbox For The Analysis of Spectral Images Recorded on Scanning Electron Microscopes.

    Science.gov (United States)

    Liebske, Christian

    2015-08-01

    iSpectra is an open source and system-independent toolbox for the analysis of spectral images (SIs) recorded on energy-dispersive spectroscopy (EDS) systems attached to scanning electron microscopes (SEMs). The aim of iSpectra is to assign pixels with similar spectral content to phases, accompanied by cumulative phase spectra with superior counting statistics for quantification. Pixel-to-phase assignment starts with a threshold-based pre-sorting of spectra to create groups of pixels with identical elemental budgets, similar to a method described by van Hoek (2014). Subsequent merging of groups and re-assignments of pixels using elemental or principle component histogram plots enables the user to generate chemically and texturally plausible phase maps. A variety of standard image processing algorithms can be applied to groups of pixels to optimize pixel-to-phase assignments, such as morphology operations to account for overlapping excitation volumes over pixels located at phase boundaries. iSpectra supports batch processing and allows pixel-to-phase assignments to be applied to an unlimited amount of SIs, thus enabling phase mapping of large area samples like petrographic thin sections.

  2. Power system dynamics and stability with synchrophasor measurement and power system toolbox

    CERN Document Server

    Sauer, Peter W; Chow, Joe H

    2017-01-01

    This new edition addresses the needs of dynamic modeling and simulation relevant to power system planning, design, and operation, including a systematic derivation of synchronous machine dynamic models together with speed and voltage control subsystems. Reduced-order modeling based on integral manifolds is used as a firm basis for understanding the derivations and limitations of lower-order dynamic models. Following these developments, a multi-machine model interconnected through the transmission network is formulated and simulated using numerical simulation methods. Energy function methods are discussed for direct evaluation of stability. Small-signal analysis is used for determining the electromechanical modes and mode-shapes, and for power system stabilizer design. Time-synchronized high-sampling-rate phasor measurement units (PMUs) to monitor power system disturbances ave been implemented throughout North America and many other countries. In this second edition, new chapters on synchrophasor measurement ...

  3. Toolbox for uncertainty; Introduction of adaptive heuristics as strategies for project decision making

    DEFF Research Database (Denmark)

    Stingl, Verena; Geraldi, Joana

    2017-01-01

    and limited information, which are the typical project decision context. This article develops a conceptual model that supports a systematic connection between adaptive heuristics and project decisions. Individual adaptive heuristics succeed only in specific decision environments, in which...

  4. The genomic and genetic toolbox of the teleost medaka (Oryzias latipes).

    Science.gov (United States)

    Kirchmaier, Stephan; Naruse, Kiyoshi; Wittbrodt, Joachim; Loosli, Felix

    2015-04-01

    The Japanese medaka, Oryzias latipes, is a vertebrate teleost model with a long history of genetic research. A number of unique features and established resources distinguish medaka from other vertebrate model systems. A large number of laboratory strains from different locations are available. Due to a high tolerance to inbreeding, many highly inbred strains have been established, thus providing a rich resource for genetic studies. Furthermore, closely related species native to different habitats in Southeast Asia permit comparative evolutionary studies. The transparency of embryos, larvae, and juveniles allows a detailed in vivo analysis of development. New tools to study diverse aspects of medaka biology are constantly being generated. Thus, medaka has become an important vertebrate model organism to study development, behavior, and physiology. In this review, we provide a comprehensive overview of established genetic and molecular-genetic tools that render medaka fish a full-fledged vertebrate system. Copyright © 2015 by the Genetics Society of America.

  5. LEA in Private: A Privacy and Data Protection Framework for a Learning Analytics Toolbox

    Science.gov (United States)

    Steiner, Christina M.; Kickmeier-Rust, Michael D.; Albert, Dietrich

    2016-01-01

    To find a balance between learning analytics research and individual privacy, learning analytics initiatives need to appropriately address ethical, privacy, and data protection issues. A range of general guidelines, model codes, and principles for handling ethical issues and for appropriate data and privacy protection are available, which may…

  6. Expanding the Tissue Toolbox : Deriving Colon Tissue from Human Pluripotent Stem Cells

    NARCIS (Netherlands)

    Bruens, Lotte; Snippert, Hugo J.G.

    2017-01-01

    Organoid technology holds great potential for disease modeling and regenerative medicine. In this issue of Cell Stem Cell, Múnera et al. (2017) establish the generation of pluripotent stem cell-derived colon organoids that upon transplantation in mice, resembling human colon to a large extent,

  7. An expression tag toolbox for microbial production of membrane bound plant cytochromes P450

    DEFF Research Database (Denmark)

    Vazquez Albacete, Dario; Cavaleiro, Mafalda; Christensen, Ulla

    2017-01-01

    tag chimeras of the model plant P450 CYP79A1 in different Escherichia coli strains. Using a high-throughput screening platform based on C-terminal GFP fusions, we identify several highly expressing and robustly performing chimeric designs. Analysis of long-term cultures by flow cytometry showed...

  8. A general XML schema and SPM toolbox for storage of neuro-imaging results and anatomical labels.

    Science.gov (United States)

    Keator, David Bryant; Gadde, Syam; Grethe, Jeffrey S; Taylor, Derek V; Potkin, Steven G

    2006-01-01

    With the increased frequency of multisite, large-scale collaborative neuro-imaging studies, the need for a general, self-documenting framework for the storage and retrieval of activation maps and anatomical labels becomes evident. To address this need, we have developed and extensible markup language (XML) schema and associated tools for the storage of neuro-imaging activation maps and anatomical labels. This schema, as part of the XML-based Clinical Experiment Data Exchange (XCEDE) schema, provides storage capabilities for analysis annotations, activation threshold parameters, and cluster and voxel-level statistics. Activation parameters contain information describing the threshold, degrees of freedom, FWHM smoothness, search volumes, voxel sizes, expected voxels per cluster, and expected number of clusters in the statistical map. Cluster and voxel statistics can be stored along with the coordinates, threshold, and anatomical label information. Multiple threshold types can be documented for a given cluster or voxel along with the uncorrected and corrected probability values. Multiple atlases can be used to generate anatomical labels and stored for each significant voxel or cluter. Additionally, a toolbox for Statistical Parametric Mapping software (http://www. fil. ion.ucl.ac.uk/spm/) was created to capture the results from activation maps using the XML schema that supports both SPM99 and SPM2 versions (http://nbirn.net/Resources/Users/ Applications/xcede/SPM_XMLTools.htm). Support for anatomical labeling is available via the Talairach Daemon (http://ric.uthscsa. edu/projects/talairachdaemon.html) and Automated Anatomical Labeling (http://www. cyceron.fr/freeware/).

  9. Analysis of Power Laws, Shape Collapses, and Neural Complexity: New Techniques and MATLAB Support via the NCC Toolbox.

    Science.gov (United States)

    Marshall, Najja; Timme, Nicholas M; Bennett, Nicholas; Ripp, Monica; Lautzenhiser, Edward; Beggs, John M

    2016-01-01

    Neural systems include interactions that occur across many scales. Two divergent methods for characterizing such interactions have drawn on the physical analysis of critical phenomena and the mathematical study of information. Inferring criticality in neural systems has traditionally rested on fitting power laws to the property distributions of "neural avalanches" (contiguous bursts of activity), but the fractal nature of avalanche shapes has recently emerged as another signature of criticality. On the other hand, neural complexity, an information theoretic measure, has been used to capture the interplay between the functional localization of brain regions and their integration for higher cognitive functions. Unfortunately, treatments of all three methods-power-law fitting, avalanche shape collapse, and neural complexity-have suffered from shortcomings. Empirical data often contain biases that introduce deviations from true power law in the tail and head of the distribution, but deviations in the tail have often been unconsidered; avalanche shape collapse has required manual parameter tuning; and the estimation of neural complexity has relied on small data sets or statistical assumptions for the sake of computational efficiency. In this paper we present technical advancements in the analysis of criticality and complexity in neural systems. We use maximum-likelihood estimation to automatically fit power laws with left and right cutoffs, present the first automated shape collapse algorithm, and describe new techniques to account for large numbers of neural variables and small data sets in the calculation of neural complexity. In order to facilitate future research in criticality and complexity, we have made the software utilized in this analysis freely available online in the MATLAB NCC (Neural Complexity and Criticality) Toolbox.

  10. Chapter 3. The Toolbox: Linguistic Tools for Analyzing the History of Russian

    OpenAIRE

    Nesset, Tore

    2015-01-01

    In chapter 1 you learned that Russian belongs to the Slavic language family, which evolved from a reconstructed ancestor language called “Proto-Slavic”. You may ask how we reconstruct ancestor languages and describe language change. This chapter addresses these questions and provides you with some linguistic tools you need in order to analyze the history of Russian. Click on the links below to learn more!3.4 Family Tree Model

  11. Stress, strain, and structural dynamics an interactive handbook of formulas, solutions, and Matlab toolboxes

    CERN Document Server

    Yang, Bingen

    2005-01-01

    Stress, Strain, and Structural Dynamics is a comprehensive and definitive reference to statics and dynamics of solids and structures, including mechanics of materials, structural mechanics, elasticity, rigid-body dynamics, vibrations, structural dynamics, and structural controls. This text integrates the development of fundamental theories, formulas and mathematical models with user-friendly interactive computer programs, written in the powerful and popular MATLAB. This unique merger of technical referencing and interactive computing allows instant solution of a variety of engineering problems

  12. Electronic audit and feedback intervention with action implementation toolbox to improve pain management in intensive care: protocol for a laboratory experiment and cluster randomised trial.

    Science.gov (United States)

    Gude, Wouter T; Roos-Blom, Marie-José; van der Veer, Sabine N; de Jonge, Evert; Peek, Niels; Dongelmans, Dave A; de Keizer, Nicolette F

    2017-05-25

    Audit and feedback is often used as a strategy to improve quality of care, however, its effects are variable and often marginal. In order to learn how to design and deliver effective feedback, we need to understand their mechanisms of action. This theory-informed study will investigate how electronic audit and feedback affects improvement intentions (i.e. information-intention gap), and whether an action implementation toolbox with suggested actions and materials helps translating those intentions into action (i.e. intention-behaviour gap). The study will be executed in Dutch intensive care units (ICUs) and will be focused on pain management. We will conduct a laboratory experiment with individual ICU professionals to assess the impact of feedback on their intentions to improve practice. Next, we will conduct a cluster randomised controlled trial with ICUs allocated to feedback without or feedback with action implementation toolbox group. Participants will not be told explicitly what aspect of the intervention is randomised; they will only be aware that there are two variations of providing feedback. ICUs are eligible for participation if they submit indicator data to the Dutch National Intensive Care Evaluation (NICE) quality registry and agree to allocate a quality improvement team that spends 4 h per month on the intervention. All participating ICUs will receive access to an online quality dashboard that provides two functionalities: gaining insight into clinical performance on pain management indicators and developing action plans. ICUs with access to the toolbox can develop their action plans guided by a list of potential barriers in the care process, associated suggested actions, and supporting materials to facilitate implementation of the actions. The primary outcome measure for the laboratory experiment is the proportion of improvement intentions set by participants that are consistent with recommendations based on peer comparisons; for the randomised

  13. Cultivo hidropônico da alface empregando substratos: uma alternativa a NFT? Growing lettuce plants in hydroponics using substrates: an alternative for the NFT?

    Directory of Open Access Journals (Sweden)

    Jerônimo L. Andriolo

    2004-12-01

    Full Text Available Foi desenvolvido um dispositivo experimental para o cultivo da alface em sistema hidropônico fechado empregando substratos. As bancadas foram constituídas por telhas de cimento amianto, cujos canais foram preenchidos com brita basáltica. Sobre a brita foram dispostos os substratos, formando uma camada de 0,05 m de altura, com a superfície revestida com filme de polietileno opaco branco. As mudas foram produzidas em bandejas de poliestireno e plantadas em orifícios feitos sobre a superfície do filme de polietileno. Uma solução nutritiva completa foi fornecida diariamente, por meio de tubos gotejadores localizados na superfície da camada de substrato e abaixo do filme de polietileno. A solução drenada foi recolhida por gravidade para dentro do reservatório principal. Foram conduzidos dois experimentos, no período entre 16 de maio e 24 de junho e 1º e 28 de outubro de 2003, empregando as cultivares Regina e Mimosa e os substratos areia média e substrato orgânico Plantmax® Folhosas HA. No decorrer dos experimentos, houve diminuição dos valores de pH da solução nutritiva, tendo sido feita apenas uma correção em cada um dos experimentos. No dia mais quente do experimento de primavera, a temperatura foi mais elevada na areia, sem diferença significativa do substrato orgânico, cuja média situou-se 5,4ºC acima da temperatura da solução nutritiva e 0,4ºC acima daquela do ar. As médias mais elevadas das variáveis de crescimento e desenvolvimento foram observadas no substrato orgânico no outono, enquanto, na primavera, foram constatadas nos tratamentos tendo areia como substrato. O emprego dos substratos permitiu uma redução em torno de 92,4% no tempo de funcionamento da motobomba e simplificou tanto o manejo da fertirrigação como os controles da solução nutritiva.An experimental set-up to grow lettuce plants in a closed hydroponic growing system using substrates was made up and tested. Commercial fibber cement tiles were used as growing beds, in which gullies were filled with basaltic gravel. Substrates were laid out over the gravel in a 0.05 m layer depth and covered with a white polyethylene sheet. Lettuce plantlets from polystyrene nursery trays were planted in gaps made by cuttings on the polyethylene sheet. A complete nutrient solution was delivered daily to plants, by means of a drip irrigation system placed just bellow the polyethylene sheet and over the substrate layer. The nutrient solution running off from gullies was conducted back to the catchment tank. Two experiments were carried out, from May 16 to June 24, and from October 1th to October 28, 2003, using the lettuce cultivars Regina and Mimosa, and sand and the organic substrate Plantmax® Folhosas HA as growing media. The pH values of the nutrient solution decreased, but only one pH correction was made during each one of the experimental periods. On the hottest day of the spring experiment, temperature was higher in sand, but did not differ significantly from the organic substrate. Average values reached 5.4ºC above that of the nutrient solution and 0.4ºC above that of the air. Growth and development plant variables showed higher values in plants growing in the organic substrate in autumn, whereas in spring they were recorded on plants grown in sand. The substrates allowed a 92.4% reduction in the time during which the pump was switched on, leading to a simplification in practices of fertigation and control of the nutrient solution.

  14. SpatTrack: an imaging toolbox for analysis of vesicle motility and distribution in living cells

    DEFF Research Database (Denmark)

    Lund, Frederik Wendelboe; Jensen, Marie Louise; Christensen, Tanja

    2014-01-01

    SpatTrack, an open source, platform-independent program collecting a variety of methods for analysis of vesicle dynamics and distribution in living cells. SpatTrack performs 2D particle tracking, trajectory analysis and fitting of diffusion models to the calculated mean square displacement. It allows...... for spatial analysis of detected vesicle patterns including calculation of the radial distribution function and particle-based colocalization. Importantly, all analysis tools are supported by Monte Carlo simulations of synthetic images. This allows the user to assess the reliability of the analysis...... and to study alternative scenarios. We demonstrate the functionality of SpatTrack by performing a detailed imaging study of internalized fluorescence-tagged Niemann Pick C2 (NPC2) protein in human disease fibroblasts. Using SpatTrack, we show that NPC2 rescued the cholesterol-storage phenotype from...

  15. Integration of 3D printing and additive manufacturing in the interventional pulmonologist's toolbox.

    Science.gov (United States)

    Guibert, Nicolas; Mhanna, Laurent; Didier, Alain; Moreno, Benjamin; Leyx, Pierre; Plat, Gavin; Mazieres, Julien; Hermant, Christophe

    2018-01-01

    New 3D technologies are rapidly entering into the surgical landscape, including in interventional pulmonology. The transition of 2D restricted data into a physical model of pathological airways by three-dimensional printing (3DP) allows rapid prototyping and fabrication of complex and patient-specific shapes and can thus help the physician to plan and guide complex procedures. Furthermore, computer-assisted designed (CAD) patient-specific devices have already helped surgeons overcome several therapeutic impasses and are likely to rapidly cover a wider range of situations. We report herein with a special focus on our clinical experience: i) how additive manufacturing is progressively integrated into the management of complex central airways diseases; ii) the appealing future directions of these new technologies, including the potential of the emerging technique of bioprinting; iii) the main pitfalls that could delay its introduction into routine care. Copyright © 2017. Published by Elsevier Ltd.

  16. Three New Lactobacillus plantarum Strains in the Probiotic Toolbox against Gut Pathogen Salmonella enterica Serotype Typhimurium

    Directory of Open Access Journals (Sweden)

    Mia Potočnjak

    2017-01-01

    Full Text Available The benefits of probiotic bacteria have been widely explored. However, fermented foods and digestive system of humans and animals are an inexhaustible source of new potentially probiotic microorganisms. In this study we present three new Lactobacillus plantarum strains isolated from different dairy products: cow′s cheese, sheep′s cheese and whey. In order to determine the antibacterial activity of yet unexplored L. plantarum strains against Salmonella enterica serotype Typhimurium, in vitro competition and co-culture tests were done. Furthermore, adhesion of these strains to Caco-2 cells and their influence on the adhesion of Salmonella were tested. Results showed the potential probiotic activity of isolated strains. L. plantarum strains survived in the presence of 1 % bile salts, they possessed acidification ability, antibacterial activity and significantly attenuated the growth of S. Typhimurium in brain heart infusion broth. All tested L. plantarum strains were able to adhere to Caco-2 cells and significantly impair the adhesion of S. Typhimurium. All three L. plantarum strains exhibited signifi cant probiotic potential and anti-Salmonella activity; therefore, further testing on in vivo models should follow.

  17. Expanding the Immunology Toolbox: Embracing Public-Data Reuse and Crowdsourcing.

    Science.gov (United States)

    Sparks, Rachel; Lau, William W; Tsang, John S

    2016-12-20

    New technologies have been propelling dramatic increases in the volume and diversity of large-scale public data, which can potentially be reused to answer questions beyond those originally envisioned. However, this often requires computational and statistical skills beyond the reach of most bench scientists. The development of educational and accessible computational tools is thus critical, as are crowdsourcing efforts that utilize the community's expertise to curate public data for hypothesis generation and testing. Here we review the history of public-data reuse and argue for greater incorporation of computational and statistical sciences into the biomedical education curriculum and the development of biologist-friendly crowdsourcing tools. Finally, we provide a resource list for the reuse of public data and highlight an illustrative crowdsourcing exercise to explore public gene-expression data of human autoimmune diseases and corresponding mouse models. Through education, tool development, and community engagement, immunologists will be poised to transform public data into biological insights. Copyright © 2016. Published by Elsevier Inc.

  18. Geocoding uncertainty analysis for the automated processing of Sentinel-1 data using Sentinel-1 Toolbox software

    Science.gov (United States)

    Dostálová, Alena; Naeimi, Vahid; Wagner, Wolfgang; Elefante, Stefano; Cao, Senmao; Persson, Henrik

    2016-10-01

    One of the major advantages of the Sentinel-1 data is its capability to provide very high spatio-temporal coverage allowing the mapping of large areas as well as creation of dense time-series of the Sentinel-1 acquisitions. The SGRT software developed at TU Wien aims at automated processing of Sentinel-1 data for global and regional products. The first step of the processing consists of the Sentinel-1 data geocoding with the help of S1TBX software and their resampling to a common grid. These resampled images serve as an input for the product derivation. Thus, it is very important to select the most reliable processing settings and assess the geocoding uncertainty for both backscatter and projected local incidence angle images. Within this study, selection of Sentinel-1 acquisitions over 3 test areas in Europe were processed manually in the S1TBX software, testing multiple software versions, processing settings and digital elevation models (DEM) and the accuracy of the resulting geocoded images were assessed. Secondly, all available Sentinel-1 data over the areas were processed using selected settings and detailed quality check was performed. Overall, strong influence of the used DEM on the geocoding quality was confirmed with differences up to 80 meters in areas with higher terrain variations. In flat areas, the geocoding accuracy of backscatter images was overall good, with observed shifts between 0 and 30m. Larger systematic shifts were identified in case of projected local incidence angle images. These results encourage the automated processing of large volumes of Sentinel-1 data.

  19. Learning GIS and exploring geolocated data with the all-in-one Geolokit toolbox for Google Earth

    Science.gov (United States)

    Watlet, A.; Triantafyllou, A.; Bastin, C.

    2016-12-01

    GIS software are today's essential tools to gather and visualize geological data, to apply spatial and temporal analysis and finally, to create and share interactive maps for further investigations in geosciences. Such skills are especially essential to learn for students who go through fieldtrips, samples collections or field experiments. However, time is generally missing to teach in detail all the aspects of visualizing geolocated geoscientific data. For these purposes, we developed Geolokit: a lightweight freeware dedicated to geodata visualization and written in Python, a high-level, cross-platform programming language. Geolokit software is accessible through a graphical user interface, designed to run in parallel with Google Earth, benefitting from the numerous interactive capabilities. It is designed as a very user-friendly toolbox that allows `geo-users' to import their raw data (e.g. GPS, sample locations, structural data, field pictures, maps), to use fast data analysis tools and to visualize these into the Google Earth environment using KML code; with no require of third party software, except Google Earth itself. Geolokit comes with a large number of geosciences labels, symbols, colours and placemarks and is applicable to display several types of geolocated data, including: Multi-points datasets Automatically computed contours of multi-points datasets via several interpolation methods Discrete planar and linear structural geology data in 2D or 3D supporting large range of structures input format Clustered stereonets and rose diagrams 2D cross-sections as vertical sections Georeferenced maps and grids with user defined coordinates Field pictures using either geo-tracking metadata from a camera built-in GPS module, or the same-day track of an external GPS In the end, Geolokit is helpful for quickly visualizing and exploring data without losing too much time in the numerous capabilities of GIS software suites. We are looking for students and teachers to

  20. Toolbox of Effects of CO2 Impurities on CO2 Transport and Storage Systems: 13th International Conference on Greenhouse Gas Control Technologies, GHGT 2016. 14 November 2016 through 18 November 2016

    NARCIS (Netherlands)

    Neele, F.; Koornneef, J.; Jakobsen, J.P.; Brunsvold, A.; Eickhoff, C.

    2017-01-01

    There is a need to gather new knowledge on the fundamental properties of CO2 mixtures with impurities and their impact on the chain integrity and economics of Carbon Capture & Storage (CCS) chains. One of the main results from the FP7 IMPACTS project is the IMPACTS toolbox, which comprises new