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Sample records for modeling toolbox nft

  1. Neuroelectromagnetic Forward Head Modeling Toolbox

    Science.gov (United States)

    Acar, Zeynep Akalin; Makeig, Scott

    2014-01-01

    This paper introduces a Neuroelectromagnetic Forward Head Modeling Toolbox (NFT) running under MATLAB (The Mathworks, Inc.) for generating realistic head models from available data (MRI and/or electrode locations) and for computing numerical solutions for the forward problem of electromagnetic source imaging. The NFT includes tools for segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues from T1-weighted magnetic resonance (MR) images. The Boundary Element Method (BEM) is used for the numerical solution of the forward problem. After extracting segmented tissue volumes, surface BEM meshes can be generated. When a subject MR image is not available, a template head model can be warped to measured electrode locations to obtain an individualized head model. Toolbox functions may be called either from a graphic user interface compatible with EEGLAB (http://sccn.ucsd.edu/eeglab), or from the MATLAB command line. Function help messages and a user tutorial are included. The toolbox is freely available under the GNU Public License for noncommercial use and open source development. PMID:20457183

  2. EEGLAB, SIFT, NFT, BCILAB, and ERICA: New Tools for Advanced EEG Processing

    Directory of Open Access Journals (Sweden)

    Arnaud Delorme

    2011-01-01

    Full Text Available We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1 a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2 a neuroelectromagnetic forward head modeling toolbox (NFT for building realistic electrical head models from available data; (3 a source information flow toolbox (SIFT for modeling ongoing or event-related effective connectivity between cortical areas; (4 a BCILAB toolbox for building online brain-computer interface (BCI models from available data, and (5 an experimental real-time interactive control and analysis (ERICA environment for real-time production and coordination of interactive, multimodal experiments.

  3. EEGLAB, SIFT, NFT, BCILAB, and ERICA: new tools for advanced EEG processing.

    Science.gov (United States)

    Delorme, Arnaud; Mullen, Tim; Kothe, Christian; Akalin Acar, Zeynep; Bigdely-Shamlo, Nima; Vankov, Andrey; Makeig, Scott

    2011-01-01

    We describe a set of complementary EEG data collection and processing tools recently developed at the Swartz Center for Computational Neuroscience (SCCN) that connect to and extend the EEGLAB software environment, a freely available and readily extensible processing environment running under Matlab. The new tools include (1) a new and flexible EEGLAB STUDY design facility for framing and performing statistical analyses on data from multiple subjects; (2) a neuroelectromagnetic forward head modeling toolbox (NFT) for building realistic electrical head models from available data; (3) a source information flow toolbox (SIFT) for modeling ongoing or event-related effective connectivity between cortical areas; (4) a BCILAB toolbox for building online brain-computer interface (BCI) models from available data, and (5) an experimental real-time interactive control and analysis (ERICA) environment for real-time production and coordination of interactive, multimodal experiments.

  4. The State Space Models Toolbox for MATLAB

    Directory of Open Access Journals (Sweden)

    Jyh-Ying Peng

    2011-05-01

    Full Text Available State Space Models (SSM is a MATLAB toolbox for time series analysis by state space methods. The software features fully interactive construction and combination of models, with support for univariate and multivariate models, complex time-varying (dy- namic models, non-Gaussian models, and various standard models such as ARIMA and structural time-series models. The software includes standard functions for Kalman fil- tering and smoothing, simulation smoothing, likelihood evaluation, parameter estimation, signal extraction and forecasting, with incorporation of exact initialization for filters and smoothers, and support for missing observations and multiple time series input with com- mon analysis structure. The software also includes implementations of TRAMO model selection and Hillmer-Tiao decomposition for ARIMA models. The software will provide a general toolbox for time series analysis on the MATLAB platform, allowing users to take advantage of its readily available graph plotting and general matrix computation capabilities.

  5. 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....

  6. 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...

  7. Modeling visual working memory with the MemToolbox.

    Science.gov (United States)

    Suchow, Jordan W; Brady, Timothy F; Fougnie, Daryl; Alvarez, George A

    2013-08-20

    The MemToolbox is a collection of MATLAB functions for modeling visual working memory. In support of its goal to provide a full suite of data analysis tools, the toolbox includes implementations of popular models of visual working memory, real and simulated data sets, Bayesian and maximum likelihood estimation procedures for fitting models to data, visualizations of data and fit, validation routines, model comparison metrics, and experiment scripts. The MemToolbox is released under the permissive BSD license and is available at http://memtoolbox.org.

  8. TMBP: A Topic Modeling Toolbox Using Belief Propagation

    CERN Document Server

    Zeng, Jia

    2012-01-01

    Latent Dirichlet allocation (LDA) is an important class of hierarchical Bayesian models for probabilistic topic modeling, which attracts worldwide interests and touches on many important applications in text mining, computer vision and computational biology. This paper introduces a topic modeling toolbox (TMBP) based on the belief propagation (BP) algorithms. This toolbox is implemented by MEX C++/MATLAB platform for either Windows or Linux. The current version includes various learning algorithms for latent Dirichlet allocation (LDA), author-topic models (ATM), relational topic models (RTM), and labeled LDA (LaLDA). This toolbox is an ongoing project and more and more BP-based learning algorithms for various LDA-based topic models will be added in the near future. Interested readers may also extend this toolbox for solving more complicated topic modeling problems. The source code is freely available under the GNU General Public Licence, Version 1.0 at http://code.google.com/p/tmbp-topicmodel-beliefpropagatio...

  9. Direct Kinematic modeling of 6R Robot using Robotics Toolbox

    Directory of Open Access Journals (Sweden)

    Prashant Badoni

    2016-01-01

    Full Text Available The traditional approaches are insufficient to solve the complex kinematics problems of the redundant robotic manipulators. To overcome such intricacy, Peter Corke’s Robotics Toolbox [1] is utilized in the present study. This paper aims to model the direct kinematics of a 6 degree of freedom (DOF Robotic arm. The Toolbox uses the Denavit-Hartenberg (DH Methodology [2] to compute the kinematic model of the robot.

  10. Direct Kinematic modeling of 6R Robot using Robotics Toolbox

    OpenAIRE

    Prashant Badoni

    2016-01-01

    The traditional approaches are insufficient to solve the complex kinematics problems of the redundant robotic manipulators. To overcome such intricacy, Peter Corke’s Robotics Toolbox [1] is utilized in the present study. This paper aims to model the direct kinematics of a 6 degree of freedom (DOF) Robotic arm. The Toolbox uses the Denavit-Hartenberg (DH) Methodology [2] to compute the kinematic model of the robot.

  11. Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) User's Guide

    Science.gov (United States)

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

    2014-01-01

    The Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) software package is an open source, MATLABSimulink toolbox (plug in) that can be used by industry professionals and academics for the development of thermodynamic and controls simulations.

  12. 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...

  13. 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...

  14. 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.

  15. 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

  16. LIMO EEG: a toolbox for hierarchical LInear MOdeling of ElectroEncephaloGraphic data

    National Research Council Canada - National Science Library

    Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

    2011-01-01

    ...). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data...

  17. LIMO EEG: A Toolbox for Hierarchical LInear MOdeling of ElectroEncephaloGraphic Data

    National Research Council Canada - National Science Library

    Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

    2011-01-01

    ...). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data...

  18. 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.

  19. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

    OpenAIRE

    2011-01-01

    Over the past decade, a growing community of researchers has emerged around the use of COnstraint-Based Reconstruction and Analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a significant update of this in silico ToolBox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis m...

  20. T-MATS Toolbox for the Modeling and Analysis of Thermodynamic Systems

    Science.gov (United States)

    Chapman, Jeffryes W.

    2014-01-01

    The Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) is a MATLABSimulink (The MathWorks Inc.) plug-in for creating and simulating thermodynamic systems and controls. The package contains generic parameterized components that can be combined with a variable input iterative solver and optimization algorithm to create complex system models, such as gas turbines.

  1. 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....

  2. A comprehensive validation toolbox for regional ocean models - Outline, implementation and application to the Baltic Sea

    Science.gov (United States)

    Jandt, Simon; Laagemaa, Priidik; Janssen, Frank

    2014-05-01

    The systematic and objective comparison between output from a numerical ocean model and a set of observations, called validation in the context of this presentation, is a beneficial activity at several stages, starting from early steps in model development and ending at the quality control of model based products delivered to customers. Even though the importance of this kind of validation work is widely acknowledged it is often not among the most popular tasks in ocean modelling. In order to ease the validation work a comprehensive toolbox has been developed in the framework of the MyOcean-2 project. The objective of this toolbox is to carry out validation integrating different data sources, e.g. time-series at stations, vertical profiles, surface fields or along track satellite data, with one single program call. The validation toolbox, implemented in MATLAB, features all parts of the validation process - ranging from read-in procedures of datasets to the graphical and numerical output of statistical metrics of the comparison. The basic idea is to have only one well-defined validation schedule for all applications, in which all parts of the validation process are executed. Each part, e.g. read-in procedures, forms a module in which all available functions of this particular part are collected. The interface between the functions, the module and the validation schedule is highly standardized. Functions of a module are set up for certain validation tasks, new functions can be implemented into the appropriate module without affecting the functionality of the toolbox. The functions are assigned for each validation task in user specific settings, which are externally stored in so-called namelists and gather all information of the used datasets as well as paths and metadata. In the framework of the MyOcean-2 project the toolbox is frequently used to validate the forecast products of the Baltic Sea Marine Forecasting Centre. Hereby the performance of any new product

  3. MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

    OpenAIRE

    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...

  4. 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.

  5. AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology

    Science.gov (United States)

    Balsa-Canto, Eva; Henriques, David; Gábor, Attila; Banga, Julio R.

    2016-01-01

    Motivation: Many problems of interest in dynamic modeling and control of biological systems can be posed as non-linear optimization problems subject to algebraic and dynamic constraints. In the context of modeling, this is the case of, e.g. parameter estimation, optimal experimental design and dynamic flux balance analysis. In the context of control, model-based metabolic engineering or drug dose optimization problems can be formulated as (multi-objective) optimal control problems. Finding a solution to those problems is a very challenging task which requires advanced numerical methods. Results: This work presents the AMIGO2 toolbox: the first multiplatform software tool that automatizes the solution of all those problems, offering a suite of state-of-the-art (multi-objective) global optimizers and advanced simulation approaches. Availability and Implementation: The toolbox and its documentation are available at: sites.google.com/site/amigo2toolbox. Contact: ebalsa@iim.csic.es Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27378288

  6. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

    Science.gov (United States)

    Schellenberger, Jan; Que, Richard; Fleming, Ronan M T; Thiele, Ines; Orth, Jeffrey D; Feist, Adam M; Zielinski, Daniel C; Bordbar, Aarash; Lewis, Nathan E; Rahmanian, Sorena; Kang, Joseph; Hyduke, Daniel R; Palsson, Bernhard Ø

    2011-08-04

    Over the past decade, a growing community of researchers has emerged around the use of constraint-based reconstruction and analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a substantial update of this in silico toolbox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include (i) network gap filling, (ii) (13)C analysis, (iii) metabolic engineering, (iv) omics-guided analysis and (v) visualization. As with the first version, the COBRA Toolbox reads and writes systems biology markup language-formatted models. In version 2.0, we improved performance, usability and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the toolbox and validate results. This toolbox lowers the barrier of entry to use powerful COBRA methods.

  7. A Matlab Toolbox for Parametric Identification of Radiation-Force Models of Ships and Offshore Structures

    Directory of Open Access Journals (Sweden)

    Tristan Perez

    2009-01-01

    Full Text Available This article describes a Matlab toolbox for parametric identification of fluid-memory models associated with the radiation forces ships and offshore structures. Radiation forces are a key component of force-to- motion models used in simulators, motion control designs, and also for initial performance evaluation of wave-energy converters. The software described provides tools for preparing non-parmatric data and for identification with automatic model-order detection. The identification problem is considered in the frequency domain.

  8. A toolbox model of evolution of metabolic pathways on networks of arbitrary topology.

    Directory of Open Access Journals (Sweden)

    Tin Yau Pang

    2011-05-01

    Full Text Available In prokaryotic genomes the number of transcriptional regulators is known to be proportional to the square of the total number of protein-coding genes. A toolbox model of evolution was recently proposed to explain this empirical scaling for metabolic enzymes and their regulators. According to its rules, the metabolic network of an organism evolves by horizontal transfer of pathways from other species. These pathways are part of a larger "universal" network formed by the union of all species-specific networks. It remained to be understood, however, how the topological properties of this universal network influence the scaling law of functional content of genomes in the toolbox model. Here we answer this question by first analyzing the scaling properties of the toolbox model on arbitrary tree-like universal networks. We prove that critical branching topology, in which the average number of upstream neighbors of a node is equal to one, is both necessary and sufficient for quadratic scaling. We further generalize the rules of the model to incorporate reactions with multiple substrates/products as well as branched and cyclic metabolic pathways. To achieve its metabolic tasks, the new model employs evolutionary optimized pathways with minimal number of reactions. Numerical simulations of this realistic model on the universal network of all reactions in the KEGG database produced approximately quadratic scaling between the number of regulated pathways and the size of the metabolic network. To quantify the geometrical structure of individual pathways, we investigated the relationship between their number of reactions, byproducts, intermediate, and feedback metabolites. Our results validate and explain the ubiquitous appearance of the quadratic scaling for a broad spectrum of topologies of underlying universal metabolic networks. They also demonstrate why, in spite of "small-world" topology, real-life metabolic networks are characterized by a broad

  9. Modeling Mechanical and Electrical Uncertain Systems using Functions of Robust Control MATLAB Toolbox®3

    Directory of Open Access Journals (Sweden)

    Mohammed Tawfik Hussein

    2015-04-01

    Full Text Available Uncertainty is inherent property of all real life control systems, and this is due to that there is nothing constant practically; all parameters are going to change under some environmental circumstances, therefore control engineers must not ignore this changing since it can affect the behavior and the performance of the system. In this paper a critical research method for modeling uncertain systems is demonstrated with the utilization of built in robust control Matlab Toolbox®3 functions. Good results were obtained for testing the stability of interval linear time invariant systems. Finally mechanical and electrical uncertain systems were implemented as practical example to validate the uncertainty.

  10. The Visible Signature Modelling and Evaluation ToolBox

    Science.gov (United States)

    2008-12-01

    Orlando, FL, USA, pp. 452– 461. 53. Doll, T. J., Home, R., Cooke, K. J., Wasilewski , A. A., Sheerin, D. T. & Hetzler, M. C. (2003) Human vision simulation...T., McWhorter, S. W., Schmieder, D. E., Hetzler, M. C., Stewart, J. M., Wasilewski , A. A., Owens, W. R., Sheffer, A. D., Galloway, G. l. & Harbert... Wasilewski , A. A. (1995) Sim- ulation of selective attention and training effects in visual search and detection, in Vision models for target

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

    Science.gov (United States)

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

    2013-12-01

    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.

  12. Toolbox model of evolution of prokaryotic metabolic networks and their regulation.

    Science.gov (United States)

    Maslov, Sergei; Krishna, Sandeep; Pang, Tin Yau; Sneppen, Kim

    2009-06-16

    It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a simple model in which metabolic and regulatory networks of prokaryotes are shaped by horizontal gene transfer of coregulated metabolic pathways. Adapting to a new environmental condition monitored by a new transcription factor (e.g., learning to use another nutrient) involves both acquiring new enzymes and reusing some of the enzymes already encoded in the genome. As the repertoire of enzymes of an organism (its toolbox) grows larger, it can reuse its enzyme tools more often and thus needs to get fewer new ones to master each new task. From this observation, it logically follows that the number of functional tasks and their regulators increases faster than linearly with the total number of genes encoding enzymes. Genomes can also shrink, e.g., because of a loss of a nutrient from the environment, followed by deletion of its regulator and all enzymes that become redundant. We propose several simple models of network evolution elaborating on this toolbox argument and reproducing the empirically observed quadratic scaling. The distribution of lengths of pathway branches in our model agrees with that of the real-life metabolic network of Escherichia coli. Thus, our model provides a qualitative explanation for broad distributions of regulon sizes in prokaryotes.

  13. VisAn MHD: a toolbox in Matlab for MHD computer model data visualisation and analysis

    Directory of Open Access Journals (Sweden)

    P. Daum

    2007-03-01

    Full Text Available Among the many challenges facing modern space physics today is the need for a visualisation and analysis package which can examine the results from the diversity of numerical and empirical computer models as well as observational data. Magnetohydrodynamic (MHD models represent the latest numerical models of the complex Earth's space environment and have the unique ability to span the enormous distances present in the magnetosphere from several hundred kilometres to several thousand kilometres above the Earth surface. This feature enables scientist to study complex structures of processes where otherwise only point measurements from satellites or ground-based instruments are available. Only by combining these observational data and the MHD simulations it is possible to enlarge the scope of the point-to-point observations and to fill the gaps left by measurements in order to get a full 3-D representation of the processes in our geospace environment. In this paper we introduce the VisAn MHD toolbox for Matlab as a tool for the visualisation and analysis of observational data and MHD simulations. We have created an easy to use tool which is capable of highly sophisticated visualisations and data analysis of the results from a diverse set of MHD models in combination with in situ measurements from satellites and ground-based instruments. The toolbox is being released under an open-source licensing agreement to facilitate and encourage community use and contribution.

  14. 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.

  15. Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System (T-MATS)

    Science.gov (United States)

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

    2014-01-01

    A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This presentation describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this presentation is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture.

  16. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models.

    Science.gov (United States)

    Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

    2014-10-07

    Constraint-based models are currently the only methodology that allows the study of metabolism at the whole-genome scale. Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic. Here we introduce MONGOOSE, a toolbox for analysing the structure of constraint-based metabolic models in exact arithmetic. We apply MONGOOSE to the analysis of 98 existing metabolic network models and find that the biomass reaction is surprisingly blocked (unable to sustain non-zero flux) in nearly half of them. We propose a principled approach for unblocking these reactions and extend it to the problems of identifying essential and synthetic lethal reactions and minimal media. Our structural insights enable a systematic study of constraint-based metabolic models, yielding a deeper understanding of their possibilities and limitations.

  17. 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.

  18. 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....

  19. Models with discrete latent variables for analysis of categorical data: a framework and a MATLAB MDLV toolbox.

    Science.gov (United States)

    Yu, Hsiu-Ting

    2013-12-01

    Studies in the social and behavioral sciences often involve categorical data, such as ratings, and define latent constructs underlying the research issues as being discrete. In this article, models with discrete latent variables (MDLV) for the analysis of categorical data are grouped into four families, defined in terms of two dimensions (time and sampling) of the data structure. A MATLAB toolbox (referred to as the "MDLV toolbox") was developed for applying these models in practical studies. For each family of models, model representations and the statistical assumptions underlying the models are discussed. The functions of the toolbox are demonstrated by fitting these models to empirical data from the European Values Study. The purpose of this article is to offer a framework of discrete latent variable models for data analysis, and to develop the MDLV toolbox for use in estimating each model under this framework. With this accessible tool, the application of data modeling with discrete latent variables becomes feasible for a broad range of empirical studies.

  20. 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

  1. von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models.

    Science.gov (United States)

    Fleming, Ronan M T; Thiele, Ines

    2011-01-01

    In flux balance analysis of genome scale stoichiometric models of metabolism, the principal constraints are uptake or secretion rates, the steady state mass conservation assumption and reaction directionality. Here, we introduce an algorithmic pipeline for quantitative assignment of reaction directionality in multi-compartmental genome scale models based on an application of the second law of thermodynamics to each reaction. Given experimental or computationally estimated standard metabolite species Gibbs energy and metabolite concentrations, the algorithms bounds reaction Gibbs energy, which is transformed to in vivo pH, temperature, ionic strength and electrical potential. This cross-platform MATLAB extension to the COnstraint-Based Reconstruction and Analysis (COBRA) toolbox is computationally efficient, extensively documented and open source. http://opencobra.sourceforge.net.

  2. Geo-PUMMA: Urban and Periurban Landscape Representation Toolbox for Hydrological Distributed Modeling

    Science.gov (United States)

    Sanzana, Pedro; Gironas, Jorge; Braud, Isabelle; Branger, Flora; Rodriguez, Fabrice; Vargas, Ximena; Hitschfeld, Nancy; Francisco Munoz, Jose

    2016-04-01

    In addition to land use changes, the process of urbanization can modify the direction of the surface and sub-surface flows, generating complex environments and increasing the types of connectivity between pervious and impervious areas. Thus, hydrological pathways in urban and periurban areas are significantly affected by artificial elements like channels, pipes, streets and other elements of storm water systems. This work presents Geo-PUMMA, a new GIS toolbox to generate vectorial meshes for distributed hydrological modeling and extract the drainage network in urban and periurban terrain. Geo-PUMMA gathers spatial information maps (e.g. cadastral, soil types, geology and digital elevation models) to produce Hydrological Response Units (HRU) and Urban Hydrological Elements (UHE). Geo-PUMMA includes tools to improve the initial mesh derived from GIS layers intersection in order to respect geometrical constraints, which ensures numerical stability while preserving the shape of the initial HRUs and minimizing the small elements to lower computing times. The geometrical constraints taken into account include: elements convexity, limitation of the number of sliver elements (e.g. roads) and of very small or very large elements. This toolbox allows the representation of basins at small scales (0.1-10km2), as it takes into account the hydrological connectivity of the main elements explicitly, and improves the representation of water pathways compared with classical raster approaches. Geo-PUMMA also allows the extraction of basin morphologic properties such as the width function, the area function and the imperviousness function. We applied this new toolbox to two periurban catchments: the Mercier catchment located near Lyon, France, and the Estero El Guindo catchment located in the Andean piedmont in the Maipo River, Chile. We use the capability of Geo-PUMMA to generate three different meshes. The first one is the initial mesh derived from the direct intersection of GIS

  3. LIMO EEG: A Toolbox for Hierarchical LInear MOdeling of ElectroEncephaloGraphic Data

    Directory of Open Access Journals (Sweden)

    Cyril R. Pernet

    2011-01-01

    Full Text Available Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip. LIMO EEG is a Matlab toolbox (EEGLAB compatible to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses.

  4. LIMO EEG: a toolbox for hierarchical LInear MOdeling of ElectroEncephaloGraphic data.

    Science.gov (United States)

    Pernet, Cyril R; Chauveau, Nicolas; Gaspar, Carl; Rousselet, Guillaume A

    2011-01-01

    Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all space and time dimensions, while accounting for single trial variability using a simple hierarchical linear modelling of the data. In addition, LIMO EEG provides robust parametric tests, therefore providing a new and complementary tool in the analysis of neural evoked responses.

  5. Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic System T-MATS

    Science.gov (United States)

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

    2014-01-01

    A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

  6. Propulsion System Simulation Using the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS)

    Science.gov (United States)

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

    2014-01-01

    A simulation toolbox has been developed for the creation of both steady-state and dynamic thermodynamic software models. This paper describes the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS), which combines generic thermodynamic and controls modeling libraries with a numerical iterative solver to create a framework for the development of thermodynamic system simulations, such as gas turbine engines. The objective of this paper is to present an overview of T-MATS, the theory used in the creation of the module sets, and a possible propulsion simulation architecture. A model comparison was conducted by matching steady-state performance results from a T-MATS developed gas turbine simulation to a well-documented steady-state simulation. Transient modeling capabilities are then demonstrated when the steady-state T-MATS model is updated to run dynamically.

  7. 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.

  8. MetaboTools: A comprehensive toolbox for analysis of genome-scale metabolic models

    Directory of Open Access Journals (Sweden)

    Maike Kathrin Aurich

    2016-08-01

    Full Text Available 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.

  9. 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.

  10. 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.

  11. Multi-Parametric Toolbox 3.0

    OpenAIRE

    Herceg, Martin; Kvasnica, Michal; Jones, Colin; Morari, Manfred

    2013-01-01

    The Multi-Parametric Toolbox is a col- lection of algorithms for modeling, control, analysis, and deployment of constrained optimal controllers developed under Matlab. It features a powerful ge- ometric library that extends the application of the toolbox beyond optimal control to various problems arising in computational geometry. The new version 3.0 is a complete rewrite of the original toolbox with a more flexible structure that offers faster integration of new algorithms. The numerical sid...

  12. A Toolbox for Rotorcraft Preliminary Design

    OpenAIRE

    Lier, Max; Krenik, Alex; Kunze, Philipp; Kohlgrüber, Dieter; Schwinn, Dominik; Lützenberger, Marius

    2015-01-01

    The German Aerospace Center (DLR) developed a toolbox, which is able to reflect the conceptual and preliminary design process of rotorcraft configuration. Such a toolbox is a valuable aid for the design engineer and can be used for the assessment of new technologies with regard to the overall configuration. This toolbox is currently extended to model novel rotorcraft configurations. Automated optimization procedures will be added in the future as well. This paper describes the too...

  13. LIMO EEG: A Toolbox for Hierarchical LInear MOdeling of ElectroEncephaloGraphic Data

    OpenAIRE

    Pernet, C. R.; Chauveau, N.; Gaspar, C.; Rousselet, G.A.

    2011-01-01

    Magnetic- and electric-evoked brain responses have traditionally been analyzed by comparing the peaks or mean amplitudes of signals from selected channels and averaged across trials. More recently, tools have been developed to investigate single trial response variability (e.g., EEGLAB) and to test differences between averaged evoked responses over the entire scalp and time dimensions (e.g., SPM, Fieldtrip). LIMO EEG is a Matlab toolbox (EEGLAB compatible) to analyse evoked responses over all...

  14. 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.

  15. 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.

  16. 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

  17. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Benveniste, J.; Knudsen, P.

    2013-12-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT 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 available as well. Recently, the second version of the GOCE User Toolbox (GUT) was developed to enhance the exploitation of GOCE level 2 data with ERS ENVISAT altimetry. The developments of GUT focused on the following issues: Data Extraction, Generation, Filtering, and Data Save and Restore Without any doubt the development of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for oceanography. The results of the preliminary analysis carried out in this phase of the GUTS project have already demonstrated a significant advance in the ability to determine the ocean's general circulation. The improved gravity models provided by the GOCE mission have enhanced the resolution and sharpened the boundaries of those features compared with earlier satellite only solutions. Calculation of the geostrophic surface currents from the MDT reveals improvements for all of the ocean's major current systems.

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

    Science.gov (United States)

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

    2014-12-01

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

  19. 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.

  20. GOCE User Toolbox and Tutorial

    Science.gov (United States)

    Benveniste, Jérôme; Knudsen, Per

    2016-07-01

    The GOCE User Toolbox GUT is a compilation of tools for the utilisation and analysis of GOCE Level 2 products. GUT support applications in Geodesy, Oceanography and Solid Earth Physics. The GUT Tutorial provides information and guidance in how to use the toolbox for a variety of applications. GUT 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 available as well. Without any doubt the development of the GOCE user toolbox have played a major role in paving the way to successful use of the GOCE data for oceanography. The GUT version 2.2 was released in April 2014 and beside some bug-fixes it adds the capability for the computation of Simple Bouguer Anomaly (Solid-Earth). During this fall a new GUT version 3 has been released. GUTv3 was further developed through a collaborative effort where the scientific communities participate aiming on an implementation of remaining functionalities facilitating a wider span of research in the fields of Geodesy, Oceanography and Solid earth studies. Accordingly, the GUT version 3 has: - An attractive and easy to use Graphic User Interface (GUI) for the toolbox, - Enhance the toolbox with some further software functionalities such as to facilitate the use of gradients, anisotropic diffusive filtering and computation of Bouguer and isostatic gravity anomalies. - An associated GUT VCM tool for analyzing the GOCE variance covariance matrices.

  1. 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...

  2. 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-invariant lin......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...

  3. Optimization of model parameters and experimental designs with the Optimal Experimental Design Toolbox (v1.0) exemplified by sedimentation in salt marshes

    Science.gov (United States)

    Reimer, J.; Schuerch, M.; Slawig, T.

    2015-03-01

    The geosciences are a highly suitable field of application for optimizing model parameters and experimental designs especially because many data are collected. In this paper, the weighted least squares estimator for optimizing model parameters is presented together with its asymptotic properties. A popular approach to optimize experimental designs called local optimal experimental designs is described together with a lesser known approach which takes into account the potential nonlinearity of the model parameters. These two approaches have been combined with two methods to solve their underlying discrete optimization problem. All presented methods were implemented in an open-source MATLAB toolbox called the Optimal Experimental Design Toolbox whose structure and application is described. In numerical experiments, the model parameters and experimental design were optimized using this toolbox. Two existing models for sediment concentration in seawater and sediment accretion on salt marshes of different complexity served as an application example. The advantages and disadvantages of these approaches were compared based on these models. Thanks to optimized experimental designs, the parameters of these models could be determined very accurately with significantly fewer measurements compared to unoptimized experimental designs. The chosen optimization approach played a minor role for the accuracy; therefore, the approach with the least computational effort is recommended.

  4. The Brain's Versatile Toolbox.

    Science.gov (United States)

    Pinker, Steven

    1997-01-01

    Considers the role of evolution and natural selection in the functioning of the modern human brain. Natural selection equipped humans with a mental toolbox of intuitive theories about the world which were used to master rocks, tools, plants, animals, and one another. The same toolbox is used today to master the intellectual challenges of modern…

  5. Using the ARTMO toolbox for automated retrieval of biophysical parameters through radiative transfer model inversion: Optimizing LUT-based inversion

    Science.gov (United States)

    Verrelst, J.; Rivera, J. P.; Leonenko, G.; Alonso, L.; Moreno, J.

    2012-04-01

    Radiative transfer (RT) modeling plays a key role for earth observation (EO) because it is needed to design EO instruments and to develop and test inversion algorithms. The inversion of a RT model is considered as a successful approach for the retrieval of biophysical parameters because of being physically-based and generally applicable. However, to the broader community this approach is considered as laborious because of its many processing steps and expert knowledge is required to realize precise model parameterization. We have recently developed a radiative transfer toolbox ARTMO (Automated Radiative Transfer Models Operator) with the purpose of providing in a graphical user interface (GUI) essential models and tools required for terrestrial EO applications such as model inversion. In short, the toolbox allows the user: i) to choose between various plant leaf and canopy RT models (e.g. models from the PROSPECT and SAIL family, FLIGHT), ii) to choose between spectral band settings of various air- and space-borne sensors or defining own sensor settings, iii) to simulate a massive amount of spectra based on a look up table (LUT) approach and storing it in a relational database, iv) to plot spectra of multiple models and compare them with measured spectra, and finally, v) to run model inversion against optical imagery given several cost options and accuracy estimates. In this work ARTMO was used to tackle some well-known problems related to model inversion. According to Hadamard conditions, mathematical models of physical phenomena are mathematically invertible if the solution of the inverse problem to be solved exists, is unique and depends continuously on data. This assumption is not always met because of the large number of unknowns and different strategies have been proposed to overcome this problem. Several of these strategies have been implemented in ARTMO and were here analyzed to optimize the inversion performance. Data came from the SPARC-2003 dataset

  6. 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.

  7. 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...

  8. 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

  9. A Dynamic Modeling Toolbox for Air Vehicle Vapor Cycle Systems (Postprint)

    Science.gov (United States)

    2013-10-01

    Transcritical Vapor Compression Systems.” Journal of Dynamic Systems, Measurement, and Control, 2004: 54-64. 7. Li, B, Otten, R, Chandan, V, Mohs , W...and Trystram, G. “Low Order Dynamic Model os a Vapor Compression Cycle for Process Control Design.” Journal of Food Process, 2003: 193-199. 13

  10. An exact arithmetic toolbox for a consistent and reproducible structural analysis of metabolic network models

    National Research Council Canada - National Science Library

    Chindelevitch, Leonid; Trigg, Jason; Regev, Aviv; Berger, Bonnie

    2014-01-01

    .... Flux balance analysis is commonly used to analyse constraint-based models. Curiously, the results of this analysis vary with the software being run, a situation that we show can be remedied by using exact rather than floating-point arithmetic...

  11. 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/Simulink...

  12. 3DIANA: 3D Domain Interaction Analysis: A Toolbox for Quaternary Structure Modeling.

    Science.gov (United States)

    Segura, Joan; Sanchez-Garcia, Ruben; Tabas-Madrid, Daniel; Cuenca-Alba, Jesus; Sorzano, Carlos Oscar S; Carazo, Jose Maria

    2016-02-23

    Electron microscopy (EM) is experiencing a revolution with the advent of a new generation of Direct Electron Detectors, enabling a broad range of large and flexible structures to be resolved well below 1 nm resolution. Although EM techniques are evolving to the point of directly obtaining structural data at near-atomic resolution, for many molecules the attainable resolution might not be enough to propose high-resolution structural models. However, accessing information on atomic coordinates is a necessary step toward a deeper understanding of the molecular mechanisms that allow proteins to perform specific tasks. For that reason, methods for the integration of EM three-dimensional maps with x-ray and NMR structural data are being developed, a modeling task that is normally referred to as fitting, resulting in the so called hybrid models. In this work, we present a novel application-3DIANA-specially targeted to those cases in which the EM map resolution is medium or low and additional experimental structural information is scarce or even lacking. In this way, 3DIANA statistically evaluates proposed/potential contacts between protein domains, presents a complete catalog of both structurally resolved and predicted interacting regions involving these domains and, finally, suggests structural templates to model the interaction between them. The evaluation of the proposed interactions is computed with DIMERO, a new method that scores physical binding sites based on the topology of protein interaction networks, which has recently shown the capability to increase by 200% the number of domain-domain interactions predicted in interactomes as compared to previous approaches. The new application displays the information at a sequence and structural level and is accessible through a web browser or as a Chimera plugin at http://3diana.cnb.csic.es.

  13. 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.

  14. DSamala toolbox software for analysing and simulating discrete, continuous, stochastic dynamic systems

    Directory of Open Access Journals (Sweden)

    Angelica María Atehortúa Labrador

    2012-09-01

    Full Text Available This article describes DSamala toolbox, a computational tool for simulating and analysing discrete, continuous, stochastic dynamic systems; It is presented as a MATLAB toolbox. DSamala toolbox makes a significant contribution to studying dynamic systems through the use of information and communication technology (ICT, especially when equations modelling these systems are difficult or impossible to solve analytically.

  15. A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences.

    Science.gov (United States)

    Eid, Sameh; Zalewski, Adam; Smieško, Martin; Ernst, Beat; Vedani, Angelo

    2013-01-04

    In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand-protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.

  16. New model systems to illuminate thyroid organogenesis. Part I: an update on the zebrafish toolbox.

    Science.gov (United States)

    Opitz, Robert; Antonica, Francesco; Costagliola, Sabine

    2013-12-01

    Thyroid dysgenesis (TD) resulting from defects during embryonic thyroid development represents a major cause of congenital hypothyroidism. The pathogenetic mechanisms of TD in human newborns, however, are still poorly understood and disease-causing genetic variants have been identified in only a small percentage of TD cases. This limited understanding of the pathogenesis of TD is partly due to a lack of knowledge on how intrinsic factors and extrinsic signalling cues orchestrate the differentiation of thyroid follicular cells and the morphogenesis of thyroid tissue. Recently, embryonic stem cells and zebrafish embryos emerged as novel model systems that allow for innovative experimental approaches in order to decipher cellular and molecular mechanisms of thyroid development and to unravel pathogenic mechanisms of TD. Zebrafish embryos offer several salient properties for studies on thyroid organogenesis including rapid and external development, optical transparency, ease of breeding, relative short generation time and amenability for genome editing. In this review, we will highlight recent advances in the zebrafish toolkit to visualize cellular dynamics of organ development and discuss specific prospects of the zebrafish model for studies on vertebrate thyroid development and human congenital thyroid diseases.

  17. Enola Gay: an integrated modelling optical toolbox applied to a wide-field telescope

    Science.gov (United States)

    Schipani, P.; Perrotta, F.

    2008-07-01

    The integrated modelling approach is fundamental in telescopes design where it is necessary to merge different disciplines together. This paper describes the integration of optical ray-tracing capabilities within the Matlab computational environment. This approach allows to write automatic procedures to implement a huge number of computations, that are very unpractical to perform in interactive mode by ray tracing software packages. Data produced by computations are stored and automatically analyzed. One of the main benefits from this approach comes from the traceability of the work, that is intrinsically impossible when the optical designer works in interactive mode. The right procedure is built and tuned just the first time and the computation software is available for inspection and check. Furthermore computations and results are easily reproducible simply re-running Matlab scripts. An automatic approach is especially helpful in wide-field telescope projects where the optical quality has to be studied over a wide field of view. This leads to repeat the same computations many times in a number of fields. In interactive mode this would cause a significant waste of optical designer time to repeat many times the same manual procedures. The solution proposed here allows to save time and prevent occasional mistakes.

  18. Enlarging the toolbox for allergen epitope definition with an allergen-type model protein.

    Science.gov (United States)

    Berkner, Hanna; Seutter von Loetzen, Christian; Hartl, Maximilian; Randow, Stefanie; Gubesch, Michaela; Vogel, Lothar; Husslik, Felix; Reuter, Andreas; Lidholm, Jonas; Ballmer-Weber, Barbara; Vieths, Stefan; Rösch, Paul; Schiller, Dirk

    2014-01-01

    Birch pollen-allergic subjects produce polyclonal cross-reactive IgE antibodies that mediate pollen-associated food allergies. The major allergen Bet v 1 and its homologs in plant foods bind IgE in their native protein conformation. Information on location, number and clinical relevance of IgE epitopes is limited. We addressed the use of an allergen-related protein model to identify amino acids critical for IgE binding of PR-10 allergens. Norcoclaurine synthase (NCS) from meadow rue is structurally homologous to Bet v 1 but does not bind Bet v 1-reactive IgE. NCS was used as the template for epitope grafting. NCS variants were tested with sera from 70 birch pollen allergic subjects and with monoclonal antibody BV16 reported to compete with IgE binding to Bet v 1. We generated an NCS variant (Δ29NCSN57/I58E/D60N/V63P/D68K) harboring an IgE epitope of Bet v 1. Bet v 1-type protein folding of the NCS variant was evaluated by 1H-15N-HSQC NMR spectroscopy. BV16 bound the NCS variant and 71% (50/70 sera) of our study population showed significant IgE binding. We observed IgE and BV16 cross-reactivity to the epitope presented by the NCS variant in a subgroup of Bet v 1-related allergens. Moreover BV16 blocked IgE binding to the NCS variant. Antibody cross-reactivity depended on a defined orientation of amino acids within the Bet v 1-type conformation. Our system allows the evaluation of patient-specific epitope profiles and will facilitate both the identification of clinically relevant epitopes as biomarkers and the monitoring of therapeutic outcomes to improve diagnosis, prognosis, and therapy of allergies caused by PR-10 proteins.

  19. Enlarging the toolbox for allergen epitope definition with an allergen-type model protein.

    Directory of Open Access Journals (Sweden)

    Hanna Berkner

    Full Text Available Birch pollen-allergic subjects produce polyclonal cross-reactive IgE antibodies that mediate pollen-associated food allergies. The major allergen Bet v 1 and its homologs in plant foods bind IgE in their native protein conformation. Information on location, number and clinical relevance of IgE epitopes is limited. We addressed the use of an allergen-related protein model to identify amino acids critical for IgE binding of PR-10 allergens.Norcoclaurine synthase (NCS from meadow rue is structurally homologous to Bet v 1 but does not bind Bet v 1-reactive IgE. NCS was used as the template for epitope grafting. NCS variants were tested with sera from 70 birch pollen allergic subjects and with monoclonal antibody BV16 reported to compete with IgE binding to Bet v 1.We generated an NCS variant (Δ29NCSN57/I58E/D60N/V63P/D68K harboring an IgE epitope of Bet v 1. Bet v 1-type protein folding of the NCS variant was evaluated by 1H-15N-HSQC NMR spectroscopy. BV16 bound the NCS variant and 71% (50/70 sera of our study population showed significant IgE binding. We observed IgE and BV16 cross-reactivity to the epitope presented by the NCS variant in a subgroup of Bet v 1-related allergens. Moreover BV16 blocked IgE binding to the NCS variant. Antibody cross-reactivity depended on a defined orientation of amino acids within the Bet v 1-type conformation.Our system allows the evaluation of patient-specific epitope profiles and will facilitate both the identification of clinically relevant epitopes as biomarkers and the monitoring of therapeutic outcomes to improve diagnosis, prognosis, and therapy of allergies caused by PR-10 proteins.

  20. Feedback control of water supply in an NFT growing system

    NARCIS (Netherlands)

    Gieling, Th.H.; Janssen, H.J.J.; Vries, de H.C.; Loef, P.

    2001-01-01

    The paper explores a concept of irrigation control, where the supply of nutrient solution is controlled without the use of predictive uptake models but rather by the use of a direct feedback of a drain flow measurement. This concept proves to be a viable approach. Results are presented, showing the

  1. Acoustic signal processing toolbox for array processing

    Science.gov (United States)

    Pham, Tien; Whipps, Gene T.

    2003-08-01

    The US Army Research Laboratory (ARL) has developed an acoustic signal processing toolbox (ASPT) for acoustic sensor array processing. The intent of this document is to describe the toolbox and its uses. The ASPT is a GUI-based software that is developed and runs under MATLAB. The current version, ASPT 3.0, requires MATLAB 6.0 and above. ASPT contains a variety of narrowband (NB) and incoherent and coherent wideband (WB) direction-of-arrival (DOA) estimation and beamforming algorithms that have been researched and developed at ARL. Currently, ASPT contains 16 DOA and beamforming algorithms. It contains several different NB and WB versions of the MVDR, MUSIC and ESPRIT algorithms. In addition, there are a variety of pre-processing, simulation and analysis tools available in the toolbox. The user can perform simulation or real data analysis for all algorithms with user-defined signal model parameters and array geometries.

  2. Broadview Radar Altimetry Toolbox

    Science.gov (United States)

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

    2016-07-01

    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 Sentinel-3 L1 and L2 products. ESA endeavoured 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'Études 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) 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 Sentinel-3 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

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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...

  8. 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.

  9. Humanitarian demining technology toolbox

    Science.gov (United States)

    Joynt, Vernon P.

    2003-09-01

    This is a keynote address surveying the field of Humanitarian Demining (HD) from the viewpoint of a participating company. The controlling bodies, funding structures and some of the important sources of R&D relevant to HD are identified. The various techniques and technologies in common use as also technologies freshly put into field use are mentioned. The way in which they all fit into the demining toolbox is explained. Finally a view of future technologies that are potentially able to change HD efficiency and safety is discussed.

  10. 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.

  11. The MULTICOM toolbox for protein structure prediction

    Directory of Open Access Journals (Sweden)

    Cheng Jianlin

    2012-04-01

    Full Text Available Abstract Background As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or Results To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map prediction, disulfide bond prediction, beta-sheet topology prediction, fold recognition, multiple template combination and alignment, template-based tertiary structure modeling, protein model quality assessment, and mutation stability prediction. Conclusions These tools have been rigorously tested by many users in the last several years and/or during the last three rounds of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7-9 from 2006 to 2010, achieving state-of-the-art or near performance. In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and scientific research. It is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.

  12. 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.

  13. 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

  14. KMUT – Project Management Toolbox

    Directory of Open Access Journals (Sweden)

    Stefanie Quade

    2013-05-01

    Full Text Available Small and medium-sized enterprises (SMEs are increasingly dealing with international projects and distributed (sometimes even virtual teams. Consequently, they are looking for project management (PM tools which fit their respective needs regarding communication and collaboration. Unfortunately, the majority of the PM software available in the market seems to be oversized for this purpose. Instead most project managers are requesting smart solutions that allow quick implementation without any significant organisational or technical change. Within the research project InterComp SME 2.0 we combine theoretical research and real business to develop hands-on solutions for SMEs. This paper describes an effective approach for a “PM Toolbox” that allows finding the right project tool for a specific project need. The toolbox has been developed in due consideration of user stories gained from business practice, a more detailed SME business survey, a theoretical PM meta model and a market of PM tools. Since the business survey revealed that the readiness to use and test a “toolbox” is highly dependent on the type of user and his or her technical background, we designed the system based on use cases and user typology. As a result, we suggest a framework of open, freely available, easy-to-install, single and multi purpose PM software tools which can be selected solely on a need basis. With this free platform we want to guide practitioners through the tool jungle with the potential to grow into a lively community.

  15. 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.

  16. Systems Biology Toolbox for MATLAB: a computational platform for research in systems biology.

    Science.gov (United States)

    Schmidt, Henning; Jirstrand, Mats

    2006-02-15

    We present a Systems Biology Toolbox for the widely used general purpose mathematical software MATLAB. The toolbox offers systems biologists an open and extensible environment, in which to explore ideas, prototype and share new algorithms, and build applications for the analysis and simulation of biological and biochemical systems. Additionally it is well suited for educational purposes. The toolbox supports the Systems Biology Markup Language (SBML) by providing an interface for import and export of SBML models. In this way the toolbox connects nicely to other SBML-enabled modelling packages. Models are represented in an internal model format and can be described either by entering ordinary differential equations or, more intuitively, by entering biochemical reaction equations. The toolbox contains a large number of analysis methods, such as deterministic and stochastic simulation, parameter estimation, network identification, parameter sensitivity analysis and bifurcation analysis.

  17. 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

  18. 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

  19. 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

  20. A Descriptor Systems Toolbox for MATLAB

    OpenAIRE

    Varga, A

    2000-01-01

    We describe a recently developed DESCRIPTOR SYSTEMS Toolbox implemented under MATLAB. This Toolbox relies on the object oriented approach for control systems analysis and design provided within the standard CONTROL Toolbox of MATLAB. The basic approach to develop the DESCRIPTOR SYSTEMS Toolbox was to exploit the powerful matrix and system object manipulation features of MATLAB via flexible and functionally rich high level m-functions, while simultaneously enforcing highly efficient and numeri...

  1. The GMT/MATLAB Toolbox

    Science.gov (United States)

    Wessel, Paul; Luis, Joaquim F.

    2017-02-01

    The GMT/MATLAB toolbox is a basic interface between MATLAB® (or Octave) and GMT, the Generic Mapping Tools, which allows MATLAB users full access to all GMT modules. Data may be passed between the two programs using intermediate MATLAB structures that organize the metadata needed; these are produced when GMT modules are run. In addition, standard MATLAB matrix data can be used directly as input to GMT modules. The toolbox improves interoperability between two widely used tools in the geosciences and extends the capability of both tools: GMT gains access to the powerful computational capabilities of MATLAB while the latter gains the ability to access specialized gridding algorithms and can produce publication-quality PostScript-based illustrations. The toolbox is available on all platforms and may be downloaded from the GMT website.

  2. 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 i

  3. 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 i

  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...

  5. CBP TOOLBOX VERSION 2.0: CODE INTEGRATION ENHANCEMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Smith, F.; Flach, G.; BROWN, K.

    2013-06-01

    This report describes enhancements made to code integration aspects of the Cementitious Barriers Project (CBP) Toolbox as a result of development work performed at the Savannah River National Laboratory (SRNL) in collaboration with Vanderbilt University (VU) in the first half of fiscal year 2013. Code integration refers to the interfacing to standalone CBP partner codes, used to analyze the performance of cementitious materials, with the CBP Software Toolbox. The most significant enhancements are: 1) Improved graphical display of model results. 2) Improved error analysis and reporting. 3) Increase in the default maximum model mesh size from 301 to 501 nodes. 4) The ability to set the LeachXS/Orchestra simulation times through the GoldSim interface. These code interface enhancements have been included in a new release (Version 2.0) of the CBP Toolbox.

  6. CONTINEX: A Toolbox for Continuation in Experiments

    DEFF Research Database (Denmark)

    Schilder, Frank; Bureau, Emil; Santos, Ilmar

    2014-01-01

    -free models. The current version of the interface for experimental set-ups implements an algorithm for tuning control parameters, a robust noise-tolerant covering algorithm, and functions for monitoring (in)stability. In this talk we will report on experiments with an impact oscillator with magnetic actuators......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...

  7. 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 (D...

  8. 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...

  9. A toolbox for European judges

    NARCIS (Netherlands)

    Hesselink, M.W.

    2011-01-01

    The forthcoming instrument on European contract law, be it in the shape of an optional code for cross-border contracts or as an official toolbox for the European legislator, is likely to have a spill-over effect on private law adjudication in Europe. Judges will have no great difficulty in finding m

  10. Extend your toolbox with R

    CERN Document Server

    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.

  11. Power system identification toolbox: Phase two progress

    Energy Technology Data Exchange (ETDEWEB)

    Trudnowski, D.J.

    1994-08-01

    This report describes current progress on a project funded by the Bonneville Power Administration (BPA) to develop a set of state-of-the-art analysis software (termed the Power System Identification [PSI] Toolbox) for fitting dynamic models to measured data. The project is being conducted as a three-phase effort. The first phase, completed in late 1992, involved investigating the characteristics of the analysis techniques by evaluating existing software and developing guidelines for best use. Phase Two includes extending current software, developing new analysis algorithms and software, and demonstrating and developing applications. The final phase will focus on reorganizing the software into a modular collection of documented computer programs and developing user manuals with instruction and application guidelines. Phase Two is approximately 50% complete; progress to date and a vision for the final product of the PSI Toolbox are described. The needs of the power industry for specialized system identification methods are particularly acute. The industry is currently pushing to operate transmission systems much closer to theoretical limits by using real-time, large-scale control systems to dictate power flows and maintain dynamic stability. Reliably maintaining stability requires extensive system-dynamic modeling and analysis capability, including measurement-based methods. To serve this need, the BPA has developed specialized system-identification computer codes through in-house efforts and university contract research over the last several years. To make full integrated use of the codes, as well as other techniques, the BPA has commissioned Pacific Northwest Laboratory (PNL) to further develop the codes and techniques into the PSI Toolbox.

  12. 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.

  13. A flexible open-source toolbox for robust end-member modelling analysis - The R-package EMMAgeo

    Science.gov (United States)

    Dietze, Michael; Dietze, Elisabeth

    2013-04-01

    Interpreting geomorphological and sedimentological processes from grain-size data in environmental archives typically runs into problems when source- and process-related grain-size distributions become mixed during deposition. A powerful approach to overcome this ambiguity is to statistically "unmix" the samples. Typical algorithms use eigenspace decomposition and techniques of dimension reduction. This contribution presents a package for the free statistical software R. Some of the great advantages of R and R-packages are the open code structure, flexibility and low programming effort. The package contains a series of flexible, ready-to-use functions to perform different tasks of data tests, preparation, modelling and visualisation. The package originated from a recently presented Matlab-based end-member modelling algorithm (Dietze et al., 2012, SedGeol). It supports simple modelling of grain-size end-member loadings and scores (eigenspace extraction, factor rotation, data scaling, non-negative least squares solving) along with several measures of model quality. The package further provides preprocessing tools (e.g. grain-size scale conversions, tests of data structure, weight factor limit inference, determination of minimum, optimum and maximum number of meaningful end-members) and allows to model data sets with artificial or user-defined end-member loadings. EMMAgeo also supports inferring uncertainty estimation from a series of plausible model runs and the determination of robust end-members. The contribution presents important package functions, thereby illustrating how large data sets of artificial and natural grain-size samples from different depositional environments can be analysed to infer quantified process-related proxies.

  14. 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 ...

  15. 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.

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

    DEFF Research Database (Denmark)

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

    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...... 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....

  17. 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...... 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....

  18. 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...

  19. 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...

  20. MTpy: A Python toolbox for magnetotellurics

    Science.gov (United States)

    Krieger, Lars; Peacock, Jared R.

    2014-11-01

    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. In its current state, modules and functions of MTpy work on raw and pre-processed MT data. However, opposite to providing a static compilation of software, we prefer to introduce MTpy as a flexible software toolbox, whose contents can be combined and utilised according to the respective needs of the user. Just as the overall functionality of a mechanical toolbox can be extended by adding new tools, MTpy is a flexible framework, which will be dynamically extended in the future. Furthermore, it can help to unify and extend existing codes and algorithms within the (academic) MT community. In this paper, we introduce the structure and concept of MTpy. Additionally, we show some examples from an everyday work-flow of MT data processing: the generation of standard EDI data files from raw electric (E-) and magnetic flux density (B-) field time series as input, the conversion into MiniSEED data format, as well as the generation of a graphical data representation in the form of a Phase Tensor pseudosection.

  1. 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.

  2. Scutellaria barbata flavonoids inhibits NFT aggregation and regulatory mechanism in rats induced by composited Aβ%半枝莲黄酮抑制复合 Aβ所致大鼠皮层细胞 NFT 沉积及其调节机制

    Institute of Scientific and Technical Information of China (English)

    郭可; 缪红; 王树松; 程建军; 商亚珍

    2016-01-01

    AIM: To investigate the effects of Scutellaria barbata flavonoids (SBF) on neurofibrillary tangle (NFT) aggregation, tau protein phosphorylation and the regulated mechanism of glycogen synthase kinase (GSK) 3βand protein phosphatase (PP) 2A in the rats induced by amyloid βprotein 25-35 (Aβ25-35) in combination with AlCl3 and re-combinant human transforming growth factor ( RHTGF)-β1( composited Aβ) .METHODS:The male SD rats were used to establish the simulated Alzheimer disease ( AD) model by intracerebroventricular injection of composited Aβ.The Morris water maze was applied for screening the successful model rats with learning and memory deficits .The successful model rats were daily and orally administrated with SBF at doses of 35, 70 and 140 mg/kg or positive control drug Ginkgo biloba leaves flavonoids ( GLF) at 140 mg/kg for 37 d.The silver nitrate staining was used to determine the cortical NFT .The protein levels of total tau, phosphorylated protein of tau at Ser199 and Ser214 sites, GSK3βand PP2A in hippocampus and cortex were determined by Western blot .The mRNA expression of GSK3βand PP2A in the hippocampus and cortex was detected by RT-PCR.RESULTS:Compared with sham group , the cell number of positive NFT with silver nitrate staining in model rat cerebral cortex was significantly increased .The protein levels of phosphorylated tau protein at Ser 199 and Ser214 sites, GSK3βin the hippocampus and cerebral cortex in the model rats dramatically elevated , and PP2A was marked decreased as compared with the sham group rats.Meanwhile, the mRNA expression of GSK-3βsignificantly increased but PP2A was de-creased.However, these above abnormalities were differently attenuated by treating with SBF at different doses or GLF at 140 mg/kg for 37 d.CONCLUSION: SBF suppresses the NFT aggregation by inhibition of the regulatory functions of GSK-3βand PP2A, thus reducing the phosphorylation of tau protein .%目的:探讨半枝莲黄酮(SBF)对复

  3. Inlet Engineering Toolbox

    Science.gov (United States)

    2014-10-31

    tools and models were developed for desktop PC and web-based use, so that District scientists and engineers can complete projects in-house rather...change and sand transport model . GenCade is run in the Surface-water Modeling System (SMS) version 11.1 or higher. Another product is the Sediment...application at Onslow Bay, NC. Figure 2. Sediment budget in SBAS, Galveston, TX. resiliency of coastal dune systems, whether natural or built

  4. Object-oriented Matlab adaptive optics toolbox

    Science.gov (United States)

    Conan, R.; Correia, C.

    2014-08-01

    Object-Oriented Matlab Adaptive Optics (OOMAO) is a Matlab toolbox dedicated to Adaptive Optics (AO) systems. OOMAO is based on a small set of classes representing the source, atmosphere, telescope, wavefront sensor, Deformable Mirror (DM) and an imager of an AO system. This simple set of classes allows simulating Natural Guide Star (NGS) and Laser Guide Star (LGS) Single Conjugate AO (SCAO) and tomography AO systems on telescopes up to the size of the Extremely Large Telescopes (ELT). The discrete phase screens that make the atmosphere model can be of infinite size, useful for modeling system performance on large time scales. OOMAO comes with its own parametric influence function model to emulate different types of DMs. The cone effect, altitude thickness and intensity profile of LGSs are also reproduced. Both modal and zonal modeling approach are implemented. OOMAO has also an extensive library of theoretical expressions to evaluate the statistical properties of turbulence wavefronts. The main design characteristics of the OOMAO toolbox are object-oriented modularity, vectorized code and transparent parallel computing. OOMAO has been used to simulate and to design the Multi-Object AO prototype Raven at the Subaru telescope and the Laser Tomography AO system of the Giant Magellan Telescope. In this paper, a Laser Tomography AO system on an ELT is simulated with OOMAO. In the first part, we set-up the class parameters and we link the instantiated objects to create the source optical path. Then we build the tomographic reconstructor and write the script for the pseudo-open-loop controller.

  5. Basic Radar Altimetry Toolbox & Tutorial

    Science.gov (United States)

    Rosmorduc, Vinca; Benveniste, Jerome; Breebaart, Leo; Bronner, Emilie; Dinardo, Salvatore; Earith, Didier; Lucas, Bruno Manuel; Niejmeier, Sander; Picot, Nicolas

    2010-12-01

    The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data, including the last mission launched, CryoSat. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. Nearly 1200 people downloaded it (as of end of June 2010), with many "newcomers" to altimetry among them. Users' feedbacks, developments in altimetry, and practice, showed that new interesting features could be added. Some have been added and/or improved in version 2. Others are ongoing, some are in discussion. The Basic Radar Altimetry Toolbox is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason- 1, Envisat, Jason- 2, CryoSat and also the future Saral and Sentinel 3 missions, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool both, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data, additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. BRAT is developed under contract with ESA and CNES. It is available at http://www.altimetry.info and http://earth.esa.int/brat/

  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. PREVIEW Behavior Modification Intervention Toolbox (PREMIT)

    DEFF Research Database (Denmark)

    Kahlert, Daniela; Unyi-Reicherz, Annelie; Stratton, Gareth

    2016-01-01

    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......) 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 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. METHODS: The program...

  10. Audition assessment using the NIH Toolbox.

    Science.gov (United States)

    Zecker, Steven G; 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

    2013-03-12

    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.

  11. The polarization-based collimated beam combiner and the proposed NOVA fringe tracker (NFT) for the VLTI

    Science.gov (United States)

    Meisner, Jeffrey A.; Jaffe, Walter J.; Le Poole, Rudolf S.; Pereira, Silvania F.; Quirrenbach, Andreas; Raban, David; Vosteen, Amir

    2010-07-01

    The Polarization-Based Collimated Beam Combiner efficiently produces pairwise interference between beams from multiple telescopes. An important feature is achieving "Photometric Symmetry" whereby interference measurements have no first-order sensitivity to wavefront perturbations (or photometric variations following spatial filtering) which otherwise entail visibility measurements with increased error, bias, and nonlinearity in phase determination. Among other proposed applications, this topology has been chosen as the basis for the design of the NOVA Fringe Tracker (NFT), a proposed 4 or 6 telescope second-generation fringe tracker for the VLTI. The NFT takes advantage of the photometric symmetry thus achieved making it capable of tracking on stars resolved beyond the first visibility null, as well as interfering a telescope beam with one which is 20 times brighter, a design goal set by ESO. By not requiring OPD modulation for interferometric detection, the detector exposure time can be increased without performance reduction due to time skew nor is sensitivity reduced by removing optical power for photometric monitoring, and use of two-phase interferometric detection saves one half of the photons being diverted for detection of the other two (mainly) unused quadrature phases. The topology is also proposed for visibility measuring interferometers with configurations proposed for the achievement of balanced quadrature or 3-phase interferometric detection. A laboratory demonstration confirms >>100:1 rejection of photometric crosstalk in a fringe tracking configuration where atmospheric OPD fluctuations were simulated using a hair dryer. Tracking with a 30:1 intensity ratio between the incoming beams was performed while rejecting large introduced photometric fluctuations.

  12. A toolbox for robust PID controller tuning using convex optimization

    OpenAIRE

    Sadeghpour, Mehdi; de Oliveira, Vinicius; Karimi, Alireza

    2012-01-01

    A robust PID controller design toolbox for Matlab is presented in this paper. The design is based on linearizing or convexifying the conventional non-convex constraints on the classical robustness margins or H∞ constraints. Then the existing optimization solvers can be used to compute the controller parameters. The software can be used in a wide range of controller design problems, including multi-model systems and gain-scheduled controllers. The models can be parametric or non-parametric whi...

  13. The SLICOT Toolboxes for Matlab | Die SLICOT-Toolboxen für Matlab

    OpenAIRE

    Benner, P; Kressner, D.; Sima, V.; Varga, A

    2010-01-01

    SLICOT is a comprehensive numerical software package for control systems analysis and design. While based on highly performant Fortran routines, Matlab and Scilab interfaces provide convenient alternative access for users. In this survey, we summarize the functionality contained in the three SLICOT toolboxes for (1) basic tasks in systems and control, (2) system identification, and (3) model and controller reduction. Several examples illustrate the use of these toolboxes for addressing freque...

  14. BioMet Toolbox: genome-wide analysis of metabolism

    DEFF Research Database (Denmark)

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

    2010-01-01

    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...... rates, substrate uptake rates and metabolic production rates by detecting relevant fluxes, simulate single and double gene deletions or detect metabolites around which major transcriptional changes are concentrated. These tools can be used for high-throughput in silico screening and allows fully...

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. Low Energy Mission Planning Toolbox Project

    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...

  20. Structural Time Domain Identification Toolbox User's Guide

    DEFF Research Database (Denmark)

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

    This manual describes the Structural Time Domain Identification toolbox for use with MA TLAB. This version of the tool box has been developed using the PC-based MA TLAB version 4.2c, but is compatible with prior versions of MATLAB and UNIX-based versions. The routines of the toolbox are the so-ca......-called m-files that can be executed from the MA TLAB command line prompt or built into other m-files....

  1. Real time wind farm emulation using SimWindFarm toolbox

    Science.gov (United States)

    Topor, Marcel

    2016-06-01

    This paper presents a wind farm emulation solution using an open source Matlab/Simulink toolbox and the National Instruments cRIO platform. This work is based on the Aeolus SimWindFarm (SWF) toolbox models developed at Aalborg university, Denmark. Using the Matlab Simulink models developed in SWF, the modeling code can be exported to a real time model using the NI Veristand model framework and the resulting code is integrated as a hardware in the loop control on the NI 9068 platform.

  2. 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.

  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

    National Research Council Canada - National Science Library

    Rafaelly Suzanye da Silva Santos; Nildo da Silva Dias; Osvaldo Nogueira de Sousa Neto; Marcelo Tavares Gurgel

    2010-01-01

    ... 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...

  4. EOSPEC: a complementary toolbox for MODTRAN calculations

    Science.gov (United States)

    Dion, Denis

    2016-09-01

    For more than a decade, Defence Research and Development Canada (DRDC) has been developing a Library of computer models for the calculations of atmospheric effects on EO-IR sensor performances. The Library, called EOSPEC-LIB (EO-IR Sensor PErformance Computation LIBrary) has been designed as a complement to MODTRAN, the radiative transfer code developed by the Air Force Research Laboratory and Spectral Science Inc. in the USA. The Library comprises modules for the definition of the atmospheric conditions, including aerosols, and provides modules for the calculation of turbulence and fine refraction effects. SMART (Suite for Multi-resolution Atmospheric Radiative Transfer), a key component of EOSPEC, allows one to perform fast computations of transmittances and radiances using MODTRAN through a wide-band correlated-k computational approach. In its most recent version, EOSPEC includes a MODTRAN toolbox whose functions help generate in a format compatible to MODTRAN 5 and 6 atmospheric and aerosol profiles, user-defined refracted optical paths and inputs for configuring the MODTRAN sea radiance (BRDF) model. The paper gives an overall description of the EOSPEC features and capacities. EOSPEC provides augmented capabilities for computations in the lower atmosphere, and for computations in maritime environments.

  5. 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

  6. 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

  7. 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

  8. 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

  9. Norming plans for the NIH Toolbox.

    Science.gov (United States)

    Beaumont, Jennifer L; Havlik, Richard; Cook, Karon F; Hays, Ron D; Wallner-Allen, Kathleen; Korper, Samuel P; Lai, Jin-Shei; Nord, Christine; Zill, Nicholas; Choi, Seung; Yost, Kathleen J; Ustsinovich, Vitali; Brouwers, Pim; Hoffman, Howard J; Gershon, Richard

    2013-03-12

    The NIH Toolbox for Assessment of Neurological and Behavioral Function (NIH Toolbox) is a comprehensive battery of brief assessment tools. The purpose of this article is to describe plans to establish normative reference values for the NIH Toolbox measures. A large sample will be obtained from the US population for the purpose of calculating normative values. The sample will be stratified by age (ages 3-85 years), sex, and language preference (English or Spanish) and have a total sample size of at least 4,205. The sample will include a minimum of 25-100 individuals in each targeted demographic and language subgroup. Norming methods will include poststratification adjustment calculated using iterative proportional fitting, also known as raking, so that the weighted sample will have the same distribution on key demographic variables as the US population described in the 2010 Census. As with any set of norms, users should be mindful of the reference population and make conclusions consistent with the limitations of normative sampling, since it is not a probability-based sample. However, the NIH Toolbox norming study has been designed to minimize bias and maximize representativeness and precision of estimates. The availability of a "toolbox" of normed measures will be an important foundation for addressing critical research questions in neurologic and behavioral health.

  10. Integrated Sensing and Control of Aeroelastic Deformation (ISCAD) Toolbox Project

    Data.gov (United States)

    National Aeronautics and Space Administration — An Integrated Sensing and Control of Aeroelastic Deformation (ISCAD) Toolbox is proposed. Specif-ically, this toolbox will provide a methodology, both hardware and...

  11. 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 hav......, expand, and develop the contents of the toolbox. This paper presents the structure and the backbone of the library. Three examples are given to visualize the possibilities of the toolbox....

  12. Computational performance of a parallelized high-order spectral and mortar element toolbox

    CERN Document Server

    Bouffanais, Roland; Gruber, Ralf; Deville, Michel O

    2007-01-01

    In this paper, a comprehensive performance review of a MPI-based high-order spectral and mortar element method C++ toolbox is presented. The focus is put on the performance evaluation of several aspects with a particular emphasis on the parallel efficiency. The performance evaluation is analyzed and compared to predictions given by a heuristic model, the so-called Gamma model. A tailor-made CFD computation benchmark case is introduced and used to carry out this review, stressing the particular interest for commodity clusters. Conclusions are drawn from this extensive series of analyses and modeling leading to specific recommendations concerning such toolbox development and parallel implementation.

  13. 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....

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

    DEFF Research Database (Denmark)

    Brandt, A.

    2013-01-01

    , 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...

  15. 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...

  16. Colloidal Toolbox Synthesis of Pt Nanoalloys

    DEFF Research Database (Denmark)

    Spanos, Ioannis

    enhancement of the activity is observeddue to the introduction of an electronic or ligand effect. The above method is however difficult to control and its reproducibility is poor. For thatreason, a colloidal method is used as a toolbox to conduct systematic studies on PtxCo1-xnanoalloys. This method provides...

  17. NUTMEG: a neuromagnetic source reconstruction toolbox.

    Science.gov (United States)

    Dalal, S S; Zumer, J M; Agrawal, V; Hild, K E; Sekihara, K; Nagarajan, S S

    2004-11-30

    We have developed an analysis toolbox called NUTMEG (Neurodynamic Utility Toolbox for Magnetoencephalography) for reconstructing the spatiotemporal dynamics of neural activations and overlaying them onto structural MR images. The toolbox runs under MATLAB in conjunction with SPM2 and can be used with the Linux/UNIX, Mac OS X, and even Windows platforms. Currently, evoked magnetic field data from 4-D Neuroimaging, CTF, and KIT systems can be imported to the toolbox for analysis. NUTMEG uses an eigenspace vector beamforming algorithm to generate a tomographic reconstruction of spatiotemporal magnetic source activity over selected time intervals and spatial regions. The MEG coordinate frame is coregistered with an anatomical MR image using fiducial locations and, optionally, head shape information. This allows the reconstruction to be superimposed onto an MRI to provide a convenient visual correspondence to neuroanatomy. Navigating through the MR volume automatically updates the displayed time series of activation for the selected voxel. Animations can also be generated to view the evolution of neural activity over time. Since NUTMEG displays activations using SPM2's engine, certain SPM functions such as brain rendering and spatial normalization may be applied as well. Finally, as a MATLAB package, the end user can easily add customized functions. Source code is available at http://bil.ucsf.edu/ and distributed under a BSD-style license.

  18. The RTMM Toolbox for DMM Applications

    DEFF Research Database (Denmark)

    Sharp, Robin; Todirica, Edward Alexandru

    2002-01-01

    This paper describes an approach to implementing distributed multimedia applications based on the use of a software toolbox. The tools in the box allow the designer to specify which components are to be used, how they are logically connected and what properties the streams of data to be passed...

  19. Emotion assessment using the NIH Toolbox.

    Science.gov (United States)

    Salsman, John M; Butt, Zeeshan; Pilkonis, Paul A; Cyranowski, Jill M; Zill, Nicholas; Hendrie, Hugh C; Kupst, Mary Jo; Kelly, Morgen A R; Bode, Rita K; Choi, Seung W; Lai, Jin-Shei; Griffith, James W; Stoney, Catherine M; Brouwers, Pim; Knox, Sarah S; Cella, David

    2013-03-12

    One of the goals of the NIH Toolbox for Assessment of Neurological and Behavioral Function was to identify or develop brief measures of emotion for use in prospective epidemiologic and clinical research. Emotional health has significant links to physical health and exerts a powerful effect on perceptions of life quality. Based on an extensive literature review and expert input, the Emotion team identified 4 central subdomains: Negative Affect, Psychological Well-Being, Stress and Self-Efficacy, and Social Relationships. A subsequent psychometric review identified several existing self-report and proxy measures of these subdomains with measurement characteristics that met the NIH Toolbox criteria. In cases where adequate measures did not exist, robust item banks were developed to assess concepts of interest. A population-weighted sample was recruited by an online survey panel to provide initial item calibration and measure validation data. Participants aged 8 to 85 years completed self-report measures whereas parents/guardians responded for children aged 3 to 12 years. Data were analyzed using a combination of classic test theory and item response theory methods, yielding efficient measures of emotional health concepts. An overview of the development of the NIH Toolbox Emotion battery is presented along with preliminary results. Norming activities led to further refinement of the battery, thus enhancing the robustness of emotional health measurement for researchers using the NIH Toolbox.

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

    Science.gov (United States)

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

    2012-05-01

    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.

  1. Toolbox or Adjustable Spanner? A Critical Comparison of Two Metaphors for Adaptive Decision Making

    Science.gov (United States)

    Söllner, Anke; Bröder, Arndt

    2016-01-01

    For multiattribute decision tasks, different metaphors exist that describe the process of decision making and its adaptation to diverse problems and situations. Multiple strategy models (MSMs) assume that decision makers choose adaptively from a set of different strategies (toolbox metaphor), whereas evidence accumulation models (EAMs) hold that a…

  2. 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.

  3. optPBN: An Optimisation Toolbox for Probabilistic Boolean Networks

    Science.gov (United States)

    Trairatphisan, Panuwat; Mizera, Andrzej; Pang, Jun; Tantar, Alexandru Adrian; Sauter, Thomas

    2014-01-01

    Background There exist several computational tools which allow for the optimisation and inference of biological networks using a Boolean formalism. Nevertheless, the results from such tools yield only limited quantitative insights into the complexity of biological systems because of the inherited qualitative nature of Boolean networks. Results We introduce optPBN, a Matlab-based toolbox for the optimisation of probabilistic Boolean networks (PBN) which operates under the framework of the BN/PBN toolbox. optPBN offers an easy generation of probabilistic Boolean networks from rule-based Boolean model specification and it allows for flexible measurement data integration from multiple experiments. Subsequently, optPBN generates integrated optimisation problems which can be solved by various optimisers. In term of functionalities, optPBN allows for the construction of a probabilistic Boolean network from a given set of potential constitutive Boolean networks by optimising the selection probabilities for these networks so that the resulting PBN fits experimental data. Furthermore, the optPBN pipeline can also be operated on large-scale computational platforms to solve complex optimisation problems. Apart from exemplary case studies which we correctly inferred the original network, we also successfully applied optPBN to study a large-scale Boolean model of apoptosis where it allows identifying the inverse correlation between UVB irradiation, NFκB and Caspase 3 activations, and apoptosis in primary hepatocytes quantitatively. Also, the results from optPBN help elucidating the relevancy of crosstalk interactions in the apoptotic network. Summary The optPBN toolbox provides a simple yet comprehensive pipeline for integrated optimisation problem generation in the PBN formalism that can readily be solved by various optimisers on local or grid-based computational platforms. optPBN can be further applied to various biological studies such as the inference of gene regulatory

  4. Evaluation of an Advanced Harmonic Filter for Adjustable Speed Drives using a Toolbox Approach

    DEFF Research Database (Denmark)

    Asiminoaei, Lucian; Hansen, Steffan; Blaabjerg, Frede

    2004-01-01

    the performance of different topologies. This paper presents a method to integrate the model of the filter into an existing harmonic calculation toolbox dedicated for harmonic analysis on the 6-pulse converter. The results are linked together into a practical PC software toolbox for harmonic estimation. By using...... harmonic reduction performance at the same time with small costs and engineering. In the event that such filters are used to replace existing solutions, the assessment of the harmonic performance before commissioning is a necessity. This assessment is possible by using software tools to compare...... a combination of a pre-stored database and new interpolation techniques the toolbox can provide the harmonic data on real applications allowing comparisons between different mitigation solutions....

  5. FAST: FAST Analysis of Sequences Toolbox.

    Science.gov (United States)

    Lawrence, Travis J; Kauffman, Kyle T; Amrine, Katherine C H; Carper, Dana L; Lee, Raymond S; Becich, Peter J; Canales, Claudia J; Ardell, David H

    2015-01-01

    FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  6. FAST: FAST Analysis of Sequences Toolbox

    Directory of Open Access Journals (Sweden)

    Travis J. Lawrence

    2015-05-01

    Full Text Available FAST (FAST Analysis of Sequences Toolbox provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU’s Not Unix Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics makes FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format. Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought.

  7. SCoT: A Python Toolbox for EEG Source Connectivity

    Directory of Open Access Journals (Sweden)

    Martin eBillinger

    2014-03-01

    Full Text Available Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG. Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs require single-trial estimation methods.In this paper, we present SCoT – a source connectivity toolbox for Python. This toolbox implements routines for blind source decomposition and connectivity estimation with theMVARICA approach. Additionally, a novel extension called CSPVARICA is available for labeled data. SCoT estimates connectivity from various spectral measures relying on vector autoregressive (VAR models. Optionally, these VAR models can be regularized to facilitate ill posed applications such as single-trial fitting.We demonstrate basic usage of SCoT on motor imagery (MI data. Furthermore, we show simulation results of utilizing SCoT for feature extraction in a BCI application. These results indicate that CSPVARICA and correct regularization can significantly improve MI classification. While SCoT was mainly designed for application in BCIs, it contains useful tools for other areas of neuroscience. SCoT is a software package that (1 brings combined source decomposition and connectivtiy estimation to the open Python platform, and (2 offers tools for single-trial connectivity estimation. The source code is released under the MIT license and is available online at github.com/SCoT-dev/SCoT.

  8. 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....

  9. 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....

  10. Radiation Detection Scenario Analysis Toolbox (RADSAT) Test Case Implementation Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Shaver, Mark W.

    2010-09-27

    Final report for the project. This project was designed to demonstrate the use of the Radiation Detection Scenario Analysis Toolbox (RADSAT) radiation detection transport modeling package (developed in a previous NA-22 project) for specific radiation detection scenarios important to proliferation detection.

  11. 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.

  12. 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

  13. Gustation assessment using the NIH Toolbox.

    Science.gov (United States)

    Coldwell, Susan E; Mennella, Julie A; Duffy, Valerie B; Pelchat, Marcia L; Griffith, James W; Smutzer, Gregory; Cowart, Beverly J; Breslin, Paul A S; Bartoshuk, Linda M; Hastings, Lloyd; Victorson, David; Hoffman, Howard J

    2013-03-12

    The NIH Toolbox for Assessment of Neurological and Behavioral Function (NIH Toolbox) is a set of brief measures for the assessment of cognitive function, emotional health, motor function, and sensory function for use in clinical trials and in epidemiologic and longitudinal studies. Gustatory perception is assessed as 1 of 6 areas of sensory function. A team of 11 scientists with expertise in taste perception selected 2 gustatory measures, 1 of which can be used in young pediatric populations. The measure selected for young pediatric populations assesses sucrose (sweet) taste preference and can also be used across the age span of 5 to 85 years. For adult populations, the selected measure is a regional test, which assesses variability in perceived intensity of quinine hydrochloride (bitter) when applied to the tongue tip as well as perceived with the whole mouth. The team also recommends the regional test for assessing other tastants, such as sodium chloride (salty). Validation studies have demonstrated that the measures modified for the NIH Toolbox correlate with more traditional assessments, and can identify known population differences in gustation.

  14. WEC Design Response Toolbox v. 1.0

    Energy Technology Data Exchange (ETDEWEB)

    2016-03-30

    The WEC Design Response Toolbox (WDRT) is a numerical toolbox for design-response analysis of wave energy converters (WECs). The WDRT was developed during a series of efforts to better understand WEC survival design. The WDRT has been designed as a tool for researchers and developers, enabling the straightforward application of statistical and engineering methods. The toolbox includes methods for short-term extreme response, environmental characterization, long-term extreme response and risk analysis, fatigue, and design wave composition.

  15. 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.

  16. 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.

  17. Toolbox Wind Energy. Manual for site selection for wind turbines; Toolbox Windenergie. Handleiding plaatsingstrajecten windturbines

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2011-01-15

    For the year 2015 the Dutch province of Zuid-Holland has set a target of 350 MW wind energy capacity and for the longer term (2020) 1000 MW. In this toolbox some practical tips are given for municipalities to realize the targets in their policies with regard to wind power. [Dutch] Voor het jaar 2015 is als doel gesteld om 350 MW wind energie vermogen in bedrijf te hebben en voor de langere termijn (2020) 1000 MW. In deze Toolbox bieden we als provinciebestuur enkele praktische handvatten waarmee gemeenten hun windenergiebeleid kracht kunnen bijzetten.

  18. 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.

  19. Assessment of self-reported negative affect in the NIH Toolbox.

    Science.gov (United States)

    Pilkonis, Paul A; Choi, Seung W; Salsman, John M; Butt, Zeeshan; Moore, Tara L; Lawrence, Suzanne M; Zill, Nicholas; Cyranowski, Jill M; Kelly, Morgen A R; Knox, Sarah S; Cella, David

    2013-03-30

    We report on the selection of self-report measures for inclusion in the NIH Toolbox that are suitable for assessing the full range of negative affect including sadness, fear, and anger. The Toolbox is intended to serve as a "core battery" of assessment tools for cognition, sensation, motor function, and emotional health that will help to overcome the lack of consistency in measures used across epidemiological, observational, and intervention studies. A secondary goal of the NIH Toolbox is the identification of measures that are flexible, efficient, and precise, an agenda best fulfilled by the use of item banks calibrated with models from item response theory (IRT) and suitable for adaptive testing. Results from a sample of 1763 respondents supported use of the adult and pediatric item banks for emotional distress from the Patient-Reported Outcomes Measurement Information System (PROMIS(®)) as a starting point for capturing the full range of negative affect in healthy individuals. Content coverage for the adult Toolbox was also enhanced by the development of a scale for somatic arousal using items from the Mood and Anxiety Symptom Questionnaire (MASQ) and scales for hostility and physical aggression using items from the Buss-Perry Aggression Questionnaire (BPAQ).

  20. HYDRORECESSION: A Matlab toolbox for streamflow recession analysis

    Science.gov (United States)

    Arciniega-Esparza, Saúl; Breña-Naranjo, José Agustín; Pedrozo-Acuña, Adrián; Appendini, Christian Mario

    2017-01-01

    Streamflow recession analysis from observed hydrographs allows to extract information about the storage-discharge relationship of a catchment and some of their groundwater hydraulic properties. The HYDRORECESSION toolbox, presented in this paper, is a graphical user interface for Matlab and it was developed to analyse streamflow recession curves with the support of different tools. The software extracts hydrograph recessions segments with three different methods (Vogel, Brutsaert and Aksoy) that are later analysed with four of the most common models to simulate recession curves (Maillet, Boussinesq, Coutagne and Wittenberg) and it includes four parameter-fitting techniques (linear regression, lower envelope, data binning and mean squared error). HYDRORECESSION offers tools to parameterize linear and nonlinear storage-outflow relationships and it is useful for regionalization purposes, catchment classification, baseflow separation, hydrological modeling and low flows prediction. HYDRORECESSION is freely available for non-commercial and academic purposes and is available at Matlab File Exchange (http://www.mathworks.com/matlabcentral/fileexchange/51332-hydroecession).

  1. 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.

  2. Desempenho de cultivares de alface crespa em dois ambientes de cultivo em sistema hidropônico Performance of lettuce cultivars grown in two environments, in the NFT hydroponic system

    National Research Council Canada - National Science Library

    SF Blat; SV Sanchez; JAC Araújo; D Bolonhezi

    2011-01-01

    ..., Belíssima, Locarno, Crespona Gigante e Verônica) em dois ambientes de cultivo (casa de vegetação climatizada e não climatizada) em sistema hidropônico NFT. O delineamento experimental foi em blocos casualizados para cada ambiente com...

  3. 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

  4. A distributed SIRT implementation for the ASTRA Toolbox

    NARCIS (Netherlands)

    Palenstijn, W.J.; Bédorf, J.; Batenburg, K.J.; King, M.; Glick, S.; Mueller, K.

    2015-01-01

    The ASTRA Toolbox is a software toolbox that enables rapid development of GPU accelerated tomography algorithms. It contains GPU implementations of forward and backprojection operations for common scanning geometries, as well as a set of algorithms for iterative reconstruction. These algorithms are

  5. 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 covari

  6. 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...... to automatically determine parameters of the different classes present in the data, and edge weighted smoothing of the final segmentation based on Markov Random Fields (MRF). The toolbox is developed for Matlab users and requires only minimal background knowledge of Matlab....

  7. The 'Toolbox' of strategies for managing Haemonchus contortus in goats: What's in and what's out.

    Science.gov (United States)

    Kearney, P E; Murray, P J; Hoy, J M; Hohenhaus, M; Kotze, A

    2016-04-15

    A dynamic and innovative approach to managing the blood-consuming nematode Haemonchus contortus in goats is critical to crack dependence on veterinary anthelmintics. H. contortus management strategies have been the subject of intense research for decades, and must be selected to create a tailored, individualized program for goat farms. Through the selection and combination of strategies from the Toolbox, an effective management program for H. contortus can be designed according to the unique conditions of each particular farm. This Toolbox investigates strategies including vaccines, bioactive forages, pasture/grazing management, behavioural management, natural immunity, FAMACHA, Refugia and strategic drenching, mineral/vitamin supplementation, copper Oxide Wire Particles (COWPs), breeding and selection/selecting resistant and resilient individuals, biological control and anthelmintic drugs. Barbervax(®), the ground-breaking Haemonchus vaccine developed and currently commercially available on a pilot scale for sheep, is prime for trialling in goats and would be an invaluable inclusion to this Toolbox. The specialised behaviours of goats, specifically their preferences to browse a variety of plants and accompanying physiological adaptations to the consumption of secondary compounds contained in browse, have long been unappreciated and thus overlooked as a valuable, sustainable strategy for Haemonchus management. These strategies are discussed in this review as to their value for inclusion into the 'Toolbox' currently, and the future implications of ongoing research for goat producers. Combining and manipulating strategies such as browsing behaviour, pasture management, bioactive forages and identifying and treating individual animals for haemonchosis, in addition to continuous evaluation of strategy effectiveness, is conducted using a model farm scenario. Selecting strategies from the Toolbox, with regard to their current availability, feasibility, economical cost

  8. A ''Toolbox''21 Equivalent Process for Safety Analysis Software

    Energy Technology Data Exchange (ETDEWEB)

    O' KULA, KR

    2004-04-30

    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

  9. A Parallel Multiscale Mixed Finite-Element Method for the Matlab Reservoir Simulation Toolbox

    OpenAIRE

    2012-01-01

    We start by giving a brief introduction to reservoirs and reservoir modelling at different scales. We introduce a mathematical model for the two-phase flow, before we look at numerical discretizations. In particular we look at the Multiscale Mixed Finite-Element (MsMFE) Method from the Matlab Reservoir Simulation Toolbox (MRST), developed by SINTEF. Next we introduce a mimetic method, (with the inverse ip_simple inner product, wich is used for solving the local flow problems required to const...

  10. 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.

  11. 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...... on the high frequency approximation of the wave-equation and ‘fat’ ray based forward models relying on finite frequency theory. In order to sample the a posteriori probability density function we make use of both least squares based inversion, for linear Gaussian inverse problems, and the extended Metropolis...... sampler, for non-linear non-Gaussian inverse problems. To illustrate the applicability of the SIPPI toolbox to a tomographic field data set we use a cross-borehole traveltime data set from Arrenæs, Denmark. Both the computer code and the data are released in the public domain using open source and open...

  12. 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...... on the angular location of residual energy. Also, the framework can be extended, for instance by post modeling of repeated faults. Furthermore, we have investigated the problem of non-stationary condition monitoring when operational changes induce angular timing changes in the observed signals. Our contribution......, the inversion of those angular timing changes called “event alignment”, has allowed for condition monitoring across operation load settings, successfully enabling a single model to be used with realistic data under varying operational conditions-...

  13. An extension of the open-source porousMultiphaseFoam toolbox dedicated to groundwater flows solving the Richards' equation

    CERN Document Server

    Horgue, Pierre; Guibert, Romain; Debenest, Gérald

    2015-01-01

    In this note, the existing porousMultiphaseFoam toolbox, developed initially for any two-phase flow in porous media is extended to the specific case of the Richards' equation which neglect the pressure gradient of the non-wetting phase. This model is typically used for saturated and unsaturated groundwater flows. A Picard's algorithm is implemented to linearize and solve the Richards' equation developed in the pressure head based form. This new solver of the porousMultiphaseFoam toolbox is named groundwaterFoam. The validation of thesolver is achieved by a comparison between numerical simulations and results obtained from the literature. Finally, a parallel efficiency test is performed on a large unstructured mesh and exhibits a super-linear behavior as observed for the other solvers of the toolbox.

  14. DOTcvpSB, a software toolbox for dynamic optimization in systems biology

    Directory of Open Access Journals (Sweden)

    Balsa-Canto Eva

    2009-06-01

    Full Text Available Abstract Background Mathematical optimization aims to make a system or design as effective or functional as possible, computing the quality of the different alternatives using a mathematical model. Most models in systems biology have a dynamic nature, usually described by sets of differential equations. Dynamic optimization addresses this class of systems, seeking the computation of the optimal time-varying conditions (control variables to minimize or maximize a certain performance index. Dynamic optimization can solve many important problems in systems biology, including optimal control for obtaining a desired biological performance, the analysis of network designs and computer aided design of biological units. Results Here, we present a software toolbox, DOTcvpSB, which uses a rich ensemble of state-of-the-art numerical methods for solving continuous and mixed-integer dynamic optimization (MIDO problems. The toolbox has been written in MATLAB and provides an easy and user friendly environment, including a graphical user interface, while ensuring a good numerical performance. Problems are easily stated thanks to the compact input definition. The toolbox also offers the possibility of importing SBML models, thus enabling it as a powerful optimization companion to modelling packages in systems biology. It serves as a means of handling generic black-box models as well. Conclusion Here we illustrate the capabilities and performance of DOTcvpSB by solving several challenging optimization problems related with bioreactor optimization, optimal drug infusion to a patient and the minimization of intracellular oscillations. The results illustrate how the suite of solvers available allows the efficient solution of a wide class of dynamic optimization problems, including challenging multimodal ones. The toolbox is freely available for academic use.

  15. psst: An Open-Source Power System Simulation Toolbox in Python

    Energy Technology Data Exchange (ETDEWEB)

    Krishnamurthy, Dheepak

    2016-11-21

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

  16. Developing a Practical Chiral Toolbox for Asymmetric Catalytic Reactions

    Institute of Scientific and Technical Information of China (English)

    ZHANG XuMu

    2001-01-01

    @@ Chiral Quest's Toolbox Approach: During the last several decades, chemists have made major progress in discovering man-made catalysts to perform challenging asymmetric transformations. However, there is no universal chiral ligand or catalyst for solving problems in enantioselective transformations. The focus of Chiral Quest's research is to develop a useful chiral toolbox for strategically important asymmetric catalytic reactions by inventing a diverse set of novel chiral ligands and combining them with transition metals as effective enantioselective catalysts. The toolbox approach addresses significant problems in organic stereochemistry and has resulted in practical methods for the synthesis of chiral pharmaceuticals and agrochemicals

  17. Developing a Practical Chiral Toolbox for Asymmetric Catalytic Reactions

    Institute of Scientific and Technical Information of China (English)

    ZHANG; XuMu

    2001-01-01

    Chiral Quest's Toolbox Approach: During the last several decades, chemists have made major progress in discovering man-made catalysts to perform challenging asymmetric transformations. However, there is no universal chiral ligand or catalyst for solving problems in enantioselective transformations. The focus of Chiral Quest's research is to develop a useful chiral toolbox for strategically important asymmetric catalytic reactions by inventing a diverse set of novel chiral ligands and combining them with transition metals as effective enantioselective catalysts. The toolbox approach addresses significant problems in organic stereochemistry and has resulted in practical methods for the synthesis of chiral pharmaceuticals and agrochemicals  ……

  18. A Toolbox for Nonlinear Regression in R: The Package nlstools

    Directory of Open Access Journals (Sweden)

    Florent Baty

    2015-08-01

    Full Text Available Nonlinear regression models are applied in a broad variety of scientific fields. Various R functions are already dedicated to fitting such models, among which the function nls( has a prominent position. Unlike linear regression fitting of nonlinear models relies on non-trivial assumptions and therefore users are required to carefully ensure and validate the entire modeling. Parameter estimation is carried out using some variant of the least- squares criterion involving an iterative process that ideally leads to the determination of the optimal parameter estimates. Therefore, users need to have a clear understanding of the model and its parameterization in the context of the application and data considered, an a priori idea about plausible values for parameter estimates, knowledge of model diagnostics procedures available for checking crucial assumptions, and, finally, an under- standing of the limitations in the validity of the underlying hypotheses of the fitted model and its implication for the precision of parameter estimates. Current nonlinear regression modules lack dedicated diagnostic functionality. So there is a need to provide users with an extended toolbox of functions enabling a careful evaluation of nonlinear regression fits. To this end, we introduce a unified diagnostic framework with the R package nlstools. In this paper, the various features of the package are presented and exemplified using a worked example from pulmonary medicine.

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

    Energy Technology Data Exchange (ETDEWEB)

    Apte, A; Veeraraghavan, H; Oh, J; Kijewski, P; Deasy, J [Memorial Sloan Kettering Cancer Center, New York, NY (United States)

    2015-06-15

    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”.

  20. 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...... to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors' viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future...... 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...

  1. 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.

  2. PREVIEW Behavior Modification Intervention Toolbox (PREMIT)

    DEFF Research Database (Denmark)

    Kahlert, Daniela; Unyi-Reicherz, Annelie; Stratton, Gareth;

    2016-01-01

    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 counseling 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...

  3. National Water-Quality Assessment (NAWQA) Area-Characterization Toolbox

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This is release 1.0 of the National Water-Quality Assessment (NAWQA) Area-Characterization Toolbox. These tools are designed to be accessed using ArcGIS Desktop...

  4. 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.

  5. V. NIH Toolbox Cognition Battery (CB): measuring working memory.

    Science.gov (United States)

    Tulsky, David S; Carlozzi, Noelle E; Chevalier, Nicolas; Espy, Kimberly A; Beaumont, Jennifer L; Mungas, Dan

    2013-08-01

    This chapter focuses on the NIH Toolbox List Sorting Working Memory Test, which was developed to assess processing speed within the NIH Toolbox Cognition Battery (CB). This test is a sequencing task requiring children and adults to process stimuli (presented both visually and auditorily) and sequence the stimuli according to size. We describe the development of the NIH Toolbox List Sorting Working Memory Test, highlighting its utility in children. We examine descriptive data, test-retest reliability, and convergent and discriminant validity. Results indicated that List Sorting performance was positively correlated with age indicating that performance on the task improved throughout childhood and early adolescence. Further, test-retest reliability coefficients were high and there was support for both convergent and discriminant validity. These data suggest that the NIH Toolbox List Sorting Working Memory Test is reliable and shows evidence of construct validity.

  6. 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...

  7. 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.

  8. EXPODE -- Advanced Exponential Time Integration Toolbox for MATLAB

    OpenAIRE

    2014-01-01

    We present a MATLAB toolbox for five different classes of exponential integrators for solving (mildly) stiff ordinary differential equations or time-dependent partial differential equations. For the efficiency of such exponential integrators it is essential to approximate the products of the matrix functions arising in these integrators with vectors in a stable, reliable and efficient way. The toolbox contains options for computing the matrix functions directly by diagonalization or by Pade a...

  9. Development of a MATLAB Toolbox for image processing.

    OpenAIRE

    Freer, Dorothy J.

    1992-01-01

    Approved for public release; distribution unlimited. This thesis provides an Image Processing Toolbox for use with MATLAB which contains ready-made tools for students and faculty who wish to continue research in image processing and related areas. The Toolbox is available for several computer environments. The documentation provided with the distribution diskette contains both a tutorial and reference section in the MATLAB style. This thesis report provides information neede...

  10. SCoT: a Python toolbox for EEG source connectivity

    OpenAIRE

    Billinger, Martin; Brunner, Clemens; Müller-Putz, Gernot R.

    2014-01-01

    Analysis of brain connectivity has become an important research tool in neuroscience. Connectivity can be estimated between cortical sources reconstructed from the electroencephalogram (EEG). Such analysis often relies on trial averaging to obtain reliable results. However, some applications such as brain-computer interfaces (BCIs) require single-trial estimation methods. In this paper, we present SCoT—a source connectivity toolbox for Python. This toolbox implements routines for blind source...

  11. 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).

  12. Dipole source localization of mouse electroencephalogram using the Fieldtrip toolbox.

    Science.gov (United States)

    Lee, Chungki; Oostenveld, Robert; Lee, Soo Hyun; Kim, Lae Hyun; Sung, Hokun; Choi, Jee Hyun

    2013-01-01

    The mouse model is an important research tool in neurosciences to examine brain function and diseases with genetic perturbation in different brain regions. However, the limited techniques to map activated brain regions under specific experimental manipulations has been a drawback of the mouse model compared to human functional brain mapping. Here, we present a functional brain mapping method for fast and robust in vivo brain mapping of the mouse brain. The method is based on the acquisition of high density electroencephalography (EEG) with a microarray and EEG source estimation to localize the electrophysiological origins. We adapted the Fieldtrip toolbox for the source estimation, taking advantage of its software openness and flexibility in modeling the EEG volume conduction. Three source estimation techniques were compared: Distribution source modeling with minimum-norm estimation (MNE), scanning with multiple signal classification (MUSIC), and single-dipole fitting. Known sources to evaluate the performance of the localization methods were provided using optogenetic tools. The accuracy was quantified based on the receiver operating characteristic (ROC) analysis. The mean detection accuracy was high, with a false positive rate less than 1.3% and 7% at the sensitivity of 90% plotted with the MNE and MUSIC algorithms, respectively. The mean center-to-center distance was less than 1.2 mm in single dipole fitting algorithm. Mouse microarray EEG source localization using microarray allows a reliable method for functional brain mapping in awake mouse opening an access to cross-species study with human brain.

  13. Dipole source localization of mouse electroencephalogram using the Fieldtrip toolbox.

    Directory of Open Access Journals (Sweden)

    Chungki Lee

    Full Text Available The mouse model is an important research tool in neurosciences to examine brain function and diseases with genetic perturbation in different brain regions. However, the limited techniques to map activated brain regions under specific experimental manipulations has been a drawback of the mouse model compared to human functional brain mapping. Here, we present a functional brain mapping method for fast and robust in vivo brain mapping of the mouse brain. The method is based on the acquisition of high density electroencephalography (EEG with a microarray and EEG source estimation to localize the electrophysiological origins. We adapted the Fieldtrip toolbox for the source estimation, taking advantage of its software openness and flexibility in modeling the EEG volume conduction. Three source estimation techniques were compared: Distribution source modeling with minimum-norm estimation (MNE, scanning with multiple signal classification (MUSIC, and single-dipole fitting. Known sources to evaluate the performance of the localization methods were provided using optogenetic tools. The accuracy was quantified based on the receiver operating characteristic (ROC analysis. The mean detection accuracy was high, with a false positive rate less than 1.3% and 7% at the sensitivity of 90% plotted with the MNE and MUSIC algorithms, respectively. The mean center-to-center distance was less than 1.2 mm in single dipole fitting algorithm. Mouse microarray EEG source localization using microarray allows a reliable method for functional brain mapping in awake mouse opening an access to cross-species study with human brain.

  14. Adaptability of Cherry Tomato to High Temperature Stress under NFT%高温胁迫条件下营养液膜水培樱桃番茄的逆境适应性

    Institute of Scientific and Technical Information of China (English)

    陈海生; 朱兆平

    2012-01-01

    The influence of high temperature stress on several physiological indices of cherry tomato in NFT and in soil was studied in this paper.The variation of physiological indices,including leaf water potential,photosynthetic rate and superoxide dismutase of cherry tomato under high temperature stress was measured.The results showed that the physiological indices above mentioned decreased dramatically when the plants were planted in soil under high temperature condition,while only a slight decrease was found from the plants planted in NFT.It can be concluded that the heat resistance of tomato seeding under NFT was stronger than that under soil culture.%通过测定高温处理后水培和土培樱桃番茄的几项生理指标,研究了樱桃番茄在高温胁迫条件下的叶水势、光合速率、SOD酶活性等生理指标的变化特征,结果表明,高温胁迫条件下土培番茄叶水势、光合速率和SOD活性大幅度下降,而水培番茄上述生理指标虽有下降,但幅度远较土培番茄为少,因此,水培樱桃番茄对高温的抵抗能力要强于土培。

  15. 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.

  16. eConnectome: A MATLAB toolbox for mapping and imaging of brain functional connectivity.

    Science.gov (United States)

    He, Bin; Dai, Yakang; Astolfi, Laura; Babiloni, Fabio; Yuan, Han; Yang, Lin

    2011-02-15

    We have developed a MATLAB-based toolbox, eConnectome (electrophysiological connectome), for mapping and imaging functional connectivity at both the scalp and cortical levels from the electroencephalogram (EEG), as well as from the electrocorticogram (ECoG). Graphical user interfaces were designed for interactive and intuitive use of the toolbox. Major functions of eConnectome include EEG/ECoG preprocessing, scalp spatial mapping, cortical source estimation, connectivity analysis, and visualization. Granger causality measures such as directed transfer function and adaptive directed transfer function were implemented to estimate the directional interactions of brain functional networks, over the scalp and cortical sensor spaces. Cortical current density inverse imaging was implemented using a generic realistic geometry brain-head model from scalp EEGs. Granger causality could be further estimated over the cortical source domain from the inversely reconstructed cortical source signals as derived from the scalp EEG. Users may implement other connectivity estimators in the framework of eConnectome for various applications. The toolbox package is open-source and freely available at http://econnectome.umn.edu under the GNU general public license for noncommercial and academic uses.

  17. 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.

  18. 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.

  19. 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)

  20. 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

  1. MOOSE2-A toolbox for least-costly application-oriented input design

    Science.gov (United States)

    Annergren, Mariette; Larsson, Christian A.

    MOOSE2 is a MATLAB®-based toolbox for solving least-costly application-oriented input design problems in system identification. MOOSE2 provides the spectrum of the input signal to be used in the identification experiment made to estimate a linear parametric model of the system. The objective is to find a spectrum that minimizes experiment cost while fulfilling constraints imposed in the experiment and on the obtained model. The constraints considered by MOOSE2 are: frequency or power constraints on the signal spectra in the experiment, and application or quality specifications on the obtained model.

  2. MOOSE2—A toolbox for least-costly application-oriented input design

    Directory of Open Access Journals (Sweden)

    Mariette Annergren

    2016-01-01

    Full Text Available MOOSE2 is a MATLAB®-based toolbox for solving least-costly application-oriented input design problems in system identification. MOOSE2 provides the spectrum of the input signal to be used in the identification experiment made to estimate a linear parametric model of the system. The objective is to find a spectrum that minimizes experiment cost while fulfilling constraints imposed in the experiment and on the obtained model. The constraints considered by MOOSE2 are: frequency or power constraints on the signal spectra in the experiment, and application or quality specifications on the obtained model.

  3. 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

  4. Towards an integrated materials characterization toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Ian M [University of Illinois, Chicago; Schuh, Christopher A. [Massachusetts Institute of Technology (MIT); Vetrano, John S [Office of Basic Energy Sciences, U.S. Dept. of Energy, Washington DC; Browning, Nigel D. [University of California, Davis; Field, D P [Washington State University; Jensen, D J [Riso National Laboratory, Roskilde, Denmark; Miller, Michael K [ORNL; Baker, Ian [Dartmouth College; Dunand, D C [Northwestern University, Evanston; Dunin-Borkowski, R [Technical University of Denmark; Kabius, B [Argonne National Laboratory (ANL); Kelly, T. F. [Imago Scientific Instruments, Madison, WI; Lozano-Perez, S [University of Oxford; Misra, A [Los Alamos National Laboratory (LANL); Rohrer, A [Carnegie Mellon University; Rollett, A [Carnegie Mellon University; Taheri, M [Drexel University; Thompson, G. B. [University of Alabama, Tuscaloosa; Uchic, M [Air Force Research Laboratory, Wright-Patterson AFB, OH; Wang, Xun-Li [ORNL; Was, G [University of Michigan

    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 to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future 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 probemicroscopy have been reviewed recently and, therefore, are not included [D.A.Bonnell et al.: Rev.Modern Phys. in Review]. In this study particular attention is paid to studies that have pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent 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, and complex structure evolution problems involving material damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.

  5. Towards an integrated materials characterization toolbox

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, Ian M.; Schuh, Christopher A.; Vetrano, John S.; Browning, Nigel; Field, David P.; Jensen, Dorte J.; Miller, Michael K.; Baker, Ian; Dunand, David C.; Dunin-Borkowski, Rafal; Kabius, Bernd C.; Kelly, Tom; Lozano-Perez, Sergio; Misra, Amit; Rohrer, Gregory S.; Rollett, D.; Taheri, Mitra L.; Thompson, Greg B.; Uchic, Michael; Wang, Xun-Li; Was, Gary S.

    2011-06-14

    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 to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors’ viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future 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 probemicroscopy have been reviewed recently and, therefore, are not included [D.A.Bonnell et al.: Rev.Modern Phys. in Review]. In this study particular attention is paid to studies that have pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent the stateof- 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, and complex structure evolution problems involving material damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.

  6. Towards an integrated materials characterization toolbox.

    Energy Technology Data Exchange (ETDEWEB)

    Robertson, I. M.; Schuh, C. A.; Vetrano, J. S.; Browning, N. D.; Field, D. P.; Jensen, D. J.; Miller, M. K.; Baker, I.; Dunand, D. C.; Dunin-Borkowski, R.; KABIUS, B.; Kelly, T.; Lozano-Perez, S.; Misra, A.; Rohrer, G. S.; Rollett, A. D.; Taheri, M. L.; Thompson, G. B.; Uchic, M.; Wang, X-L.; Was, G. (Materials Science Division); (Univ. Illinois-Urbana); (Massachusetts Inst. Tech.); (US DOE); (Univ. California-Davis); (Lawrence Livermore Nat. Lab.); (Washington State Univ.); (Tech. Univ. Denmark); (Oak Ridge Nat. Lab.); (Dartmouth College); (Northwestern Univ.); (Cameca Instruments Corp.); (Univ. Oxford); (Los Alamos Nat. Lab.); (Carnegie Mellon Univ.); (Drexel Univ.)

    2011-06-01

    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 to reaction dynamics in four-dimensions, spanning multiple orders of magnitude in both temporal and spatial space. This study presents the authors viewpoint on the material characterization field, reviewing its recent past, evaluating its present capabilities, and proposing directions for its future 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 and, therefore, are not included [D.A. Bonnell et al.: Rev. Modern Phys. in Review]. In this study particular attention is paid to studies that have pioneered the synergetic use of multiple techniques to provide complementary views of a single structure or process; several of these studies represent 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, and complex structure evolution problems involving material damage. The future of microstructural characterization is proposed to be one not only where individual techniques are pushed to their limits, but where the community devises strategies of technique synergy to address complex multiscale problems in materials science and engineering.

  7. 40 CFR 141.717 - Pre-filtration treatment toolbox components.

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Pre-filtration treatment toolbox... Cryptosporidium Requirements for Microbial Toolbox Components § 141.717 Pre-filtration treatment toolbox... softening stages prior to filtration. Both softening stages must treat the entire plant flow taken from...

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

    Science.gov (United States)

    Andrew, Marion; Barua, Reeta; Short, Steven M; Kohn, Linda M

    2012-01-01

    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 host range

  9. 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

  10. Harmonic Calculation Toolbox in Industry Application for Adjustable Speed Drive

    DEFF Research Database (Denmark)

    Asiminoaei, Lucian; Blaabjerg, Frede; Hansen, Steffan

    2004-01-01

    parameters to be aware oFrede This paper focuses on estimation of line-side harmonic distortion when connecting one or multiple six-pulse diode rectifiers to any supply transformer. Results are put into a practical PC software toolbox for harmonic estimation on real applications. Through a combination...... of an off-line database and new interpolation techniques very good results have been achieved. The final results obtained are very close to the measurements on real applications and the toolbox can be used for future ASD designs and installations....

  11. 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...

  12. 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.

  13. 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/).

  14. GAPinch: genetic algorithm toolbox for water pinch technology

    Energy Technology Data Exchange (ETDEWEB)

    Prakotpol, D. [Department of Chemical Engineering, Faculty of Engineering, King Mongkut' s University of Technology Thonburi, Bangkok (Thailand); Srinophakun, T. [Department of Chemical Engineering, Faculty of Engineering, Kasetsart University, Bangkok (Thailand)

    2004-07-01

    Wastewater in the chemical industry can be minimized by water reuse. The optimum water usage network leads to a minimum freshwater consumption and wastewater treatment. Genetic algorithm, an objective of this work, is developed for solving the wastewater minimization problem. The optimization model is formulated for both single and multiple contaminants in the class of mixed integer nonlinear programming (MINLP). In this model, there is a set of equality constraints from mass balance that drives the genetic algorithm from addressing the feasible solution. To elucidate this problem, all variables have to be divided into two groups: independent and dependent variables. The values of independent variables come from randomization, whereas the values of dependent variables come from simultaneous solutions of a set of equality constraints after assigning the values of independent variables. This method is applied to the steps of initialization, crossover and mutation. The developed program is the MATLAB{sup TM} toolbox that consists of 29 m-file. The graphic user interface was created in order to make the program easy and convenient. After a user inputs the process condition of the problem into the blank form of GUI, the program will formulate the optimization model and solve for the solution automatically. Then, the optimum results are returned to the user. The program is tested with a process that contains a certain number of water-using operations in which water is used to remove a fixed content of contaminant. In the single contaminant system, this program and Lingo can find the minimum freshwater consumption, but the solutions are different in the configuration of water usage network. These alternative configurations give a wide-vision on the analysis of the system. In the multiple contaminants system, this program can find the same or better results in some test problems. (author)

  15. A disulfide intercalator toolbox for the site-directed modification of polypeptides.

    Science.gov (United States)

    Wang, Tao; Wu, Yuzhou; Kuan, Seah Ling; Dumele, Oliver; Lamla, Markus; Ng, David Y W; Arzt, Matthias; Thomas, Jessica; Mueller, Jan O; Barner-Kowollik, Christopher; Weil, Tanja

    2015-01-02

    A disulfide intercalator toolbox was developed for site-specific attachment of a broad variety of functional groups to proteins or peptides under mild, physiological conditions. The peptide hormone somatostatin (SST) served as model compound for intercalation into the available disulfide functionalization schemes starting from the intercalator or the reactive SST precursor before or after bioconjugation. A tetrazole-SST derivative was obtained that undergoes photoinduced cycloaddition in mammalian cells, which was monitored by live-cell imaging. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. 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.

  17. X-tra as a toolbox for truth maintenance

    OpenAIRE

    Charpillet, François; Marquis, Pierre; Haton, Jean-Paul

    1991-01-01

    X-TRA is a development tool for knowledge-based systems. It integrates a toolbox for truth maintenance based on both TMS and ATMS techniques. In this paper we present facilities provided in X-TRA for the truth maintenance task.

  18. 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...

  19. 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...

  20. 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...

  1. 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.

  2. Utilization of BEAM and NEST open source toolboxes in education and research

    Directory of Open Access Journals (Sweden)

    Markéta Potůčková

    2011-05-01

    Full Text Available European Space Agency (ESA provides several open source toolboxes for visualization, processing and analyzing satellite images acquired both in optical and microwave domains. Basic ERS & Envisat (AATSR and MERIS Toolbox (BEAM was originally developed for easier handling ENVISAT optical data. Today this toolbox supports several raster data formats and datasets collected with other EO instruments such as MODIS, AVHRR, CHRIS/Proba. The NEXT ESA SAR Toolbox (NEST has been created for processing radar data acquired from different satellites such as ERS 1&2, ENVISAT, RADARSAT or TerraSAR X. Both toolboxes are suitable for the education of the basic principles of data processing (geometric and radiometric corrections, classification, filtering of radar data but also for research. Possibilities for utilization of these toolboxes in remote sensing courses based on two examples of practical exercises are described. Use of the NEST toolbox is demonstrated on a research project dealing with snow cover detection from SAR imagery.

  3. 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

  4. 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.

  5. FracPaQ: A MATLAB™ toolbox for the quantification of fracture patterns

    Science.gov (United States)

    Healy, David; Rizzo, Roberto E.; Cornwell, David G.; Farrell, Natalie J. C.; Watkins, Hannah; Timms, Nick E.; Gomez-Rivas, Enrique; Smith, Michael

    2017-02-01

    The patterns of fractures in deformed rocks are rarely uniform or random. Fracture orientations, sizes, and spatial distributions often exhibit some kind of order. In detail, relationships may exist 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 attributes and patterns. This paper describes FracPaQ, a new open source, cross-platform 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 previously 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, rock types and tectonic settings. The implemented methods presented are inherently scale independent, and a key task where applicable is analysing and integrating quantitative fracture pattern data from micro-to macro-scales. The toolbox was developed in MATLAB™ and the source code is publicly available on GitHub™ and the Mathworks™ FileExchange. The code runs on any computer with MATLAB installed, including PCs with Microsoft Windows, Apple Macs with Mac OS X, and machines running different flavours of Linux. The application, source code and sample input files are available in open repositories in the hope that other developers and researchers will optimise and extend the

  6. 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.

  7. GIAnT - Generic InSAR Analysis Toolbox

    Science.gov (United States)

    Agram, P.; Jolivet, R.; Riel, B. V.; Simons, M.; Doin, M.; Lasserre, C.; Hetland, E. A.

    2012-12-01

    noise covariance models through the processing chain for robust estimation of uncertainties in the deformation estimates. We will demonstrate the ease of use of our framework with results ranging from regional scale analysis around Long Valley, CA and Parkfield, CA to continental scale analysis in Western South America. We will also present preliminary results from a new time-series approach that simultaneously estimates deformation over the complete spatial domain at all time epochs on a distributed computing platform. GIAnT has been developed entirely using open source tools and uses Python as the underlying platform. We build on the extensive numerical (NumPy) and scientific (SciPy) computing Python libraries to develop an object-oriented, flexible and modular framework for time-series InSAR applications. The toolbox is currently configured to work with outputs from ROI-PAC, ISCE and DORIS, but can easily be extended to support products from other SAR/InSAR processors. The toolbox libraries include support for hierarchical data format (HDF5) memory mapped files, parallel processing with Python's multi-processing module and support for many convex optimization solvers like CSDP, CVXOPT etc. An extensive set of routines to deal with ASCII and XML files has also been included for controlling the processing parameters.

  8. Dynamic prediction of gas emission based on wavelet neural network toolbox

    Institute of Scientific and Technical Information of China (English)

    Yu-Min PAN; Yong-Hong DENG; Quan-Zhu ZHANG; Peng-Qian XUE

    2013-01-01

    This paper presents a method for dynamically predicting gas emission quantity based on the wavelet neural network (WNN) toolbox.Such a method is able to predict the gas emission quantity in adjacent subsequent time intervals through training the WNN with even time-interval samples.The method builds successive new model with the width of sliding window remaining invariable so as to obtain a dynamic prediction method for gas emission quantity.Furthermore,the method performs prediction by a self-developed WNN toolbox.Experiments indicate that such a model can overcome the deficiencies of the traditional static prediction model and can fully make use of the feature extraction capability of wavelet base function to reflect the geological feature of gas emission quantity dynamically.The method is characterized by simplicity,flexibility,small data scale,fast convergence rate and high prediction precision.In addition,the method is also characterized by certainty and repeatability of the predicted results.The effectiveness of this method is confirmed by simulation results.Therefore,this method will exert practical significance on promoting the application of WNN.

  9. Efeito da concentração da solução nutritiva no crescimento da alface em cultivo hidropônico-sistema NFT Effects of the concentration of nutrient solution on lettuce growth in hydroponics-NFT system

    Directory of Open Access Journals (Sweden)

    Nilton Nélio Cometti

    2008-06-01

    Full Text Available Foi avaliado o crescimento da alface (Lactuca sativa L. cv 'Vera' em um sistema hidropônico NFT com diferentes concentrações da solução nutritiva. O experimento foi realizado em casa de vegetação de abril a maio de 2000, na UFRRJ, Seropédica (RJ. Os tratamentos constaram de quatro soluções nutritivas, diferentes quanto à concentração de macronutrientes: 100; 50; 25 e 12,5% da concentração original proposta por Furlani (1997. A produção de massa seca (parte comercial em solução nutritiva a 50% da concentração original, e condutividade elétrica em torno de 0,98 dS m-1, foi semelhante à solução a 100% da força iônica. As produções obtidas com 100 e 50% da força iônica estiveram dentro da faixa de 90% da produção máxima, calculada em 75±1% da força iônica da solução nutritiva, simulada por equação de regressão. Entretanto, o uso de concentrações menores resultou em redução no crescimento de 50% com a solução a 25% e 80% com a solução a 12,5% da força iônica, nas condições de luz e temperatura em que o experimento foi conduzido. A redução da concentração da solução nutritiva permite uma economia de pelo menos 50% no custo da solução nutritiva básica, reduzindo-se a solução inicial para 1,00 dS m-1, sem comprometer a produtividade.The growth of lettuce (Lactuca sativa L. cv 'Vera' was evaluated in a NFT hydroponic system with different nutrient solution concentrations. An experiment was carried out in a greenhouse from April to May, 2000 in Rio de Janeiro State, Brazil. Four treatments were used differing in macro nutrient concentration: 100; 50; 25 and 12.5% of the original concentration of the solution proposed by Furlani (1997. Using 50% of the original concentration with electric conductivity around 0,98 dS m-1, plants produced the same shoot dry mass as using 100% of the ionic strength. In this trial, the phytomass yield using 100 and 50% of the ionic strength was within the range

  10. Modeling and Analysis of a Constant Power Series-Loaded Resonant Converter

    Science.gov (United States)

    2011-06-01

    Field Programmable Gate Array (FPGA) was programmed using a Xilinx Simulink System Generator toolbox. Using Naval xvi Postgraduate School‟s Student...Xilinx blocks using the Xilinx System Generator Toolbox. The advantage of modeling first with Simulink and then with the Xilinx System Generator Toolbox...gate driver signals. The one aspect of the Xilinx System Generator Toolbox that is different than the Simulink blocks is that Xilinx blocks are going

  11. MatArray: a Matlab toolbox for microarray data.

    Science.gov (United States)

    Venet, David

    2003-03-22

    The microarray technology allows the high-throughput quantification of the mRNA level of thousands of genes under dozens of conditions, generating a wealth of data which must be analyzed using some form of computational means. A popular framework for such analysis is Matlab, a powerful computing language for which many functions have been written. However, although complex topics like neural networks or principal component analysis are freely available in Matlab, functions to perform more basic tasks like data normalization or hierarchical clustering in an efficient manner are not. The MatArray toolbox aims at filling this gap by offering efficient implementations of the most needed functions for microarray analysis. The functions in the toolbox are command-line only, since it is geared toward seasoned Matlab users.

  12. 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

  13. 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.

  14. Service Dominant Logic. Changing perspective, revising the toolbox

    DEFF Research Database (Denmark)

    Morelli, Nicola; Götzen, Amalia De

    2016-01-01

    This paper analyses the perspective shift that has happened in service design practice with the introduction of the Service Dominant Logic. Three different levels of design action are presented with their methodological implications. In the fluid context where diffuse design, expert design...... and strategic design take place, relevant case studies are shortly presented in order to describe the designer’s role in the value-creation process and the consequent necessary revision of his own toolbox....

  15. 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.

  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

    for solving such probabilistically formulated inverse problems by sampling the a posteriori probability density function. In order to describe the a priori probability density function, we consider both simple Gaussian models and more complex (and realistic) a priori models based on higher order statistics....... These a priori models can be used with both linear and non-linear inverse problems. For linear inverse Gaussian problems we make use of least-squares and kriging-based methods to describe the a posteriori probability density function directly. For general non-linear (i.e. non-Gaussian) inverse problems, we make...... use of the extended Metropolis algorithm to sample the a posteriori probability density function. Together with the extended Metropolis algorithm, we use sequential Gibbs sampling that allow computationally efficient sampling of complex a priori models. The toolbox can be applied to any inverse...

  17. ArcGeomorphometry: A toolbox for geomorphometric characterisation of DEMs in the ArcGIS environment

    Science.gov (United States)

    Rigol-Sanchez, Juan P.; Stuart, Neil; Pulido-Bosch, Antonio

    2015-12-01

    A software tool is described for the extraction of geomorphometric land surface variables and features from Digital Elevation Models (DEMs). The ArcGeomorphometry Toolbox consists of a series of Python/Numpy processing functions, presented through an easy-to-use graphical menu for the widely used ArcGIS package. Although many GIS provide some operations for analysing DEMs, the methods are often only partially implemented and can be difficult to find and used effectively. Since the results of automated characterisation of landscapes from DEMs are influenced by the extent being considered, the resolution of the source DEM and the size of the kernel (analysis window) used for processing, we have developed a tool to allow GIS users to flexibly apply several multi-scale analysis methods to parameterise and classify a DEM into discrete land surface units. Users can control the threshold values for land surface classifications. The size of the processing kernel can be used to identify land surface features across a range of landscape scales. The pattern of land surface units from each attempt at classification is displayed immediately and can then be processed in the GIS alongside additional data that can assist with a visual assessment and comparison of a series of results. The functionality of the ArcGeomorphometry toolbox is described using an example DEM.

  18. A finite-element toolbox for the stationary Gross-Pitaevskii equation with rotation

    Science.gov (United States)

    Vergez, Guillaume; Danaila, Ionut; Auliac, Sylvain; Hecht, Frédéric

    2016-12-01

    We present a new numerical system using classical finite elements with mesh adaptivity for computing stationary solutions of the Gross-Pitaevskii equation. The programs are written as a toolbox for FreeFem++ (www.freefem.org), a free finite-element software available for all existing operating systems. This offers the advantage to hide all technical issues related to the implementation of the finite element method, allowing to easily code various numerical algorithms. Two robust and optimized numerical methods were implemented to minimize the Gross-Pitaevskii energy: a steepest descent method based on Sobolev gradients and a minimization algorithm based on the state-of-the-art optimization library Ipopt. For both methods, mesh adaptivity strategies are used to reduce the computational time and increase the local spatial accuracy when vortices are present. Different run cases are made available for 2D and 3D configurations of Bose-Einstein condensates in rotation. An optional graphical user interface is also provided, allowing to easily run predefined cases or with user-defined parameter files. We also provide several post-processing tools (like the identification of quantized vortices) that could help in extracting physical features from the simulations. The toolbox is extremely versatile and can be easily adapted to deal with different physical models.

  19. 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.

  20. MBEToolbox: a Matlab toolbox for sequence data analysis in molecular biology and evolution

    Directory of Open Access Journals (Sweden)

    Xia Xuhua

    2005-03-01

    Full Text Available Abstract Background MATLAB is a high-performance language for technical computing, integrating computation, visualization, and programming in an easy-to-use environment. It has been widely used in many areas, such as mathematics and computation, algorithm development, data acquisition, modeling, simulation, and scientific and engineering graphics. However, few functions are freely available in MATLAB to perform the sequence data analyses specifically required for molecular biology and evolution. Results We have developed a MATLAB toolbox, called MBEToolbox, aimed at filling this gap by offering efficient implementations of the most needed functions in molecular biology and evolution. It can be used to manipulate aligned sequences, calculate evolutionary distances, estimate synonymous and nonsynonymous substitution rates, and infer phylogenetic trees. Moreover, it provides an extensible, functional framework for users with more specialized requirements to explore and analyze aligned nucleotide or protein sequences from an evolutionary perspective. The full functions in the toolbox are accessible through the command-line for seasoned MATLAB users. A graphical user interface, that may be especially useful for non-specialist end users, is also provided. Conclusion MBEToolbox is a useful tool that can aid in the exploration, interpretation and visualization of data in molecular biology and evolution. The software is publicly available at http://web.hku.hk/~jamescai/mbetoolbox/ and http://bioinformatics.org/project/?group_id=454.

  1. 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.

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

    Science.gov (United States)

    MacDonell, Margaret M.; Haroun, Lynne A.; Teuschler, Linda K.; Rice, Glenn E.; Hertzberg, Richard C.; Butler, James P.; Chang, Young-Soo; Clark, Shanna L.; Johns, Alan P.; Perry, Camarie S.; Garcia, Shannon S.; Jacobi, John H.; Scofield, Marcienne A.

    2013-01-01

    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. PMID:23762048

  3. A transcription activator-like effector toolbox for genome engineering.

    Science.gov (United States)

    Sanjana, Neville E; Cong, Le; Zhou, Yang; Cunniff, Margaret M; Feng, Guoping; Zhang, Feng

    2012-01-05

    Transcription activator-like effectors (TALEs) are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas sp. The DNA-binding domain of each TALE consists of tandem 34-amino acid repeat modules that can be rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Here we describe a toolbox for rapid construction of custom TALE transcription factors (TALE-TFs) and nucleases (TALENs) using a hierarchical ligation procedure. This toolbox facilitates affordable and rapid construction of custom TALE-TFs and TALENs within 1 week and can be easily scaled up to construct TALEs for multiple targets in parallel. We also provide details for testing the activity in mammalian cells of custom TALE-TFs and TALENs using quantitative reverse-transcription PCR and Surveyor nuclease, respectively. The TALE toolbox described here will enable a broad range of biological applications.

  4. 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.

  5. 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.

  6. Characterization of disease-related covariance topographies with SSMPCA toolbox: effects of spatial normalization and PET scanners.

    Science.gov (United States)

    Peng, Shichun; Ma, Yilong; Spetsieris, Phoebe G; Mattis, Paul; Feigin, Andrew; Dhawan, Vijay; Eidelberg, David

    2014-05-01

    To generate imaging biomarkers from disease-specific brain networks, we have implemented a general toolbox to rapidly perform scaled subprofile modeling (SSM) based on principal component analysis (PCA) on brain images of patients and normals. This SSMPCA toolbox can define spatial covariance patterns whose expression in individual subjects can discriminate patients from controls or predict behavioral measures. The technique may depend on differences in spatial normalization algorithms and brain imaging systems. We have evaluated the reproducibility of characteristic metabolic patterns generated by SSMPCA in patients with Parkinson's disease (PD). We used [(18) F]fluorodeoxyglucose PET scans from patients with PD and normal controls. Motor-related (PDRP) and cognition-related (PDCP) metabolic patterns were derived from images spatially normalized using four versions of SPM software (spm99, spm2, spm5, and spm8). Differences between these patterns and subject scores were compared across multiple independent groups of patients and control subjects. These patterns and subject scores were highly reproducible with different normalization programs in terms of disease discrimination and cognitive correlation. Subject scores were also comparable in patients with PD imaged across multiple PET scanners. Our findings confirm a very high degree of consistency among brain networks and their clinical correlates in PD using images normalized in four different SPM platforms. SSMPCA toolbox can be used reliably for generating disease-specific imaging biomarkers despite the continued evolution of image preprocessing software in the neuroimaging community. Network expressions can be quantified in individual patients independent of different physical characteristics of PET cameras.

  7. 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.

  8. An analytical tool-box for comprehensive biochemical, structural and transcriptome evaluation of oral biofilms mediated by mutans streptococci.

    Science.gov (United States)

    Klein, Marlise I; Xiao, Jin; Heydorn, Arne; Koo, Hyun

    2011-01-25

    Biofilms are highly dynamic, organized and structured communities of microbial cells enmeshed in an extracellular matrix of variable density and composition (1, 2). In general, biofilms develop from initial microbial attachment on a surface followed by formation of cell clusters (or microcolonies) and further development and stabilization of the microcolonies, which occur in a complex extracellular matrix. The majority of biofilm matrices harbor exopolysaccharides (EPS), and dental biofilms are no exception; especially those associated with caries disease, which are mostly mediated by mutans streptococci (3). The EPS are synthesized by microorganisms (S. mutans, a key contributor) by means of extracellular enzymes, such as glucosyltransferases using sucrose primarily as substrate (3). Studies of biofilms formed on tooth surfaces are particularly challenging owing to their constant exposure to environmental challenges associated with complex diet-host-microbial interactions occurring in the oral cavity. Better understanding of the dynamic changes of the structural organization and composition of the matrix, physiology and transcriptome/proteome profile of biofilm-cells in response to these complex interactions would further advance the current knowledge of how oral biofilms modulate pathogenicity. Therefore, we have developed an analytical tool-box to facilitate biofilm analysis at structural, biochemical and molecular levels by combining commonly available and novel techniques with custom-made software for data analysis. Standard analytical (colorimetric assays, RT-qPCR and microarrays) and novel fluorescence techniques (for simultaneous labeling of bacteria and EPS) were integrated with specific software for data analysis to address the complex nature of oral biofilm research. The tool-box is comprised of 4 distinct but interconnected steps (Figure 1): 1) Bioassays, 2) Raw Data Input, 3) Data Processing, and 4) Data Analysis. We used our in vitro biofilm model and

  9. Offsets, one tool in the toolbox

    CSIR Research Space (South Africa)

    Garland, Rebecca M

    2014-01-01

    Full Text Available emissions inventory as we can  but this is largest stumbling block to provide policy support • How can a regulator be certain of the impact of an offset without being able to accurately model it? N a id o o, 2 0 1 2 7 What modelling... ambient air quality – Comprehensive, transparent, agreed upon modelling platform – Active regulator who decides on the interventions and policies in their airshed and has capacity required to decide on the needed suite of interventions, regulations...

  10. An optical toolbox for astronomical instrumentation

    Science.gov (United States)

    Sutin, Brian M.

    2016-08-01

    The author has open-sourced a program for optical modeling of astronomical instrumentation. The code allows for optical systems to be described in a programming language. An optical prescription may contain coordinate systems and transformations, arbitrary polynomial aspheric surfaces and complex volumes. Rather than using a plethora of rays to evaluate performance, all the derivatives along a ray are computed by automatic differentiation. By adaptively controlling the patches around each ray, the system can be modeled to a guaranteed known precision. The code currently consists of less than 10,000 lines of C++/stdlib code.

  11. nSTAT: open-source neural spike train analysis toolbox for Matlab.

    Science.gov (United States)

    Cajigas, I; Malik, W Q; Brown, E N

    2012-11-15

    Over the last decade there has been a tremendous advance in the analytical tools available to neuroscientists to understand and model neural function. In particular, the point process - generalized linear model (PP-GLM) framework has been applied successfully to problems ranging from neuro-endocrine physiology to neural decoding. However, the lack of freely distributed software implementations of published PP-GLM algorithms together with problem-specific modifications required for their use, limit wide application of these techniques. In an effort to make existing PP-GLM methods more accessible to the neuroscience community, we have developed nSTAT--an open source neural spike train analysis toolbox for Matlab®. By adopting an object-oriented programming (OOP) approach, nSTAT allows users to easily manipulate data by performing operations on objects that have an intuitive connection to the experiment (spike trains, covariates, etc.), rather than by dealing with data in vector/matrix form. The algorithms implemented within nSTAT address a number of common problems including computation of peri-stimulus time histograms, quantification of the temporal response properties of neurons, and characterization of neural plasticity within and across trials. nSTAT provides a starting point for exploratory data analysis, allows for simple and systematic building and testing of point process models, and for decoding of stimulus variables based on point process models of neural function. By providing an open-source toolbox, we hope to establish a platform that can be easily used, modified, and extended by the scientific community to address limitations of current techniques and to extend available techniques to more complex problems.

  12. 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

  13. Basic Radar Altimetry Toolbox: tools to teach altimetry for ocean

    Science.gov (United States)

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

    2013-04-01

    The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data, including the next mission to be launched, CryoSat. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. More than 2000 people downloaded it (January 2013), with many "newcomers" to altimetry among them. Users' feedbacks, developments in altimetry, and practice, showed that new interesting features could be added. Some have been added and/or improved in version 2 and 3. Others are in discussion for the future, including addition of the future Sentinel-3. The Basic Radar Altimetry Toolbox is able: - to read most distributed radar altimetry data, including the one from future missions like Saral, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways, including as an educational tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. Example from education uses will be presented, and feedback from those who used it as such will be most welcome. BRAT is developed under contract with ESA and CNES. It is available at http://www.altimetry.info and http://earth.esa.int/brat/

  14. 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,

  15. 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.

  16. 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.

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    Focusing and apodization are an essential part of signal processing in ultrasound imaging. Although the fun- damental principles are simple, the dramatic increase in computational power of CPUs, GPUs, and FPGAs motivates the development of software based beamformers, which further improves image...... quality (and the accu- racy of velocity estimation). For developing new imaging methods, it is important to establish proof-of-concept before using resources on real-time implementations. With this in mind, an eective and versatile Matlab toolbox written in C++ has been developed to assist in developing...

  18. Sequence Handling by Sequence Analysis Toolbox v1.0

    DEFF Research Database (Denmark)

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

    2006-01-01

    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...... 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...

  19. Adding tools to the open source toolbox: The Internet

    Science.gov (United States)

    Porth, Tricia

    1994-01-01

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

  20. MatSWMM – An open-source toolbox for designing real-time control of urban drainage systems

    OpenAIRE

    2016-01-01

    This manuscript describes the MatSWMM toolbox, an open-source Matlab, Python, and LabVIEW-based software package for the analysis and design of real-time control (RTC) strategies in urban drainage systems (UDS). MatSWMM includes control-oriented models of UDS, and the storm water management model (SWMM) of the US Environmental Protection Agency (EPA), as well as systematic-system edition functionalities. Furthermore, MatSWMM is also provided with a population-dynamics-based controller for UDS...

  1. 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.

  2. ZonalMetrics - a Python toolbox for zonal landscape structure analysis

    Science.gov (United States)

    Adamczyk, Joanna; Tiede, Dirk

    2017-02-01

    We present a Python toolbox for the calculation of zonal landscape metrics. Instead of global calculations focusing on the whole landscape, the proposed ZonalMetrics toolbox allows the calculation of landscape metrics for user-defined zones. Such zones can be defined through regular units (e.g. hexagons, grids) that can be created within the toolbox. In addition, any polygonal set specified by the user (e.g. administrative units) can be used. The implemented set of landscape metrics is specifically selected and valid for calculations within zones. The tool is demonstrated based on a case study for the Warsaw metropolitan area and the possibilities of applying the toolbox for different zonal layers are illustrated. The implementation is based on the Python toolbox introduced in ArcGIS 10.1, offering an easy to use graphical user interface and batch calculation possibilities. The source code is free and open to the community and extendable to specific needs.

  3. SPATIAL DATA MINING TOOLBOX FOR MAPPING SUITABILITY OF LANDFILL SITES USING NEURAL NETWORKS

    Directory of Open Access Journals (Sweden)

    S. K. M. Abujayyab

    2016-09-01

    Full Text Available 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.

  4. 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.

  5. 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.

  6. External Verification of the Bundle Adjustment in Photogrammetric Software Using the Damped Bundle Adjustment Toolbox

    Science.gov (United States)

    Börlin, Niclas; Grussenmeyer, Pierre

    2016-06-01

    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.

  7. Expanding the Imine Reductase Toolbox by Exploring the Bacterial Protein-Sequence Space.

    Science.gov (United States)

    Wetzl, Dennis; Berrera, Marco; Sandon, Nicolas; Fishlock, Dan; Ebeling, Martin; Müller, Michael; Hanlon, Steven; Wirz, Beat; Iding, Hans

    2015-08-17

    Recent investigations on imine reductases (IREDs) have enriched the toolbox of potential catalysts for accessing chiral amines, which are important building blocks for the pharmaceutical industry. Herein, we describe the characterization of 20 new IREDs. A C-terminal domain clustering of the bacterial protein-sequence space was performed to identify the novel IRED candidates. Each of the identified enzymes was characterized against a set of nine cyclic imine model substrates. A refined clustering towards putative active-site residues was performed and was consistent both with our screening and previously reported results. Finally, preparative scale experiments on a 100 mg scale with two purified IREDs, IR_20 from Streptomyces tsukubaensis and IR_23 from Streptomyces vidiochromogenes, were carried out to provide (R)-2-methylpiperidine in 98% ee (71% yield) and (R)-1-methyl-1,2,3,4-tetrahydroisoquinoline in >98% ee (82% yield). © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. 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....

  9. Extending the Schizosaccharomyces pombe molecular genetic toolbox.

    Directory of Open Access Journals (Sweden)

    Dorota Fennessy

    Full Text Available Targeted alteration of the genome lies at the heart of the exploitation of S. pombe as a model system. The rate of analysis is often determined by the efficiency with which a target locus can be manipulated. For most loci this is not a problem, however for some loci, such as fin1+, rates of gene targeting below 5% can limit the scope and scale of manipulations that are feasible within a reasonable time frame. We now describe a simple modification of transformation procedure for directing integration of genomic sequences that leads to a 5-fold increase in the transformation efficiency when antibiotic based dominant selection markers are used. We also show that removal of the pku70+ and pku80+ genes, which encode DNA end binding proteins required for the non-homologous end joining DNA repair pathway, increases the efficiency of gene targeting at fin1+ to around 75-80% (a 16-fold increase. We describe how a natMX6/rpl42+ cassette can be used for positive and negative selection for integration at a targeted locus. To facilitate the evaluation of the impact of a series of mutations on the function of a gene of interest we have generated three vector series that rely upon different selectable markers to direct the expression of tagged/untagged molecules from distinct genomic integration sites. pINTL and pINTK vectors use ura4+ selection to direct disruptive integration of leu1+ and lys1+ respectively, while pINTH vectors exploit nourseothricin resistance to detect the targeted disruption of a hygromycin B resistance conferring hphMX6 cassette that has been integrated on chromosome III. Finally, we have generated a series of multi-copy expression vectors that use resistance to nourseothricin or kanamycin/G418 to select for propagation in prototrophic hosts. Collectively these protocol modifications and vectors extend the versatility of this key model system.

  10. 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.

  11. 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

  12. The genetic toolbox for Leishmania parasites.

    Science.gov (United States)

    Roberts, Sigrid C

    2011-01-01

    Leishmania parasites cause a variety of devastating diseases in tropical areas around the world. Due to the lack of vaccines and limited availability of drugs, new therapeutic targets are urgently needed. A variety of genetic tools have been developed to investigate the complex biology of this parasite and its interactions with the host. One of the main techniques is the generation of knock-out parasites via targeted gene replacement, a process that takes advantage of the parasites ability to undergo homologous recombination. Studying the effect of gene deletions in vitro and in infectivity models in vivo allows understanding the function of a target gene and its potential as a therapeutic target. Other genetic manipulations available include episomal and chromosomal complementation and the generation of overproducer strains. However, there are also limitations, such as the lack of RNA interference machinery in most Leishmania species and limited options for inducible expression systems. The genomes of several Leishmania species have now been sequenced and will provide powerful resources in combination with the genetic tools that are available. The increasing knowledge of parasite biology and host parasite interactions derived from these studies will raise the number of potential therapeutic targets, which are sorely needed to combat leishmaniasis.

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

    Science.gov (United States)

    Conway, R; Kavanagh, R; Coughlan, R J; Carey, J J

    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 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.

  14. A toolbox for rockfall Quantitative Risk Assessment

    Science.gov (United States)

    Agliardi, F.; Mavrouli, O.; Schubert, M.; Corominas, J.; Crosta, G. B.; Faber, M. H.; Frattini, P.; Narasimhan, H.

    2012-04-01

    Rockfall Quantitative Risk Analysis for mitigation design and implementation requires evaluating the probability of rockfall events, the probability and intensity of impacts on structures (elements at risk and countermeasures), their vulnerability, and the related expected costs for different scenarios. A sound theoretical framework has been developed during the last years both for spatially-distributed and local (i.e. single element at risk) analyses. Nevertheless, the practical application of existing methodologies remains challenging, due to difficulties in the collection of required data and to the lack of simple, dedicated analysis tools. In order to fill this gap, specific tools have been developed in the form of Excel spreadsheets, in the framework of Safeland EU project. These tools can be used by stakeholders, practitioners and other interested parties for the quantitative calculation of rock fall risk through its key components (probabilities, vulnerability, loss), using combinations of deterministic and probabilistic approaches. Three tools have been developed, namely: QuRAR (by UNIMIB), VulBlock (by UPC), and RiskNow-Falling Rocks (by ETH Zurich). QuRAR implements a spatially distributed, quantitative assessment methodology of rockfall risk for individual buildings or structures in a multi-building context (urban area). Risk is calculated in terms of expected annual cost, through the evaluation of rockfall event probability, propagation and impact probability (by 3D numerical modelling of rockfall trajectories), and empirical vulnerability for different risk protection scenarios. Vulblock allows a detailed, analytical calculation of the vulnerability of reinforced concrete frame buildings to rockfalls and related fragility curves, both as functions of block velocity and the size. The calculated vulnerability can be integrated in other methodologies/procedures based on the risk equation, by incorporating the uncertainty of the impact location of the rock

  15. A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure

    Science.gov (United States)

    Richards, V. M.; Dai, W.

    2014-01-01

    A MATLAB toolbox for the efficient estimation of the threshold, slope, and lapse rate of the psychometric function is described. The toolbox enables the efficient implementation of the updated maximum-likelihood (UML) procedure. The toolbox uses an object-oriented architecture for organizing the experimental variables and computational algorithms, which provides experimenters with flexibility in experimental design and data management. Descriptions of the UML procedure and the UML Toolbox are provided, followed by toolbox use examples. Finally, guidelines and recommendations of parameter configurations are given. PMID:24671826

  16. A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure.

    Science.gov (United States)

    Shen, Yi; Dai, Wei; Richards, Virginia M

    2015-03-01

    A MATLAB toolbox for the efficient estimation of the threshold, slope, and lapse rate of the psychometric function is described. The toolbox enables the efficient implementation of the updated maximum-likelihood (UML) procedure. The toolbox uses an object-oriented architecture for organizing the experimental variables and computational algorithms, which provides experimenters with flexibility in experimental design and data management. Descriptions of the UML procedure and the UML Toolbox are provided, followed by toolbox use examples. Finally, guidelines and recommendations of parameter configurations are given.

  17. 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

  18. 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 performance......, e.g., by the use of in-situ product removal (ISPR).This review provides a general overview of currently available tools in a microfluidic toolbox and how this toolbox can be applied to the development of advanced biocatalytic process concepts. Emphasis is placed on describing the possibilities...

  19. TOM software toolbox: acquisition and analysis for electron tomography.

    Science.gov (United States)

    Nickell, Stephan; Förster, Friedrich; Linaroudis, Alexandros; Net, William Del; Beck, Florian; Hegerl, Reiner; Baumeister, Wolfgang; Plitzko, Jürgen M

    2005-03-01

    Automated data acquisition procedures have changed the perspectives of electron tomography (ET) in a profound manner. Elaborate data acquisition schemes with autotuning functions minimize exposure of the specimen to the electron beam and sophisticated image analysis routines retrieve a maximum of information from noisy data sets. "TOM software toolbox" integrates established algorithms and new concepts tailored to the special needs of low dose ET. It provides a user-friendly unified platform for all processing steps: acquisition, alignment, reconstruction, and analysis. Designed as a collection of computational procedures it is a complete software solution within a highly flexible framework. TOM represents a new way of working with the electron microscope and can serve as the basis for future high-throughput applications.

  20. 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

  1. The Expanding Toolbox of In Vivo Bioluminescent Imaging

    Science.gov (United States)

    Xu, Tingting; Close, Dan; Handagama, Winode; Marr, Enolia; Sayler, Gary; Ripp, Steven

    2016-01-01

    In vivo bioluminescent imaging (BLI) permits the visualization of engineered bioluminescence from living cells and tissues to provide a unique perspective toward the understanding of biological processes as they occur within the framework of an authentic in vivo environment. The toolbox of in vivo BLI includes an inventory of luciferase compounds capable of generating bioluminescent light signals along with sophisticated and powerful instrumentation designed to detect and quantify these light signals non-invasively as they emit from the living subject. The information acquired reveals the dynamics of a wide range of biological functions that play key roles in the physiological and pathological control of disease and its therapeutic management. This mini review provides an overview of the tools and applications central to the evolution of in vivo BLI as a core technology in the preclinical imaging disciplines. PMID:27446798

  2. Expanding the metabolic engineering toolbox with directed evolution.

    Science.gov (United States)

    Abatemarco, Joseph; Hill, Andrew; Alper, Hal S

    2013-12-01

    Cellular systems can be engineered into factories that produce high-value chemicals from renewable feedstock. Such an approach requires an expanded toolbox for metabolic engineering. Recently, protein engineering and directed evolution strategies have started to play a growing and critical role within metabolic engineering. This review focuses on the various ways in which directed evolution can be applied in conjunction with metabolic engineering to improve product yields. Specifically, we discuss the application of directed evolution on both catalytic and non-catalytic traits of enzymes, on regulatory elements, and on whole genomes in a metabolic engineering context. We demonstrate how the goals of metabolic pathway engineering can be achieved in part through evolving cellular parts as opposed to traditional approaches that rely on gene overexpression and deletion. Finally, we discuss the current limitations in screening technology that hinder the full implementation of a metabolic pathway-directed evolution approach.

  3. The NIH Toolbox Pattern Comparison Processing Speed Test: Normative Data

    Science.gov (United States)

    Carlozzi, Noelle E.; Beaumont, Jennifer L.; Tulsky, David S.; Gershon, Richard C.

    2015-01-01

    The NIH Toolbox Pattern Comparison Processing Speed Test was developed to assess processing speed. While initial validation work provides preliminary support for this test in both children and adults, more work is needed to ensure dependability and generalizability. Thus, this replication study examines descriptive data (including age effects), test–retest reliability, and construct validity in n = 4,859 participants ages 3–85 years (matched to 2010 census data). Although the Pattern Comparison was not appropriate for all 3 and 4 years old, by ages 5 and 6, more meaningful scores were apparent. There was evidence for convergent and discriminant validity. There was also a moderate practice effect (i.e., increase of 5.5 points) over a 1-week time frame. Pattern Comparison exhibits a number of strengths: it is appropriate for use across the lifespan (ages 5–85), it is short and easy to administer, and there is support for construct validity. PMID:26025230

  4. 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.

  5. Service Dominant Logic. Changing perspective, revising the toolbox

    DEFF Research Database (Denmark)

    Morelli, Nicola; Götzen, Amalia De

    2016-01-01

    This paper analyses the perspective shift that has happened in service design practice with the introduction of the Service Dominant Logic. Three different levels of design action are presented with their methodological implications. In the fluid context where diffuse design, expert design and st...... and strategic design take place, relevant case studies are shortly presented in order to describe the designer’s role in the value-creation process and the consequent necessary revision of his own toolbox.......This paper analyses the perspective shift that has happened in service design practice with the introduction of the Service Dominant Logic. Three different levels of design action are presented with their methodological implications. In the fluid context where diffuse design, expert design...

  6. Complete experimental toolbox for alignment-free quantum communication

    CERN Document Server

    D'Ambrosio, Vincenzo; Walborn, Stephen P; Aolita, Leandro; Slussarenko, Sergei; Marrucci, Lorenzo; Sciarrino, Fabio

    2012-01-01

    Quantum communication employs the counter-intuitive features of quantum physics to perform tasks that are im- possible in the classical world. It is crucial for testing the foundations of quantum theory and promises to rev- olutionize our information and communication technolo- gies. However, for two or more parties to execute even the simplest quantum transmission, they must establish, and maintain, a shared reference frame. This introduces a considerable overhead in communication resources, par- ticularly if the parties are in motion or rotating relative to each other. We experimentally demonstrate how to circumvent this problem with the efficient transmission of quantum information encoded in rotationally invariant states of single photons. By developing a complete toolbox for the efficient encoding and decoding of quantum infor- mation in such photonic qubits, we demonstrate the fea- sibility of alignment-free quantum key-distribution, and perform a proof-of-principle alignment-free entanglement distribut...

  7. Towards a Toolbox for a Process Innovation Laboratory

    DEFF Research Database (Denmark)

    2012-01-01

    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......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...... 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....

  8. Towards a Toolbox for a Process Innovation Laboratory

    DEFF Research Database (Denmark)

    2011-01-01

    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......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...... 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....

  9. Embedded target toolbox for DSP control applications of BLDC motor

    Directory of Open Access Journals (Sweden)

    Benk Enikö

    2009-10-01

    Full Text Available This paper presents a Matlab embedded target toolbox used for the DC brushless (BLDC motor applications. The synthesis, code generation, and the implementation of the control program, and also the control task itself are carried out on the host PC, under the Simulink. The target system is a brushless DC motor control kit – MSK243, connected on serial port COM to the host computer. With this real time library, it is possible to develop a Rapid Control Prototyping and Hardware-in-the-Loop Simulations. During the running control task on the target, the full functionality of Matlab/Simulink can be used for parameter’s visualization without interrupting or impeding the control process on the MSK240 board.

  10. Towards a Toolbox for a Process Innovation Laboratory

    DEFF Research Database (Denmark)

    Gong, Jie; Møller, Charles

    2012-01-01

    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...... 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...

  11. A fractured rock geophysical toolbox method selection tool

    Science.gov (United States)

    Day-Lewis, F. D.; Johnson, C.D.; Slater, L.D.; Robinson, J.L.; Williams, J.H.; Boyden, C.L.; Werkema, D.D.; Lane, J.W.

    2016-01-01

    Geophysical technologies have the potential to improve site characterization and monitoring in fractured rock, but the appropriate and effective application of geophysics at a particular site strongly depends on project goals (e.g., identifying discrete fractures) and site characteristics (e.g., lithology). No method works at every site or for every goal. New approaches are needed to identify a set of geophysical methods appropriate to specific project goals and site conditions while considering budget constraints. To this end, we present the Excel-based Fractured-Rock Geophysical Toolbox Method Selection Tool (FRGT-MST). We envision the FRGT-MST (1) equipping remediation professionals with a tool to understand what is likely to be realistic and cost-effective when contracting geophysical services, and (2) reducing applications of geophysics with unrealistic objectives or where methods are likely to fail.

  12. TRIQS: A toolbox for research on interacting quantum systems

    Science.gov (United States)

    Parcollet, Olivier; Ferrero, Michel; Ayral, Thomas; Hafermann, Hartmut; Krivenko, Igor; Messio, Laura; Seth, Priyanka

    2015-11-01

    We present the TRIQS library, a Toolbox for Research on Interacting Quantum Systems. It is an open-source, computational physics library providing a framework for the quick development of applications in the field of many-body quantum physics, and in particular, strongly-correlated electronic systems. It supplies components to develop codes in a modern, concise and efficient way: e.g. Green's function containers, a generic Monte Carlo class, and simple interfaces to HDF5. TRIQS is a C++/Python library that can be used from either language. It is distributed under the GNU General Public License (GPLv3). State-of-the-art applications based on the library, such as modern quantum many-body solvers and interfaces between density-functional-theory codes and dynamical mean-field theory (DMFT) codes are distributed along with it.

  13. Advanced photoacoustic image reconstruction using the k-Wave toolbox

    Science.gov (United States)

    Treeby, B. E.; Jaros, J.; Cox, B. T.

    2016-03-01

    Reconstructing images from measured time domain signals is an essential step in tomography-mode photoacoustic imaging. However, in practice, there are many complicating factors that make it difficult to obtain high-resolution images. These include incomplete or undersampled data, filtering effects, acoustic and optical attenuation, and uncertainties in the material parameters. Here, the processing and image reconstruction steps routinely used by the Photoacoustic Imaging Group at University College London are discussed. These include correction for acoustic and optical attenuation, spatial resampling, material parameter selection, image reconstruction, and log compression. The effect of each of these steps is demonstrated using a representative in vivo dataset. All of the algorithms discussed form part of the open-source k-Wave toolbox (available from http://www.k-wave.org).

  14. MOTO: a Matlab object-oriented programming toolbox for optics

    Science.gov (United States)

    Anterrieu, Eric; Pérez, José-Philippe

    2007-06-01

    The ray optics is the branch of optics in which all the wave effects are neglected: the light is considered as travelling along rays which can only change their direction by refraction or reflection. On one hand, a further simplifying approximation can be made if attention is restricted to rays travelling close to the optical axis and at small angles: the well-known linear or paraxial approximation introduced by Gauss. On the other hand, in order to take into account the geometrical aberrations, it is sometimes necessary to pay attention to marginal rays with the aid of a ray tracing procedure. This contribution describes a toolbox for the study of optical systems which implements both approaches. It has been developed in the framework of an educational project, but it is general enough to be useful in most of the cases.

  15. Research on prediction for coal and gas outburst based on Matlab neural network toolbox and its application

    Institute of Scientific and Technical Information of China (English)

    XIAO Hong-fei; XU Zhi-sheng; TIAN Yun-li

    2007-01-01

    In order to predict the danger of coal and gas outburst in mine coal layer correctly,on the basis of the VLBP and LMBP algorithm in Matlab neural network toolbox.one kind of modified BP neural network was put forth to speed up the network convergence speed in this paper.Firstly,according to the characteristics of coal and gas outburst.five key influencing factors such as excavation depth,pressure of gas,and geologic destroy degree were selected as the judging indexes of coal and gas outburst.Secondly,the prediction model for coal and gas outburst was built.Finally,it was verified by practical examples.Practical application demonstrates that,on the one hand,the modified BP prediction model based on the Matlab neural network toolbox can overcome the disadvantages of constringency and,on the other hand,it has fast convergence speed and good prediction accuracy.The analysis and computing results show that the computing speed by LMBP algorithm is faster than by VLBP algonthm but needs more memory.And the resuits show that the prediction results are identical with actual results and this model is a very efficient prediction method for mine coal and gas outburst,and has an important practical meaning for the mine production safety.So we conclude that it can be used to predict coal and gas outburst precisely in actual engineering.

  16. Developing a Conceptual Design Engineering Toolbox and its Tools

    Directory of Open Access Journals (Sweden)

    R. W. Vroom

    2004-01-01

    Full Text Available In order to develop a successful product, a design engineer needs to pay attention to all relevant aspects of that product. Many tools are available, software, books, websites, and commercial services. To unlock these potentially useful sources of knowledge, we are developing C-DET, a toolbox for conceptual design engineering. The idea of C-DET is that designers are supported by a system that provides them with a knowledge portal on one hand, and a system to store their current work on the other. The knowledge portal is to help the designer to find the most appropriate sites, experts, tools etc. at a short notice. Such a toolbox offers opportunities to incorporate extra functionalities to support the design engineering work. One of these functionalities could be to help the designer to reach a balanced comprehension in his work. Furthermore C-DET enables researchers in the area of design engineering and design engineers themselves to find each other or their work earlier and more easily. Newly developed design tools that can be used by design engineers but have not yet been developed up to a commercial level could be linked to by C-DET. In this way these tools can be evaluated in an early stage by design engineers who would like to use them. This paper describes the first prototypes of C-DET, an example of the development of a design tool that enables designers to forecast the use process and an example of the future functionalities of C-DET such as balanced comprehension.

  17. 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

  18. 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.

  19. 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/.

  20. 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.

  1. 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.

  2. Production de minitubercules de pomme de terre par hydroponie: évaluation d'un système combinant les techniques NFT et Gravel Culture pour deux types de solutions nutritives

    Directory of Open Access Journals (Sweden)

    Rolot J.L.

    2002-01-01

    Full Text Available Potato minituber production through hydropony: assessment of a system combining the NFT and Gravel Culture techniques for two types of nutrient solutions. The potato minituber production is the classical intermediate stage enabling field use of potato materials with an in vitro origin. This production of minitubers may be achieved through various techniques. Most often however they are based upon bedding vitroplantlets or vitroplantlets cuttings in an organic substratum which is disinfected or not. The soilless culture of plants stemming from vitrotubers to produce minitubers with a superior health quality was tested within a hydroponic system. Two types of nutrient solutions were compared: a nitrogen rich one (NPK, mg/l, 180-40-300 and a phosphorus rich one (NPK, mg/l, 60-150-300. In order to initiate the cultures, presprouting microtubers of several varieties (Bintje, Kennebec, Spunta, Saturna, Desiree and Gasore were used. Multiplication rates ranged between 13.2 (Saturna and 3.8 (Kennebec minitubers with a grade higher than 10 mm (more than 1.5 g. As the selected density of the plants was 59 plants per square metre, the yield per square metre varied from 224 to 779 minitubers with a grade higher than 10 mm. The obtained number of minitubers depended especially on the variety. The phosphorus enrichment of the nutrient solution induced an increased number of minitubers produced with a grade higher than 15 mm (more than 5 g. The health state of the produced tubers was excellent.

  3. TEMPERATURA DO AR NO INTERIOR DO CANAL DE CULTIVO E CRESCIMENTO DA ALFACE EM FUNÇÃO DO MATERIAL DE COBERTURA DA MESA DE CULTIVO HIDROPÔNICO - NFT

    Directory of Open Access Journals (Sweden)

    MATTOS KAREN MARIA DA COSTA

    2001-01-01

    Full Text Available Estudou-se o efeito de diferentes tipos de material de cobertura de mesas de cultivo hidropônico-NFT na temperatura do interior das canaletas e no crescimento da alface (Lactuca sativa L., cv. Verônica. Em comparação ao tratamento-controle (tubos de polipropileno, utilizaram-se mantas de polietileno dupla face (branco e preto e de Tetra-Pak®. O experimento foi realizado no Núcleo Experimental de Campinas, do Instituto Agronômico (22°54'S, 47°05'W, 674 m de altitude, usando-se mesas de cultivo com 24 m de comprimento, dividida em quatro blocos simétricos com os tratamentos distribuídos ao acaso. Sessenta termopares foram instalados no interior dos tubos para avaliar a temperatura interna do ar; armazenaram-se os sinais em um datalogger. Os valores medidos no interior dos tubos foram sempre superiores aos externos. Entretanto, nos tubos protegidos com Tetra-Pak®, os dados da temperatura interna do ar foram sempre de menor magnitude e, os de massa fresca de plantas de alface, superiores aos demais tratamentos. Essas diferenças foram estatisticamente significativas pelo teste de Tukey ao nível de 5%. No período noturno, nenhuma diferença de comportamento foi obtida entre os três tratamentos usados.

  4. Object oriented design provides flexible framework for electrophysiolgy software toolbox - biomed 2010.

    Science.gov (United States)

    Gruner, Charlotte M

    2010-01-01

    This work describes a software platform to support an expandible toolbox for electrophysiology data analysis. The current focus of the toolbox, known as NeuroMAX is spike-sorting and spike-time analysis tools. A key feature of the toolbox is the ability for a user to connect tools into a workspace toolchain in a flexible, intelligent feed-forward manner that allows a tool to use any previously computed data set as input. Tool parameters can be saved and applied to other data sets. Tools and workspaces can be accessed to process data either directly from the MATLAB command line or from the NeuroMAX GUI. This work discusses the object-oriented design of the toolbox, including the data classes, workspace classes, and tool classes created to achieve this functionality.

  5. 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.

  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 CRISPR-Based Toolbox for Studying T Cell Signal Transduction

    Science.gov (United States)

    Chi, Shen; Weiss, Arthur; Wang, Haopeng

    2016-01-01

    CRISPR/Cas9 system is a powerful technology to perform genome editing in a variety of cell types. To facilitate the application of Cas9 in mapping T cell signaling pathways, we generated a toolbox for large-scale genetic screens in human Jurkat T cells. The toolbox has three different Jurkat cell lines expressing distinct Cas9 variants, including wild-type Cas9, dCas9-KRAB, and sunCas9. We demonstrated that the toolbox allows us to rapidly disrupt endogenous gene expression at the DNA level and to efficiently repress or activate gene expression at the transcriptional level. The toolbox, in combination with multiple currently existing genome-wide sgRNA libraries, will be useful to systematically investigate T cell signal transduction using both loss-of-function and gain-of-function genetic screens. PMID:27057542

  8. Planetary Geologic Mapping Python Toolbox: A Suite of Tools to Support Mapping Workflows

    Science.gov (United States)

    Hunter, M. A.; Skinner, J. A.; Hare, T. M.; Fortezzo, C. M.

    2017-06-01

    The collective focus of the Planetary Geologic Mapping Python Toolbox is to provide researchers with additional means to migrate legacy GIS data, assess the quality of data and analysis results, and simplify common mapping tasks.

  9. A CRISPR-Based Toolbox for Studying T Cell Signal Transduction

    Directory of Open Access Journals (Sweden)

    Shen Chi

    2016-01-01

    Full Text Available CRISPR/Cas9 system is a powerful technology to perform genome editing in a variety of cell types. To facilitate the application of Cas9 in mapping T cell signaling pathways, we generated a toolbox for large-scale genetic screens in human Jurkat T cells. The toolbox has three different Jurkat cell lines expressing distinct Cas9 variants, including wild-type Cas9, dCas9-KRAB, and sunCas9. We demonstrated that the toolbox allows us to rapidly disrupt endogenous gene expression at the DNA level and to efficiently repress or activate gene expression at the transcriptional level. The toolbox, in combination with multiple currently existing genome-wide sgRNA libraries, will be useful to systematically investigate T cell signal transduction using both loss-of-function and gain-of-function genetic screens.

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

    Directory of Open Access Journals (Sweden)

    H. Ihshaish

    2015-01-01

    Full Text Available 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 O (106 and of edges (up to at least O (1012. The key innovation is an efficient set of parallel software tools designed to leverage the inherited hybrid parallelism in distributed-memory clusters of multi-core machines. The performance of the toolbox is illustrated through networks derived from sea surface height (SSH data of a global high-resolution ocean model. Less than 8 min are needed on 90 Intel Xeon E5-4650 processors to construct a climate network including the preprocessing and the correlation of 3 × 105 SSH time series, resulting in a weighted graph with the same number of vertices and about 3 × 106 edges. In less than 5 min on 30 processors, the resulted graph's degree centrality, strength, connected components, eigenvector centrality, entropy and clustering coefficient metrics were obtained. These results indicate that a complete cycle to construct and analyze a large-scale climate network is available under 13 min. Par@Graph therefore facilitates the application of climate network analysis on high-resolution observations and model results, by enabling fast network construction from the calculation of statistical similarities between climate time series. It also enables network analysis at unprecedented scales on a variety of different sizes of input data sets.

  11. CERENA: ChEmical REaction Network Analyzer--A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics.

    Science.gov (United States)

    Kazeroonian, Atefeh; Fröhlich, Fabian; Raue, Andreas; Theis, Fabian J; Hasenauer, Jan

    2016-01-01

    Gene expression, signal transduction and many other cellular processes are subject to stochastic fluctuations. The analysis of these stochastic chemical kinetics is important for understanding cell-to-cell variability and its functional implications, but it is also challenging. A multitude of exact and approximate descriptions of stochastic chemical kinetics have been developed, however, tools to automatically generate the descriptions and compare their accuracy and computational efficiency are missing. In this manuscript we introduced CERENA, a toolbox for the analysis of stochastic chemical kinetics using Approximations of the Chemical Master Equation solution statistics. CERENA implements stochastic simulation algorithms and the finite state projection for microscopic descriptions of processes, the system size expansion and moment equations for meso- and macroscopic descriptions, as well as the novel conditional moment equations for a hybrid description. This unique collection of descriptions in a single toolbox facilitates the selection of appropriate modeling approaches. Unlike other software packages, the implementation of CERENA is completely general and allows, e.g., for time-dependent propensities and non-mass action kinetics. By providing SBML import, symbolic model generation and simulation using MEX-files, CERENA is user-friendly and computationally efficient. The availability of forward and adjoint sensitivity analyses allows for further studies such as parameter estimation and uncertainty analysis. The MATLAB code implementing CERENA is freely available from http://cerenadevelopers.github.io/CERENA/.

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

    Directory of Open Access Journals (Sweden)

    Thaleia Konstantinou

    2014-07-01

    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 facilitates

  13. 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...

  14. 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

  15. An adaptive toolbox approach to the route to expertise in sport.

    Science.gov (United States)

    de Oliveira, Rita F; Lobinger, Babett H; Raab, Markus

    2014-01-01

    Expertise is characterized by fast decision-making which is highly adaptive to new situations. Here we propose that athletes use a toolbox of heuristics which they develop on their route to expertise. The development of heuristics occurs within the context of the athletes' natural abilities, past experiences, developed skills, and situational context, but does not pertain to any of these factors separately. This is a novel approach because it integrates separate factors into a comprehensive heuristic description. The novelty of this approach lies within the integration of separate factors determining expertise into a comprehensive heuristic description. It is our contention that talent identification methods and talent development models should therefore be geared toward the assessment and development of specific heuristics. Specifically, in addition to identifying and developing separate natural abilities and skills as per usual, heuristics should be identified and developed. The application of heuristics to talent and expertise models can bring the field one step away from dichotomized models of nature and nurture toward a comprehensive approach to the route to expertise.

  16. An adaptive toolbox approach to the route to expertise in sport

    Directory of Open Access Journals (Sweden)

    Rita F De Oliveira

    2014-07-01

    Full Text Available Expertise is characterized by fast decision-making which is highly adaptive to new situations. Here we propose that athletes use a toolbox of heuristics which they develop on their route to expertise. The development of heuristics occurs within the context of the athletes’ natural abilities, past experiences, developed skills, and situational context, but does not pertain to any of these factors separately. This is a novel approach because it integrates separate factors into a comprehensive heuristic description. The novelty of this approach lies within the integration of separate factors determining expertise into a comprehensive heuristic description. It is our contention that talent identification methods and talent development models should therefore be geared towards the assessment and development of specific heuristics. Specifically, in addition to identifying and developing separate natural abilities and skills as per usual, heuristics should be identified and developed. The application of heuristics to talent and expertise models can bring the field one step away from dichotomized models of nature and nurture towards a comprehensive approach to the route to expertise.

  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. Optics Toolbox: An Intelligent Relational Database System For Optical Designers

    Science.gov (United States)

    Weller, Scott W.; Hopkins, Robert E.

    1986-12-01

    Optical designers were among the first to use the computer as an engineering tool. Powerful programs have been written to do ray-trace analysis, third-order layout, and optimization. However, newer computing techniques such as database management and expert systems have not been adopted by the optical design community. For the purpose of this discussion we will define a relational database system as a database which allows the user to specify his requirements using logical relations. For example, to search for all lenses in a lens database with a F/number less than two, and a half field of view near 28 degrees, you might enter the following: FNO English-like language, and which are easily modified by the user. An example rule is: IF require microscope objective in air and require NA > 0.9 THEN suggest the use of an oil immersion objective The heart of the expert system is the rule interpreter, sometimes called an inference engine, which reads the rules and forms conclusions based on them. The use of a relational database system containing lens prototypes seems to be a viable prospect. However, it is not clear that expert systems have a place in optical design. In domains such as medical diagnosis and petrology, expert systems are flourishing. These domains are quite different from optical design, however, because optical design is a creative process, and the rules are difficult to write down. We do think that an expert system is feasible in the area of first order layout, which is sufficiently diagnostic in nature to permit useful rules to be written. This first-order expert would emulate an expert designer as he interacted with a customer for the first time: asking the right questions, forming conclusions, and making suggestions. With these objectives in mind, we have developed the Optics Toolbox. Optics Toolbox is actually two programs in one: it is a powerful relational database system with twenty-one search parameters, four search modes, and multi

  19. 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.

  20. Scientific Opinion on the development of a risk ranking toolbox for the EFSA BIOHAZ Panel

    Directory of Open Access Journals (Sweden)

    EFSA Panel on Biological Hazards (BIOHAZ

    2015-01-01

    Full Text Available Eight tools relevant to risk ranking of biological hazards in food were identified and assessed using two case studies. Differences in their performance were observed, related to the risk metrics, data requirements, ranking approach, model type, model variables and data integration. Quantitative stochastic models are the most reliable for risk ranking. However, this approach needs good characterisation of input parameters. The use of deterministic models that ignore variability may result in risk ranking errors. The ordinal scoring approaches in semi-quantitative models provide ranking with more errors than the deterministic approaches. FDA (Food and Drug Administration-iRISK was identified as the most appropriate tool for risk ranking of microbiological hazards. The Burden of Communicable Diseases in Europe (BCoDE toolkit can be used in combination with the outputs from FDA-iRISK or as a top-down tool to rank pathogens. Uncertainty needs to be addressed and communicated to decision makers and stakeholders as one of the outcomes of the risk ranking process. Uncertainty and variability can be represented by means of probability distributions. Techniques such as the NUSAP (numeral, unit, spread, assessment and pedigree approach can also be used to prioritise factors for sensitivity and scenario analysis or stochastic modelling. Quantitative risk ranking models are preferred over semi-quantitative models. When data and time constraints do not allow quantitative risk ranking, semi-quantitative models could be used, but the limitations of these approaches linked to the selection and integration of the ordinal scores should be made explicit. Decision trees should be used only to show how decisions are made about classifying food–pathogen combinations into broad categories. BCoDE and FDA-iRISK, in combination with a network of available predictive microbiology tools, databases and information sources, can form a risk ranking toolbox and be applied

  1. A broadband toolbox for scanning microwave microscopy transmission measurements

    Science.gov (United States)

    Lucibello, Andrea; Sardi, Giovanni Maria; Capoccia, Giovanni; Proietti, Emanuela; Marcelli, Romolo; Kasper, Manuel; Gramse, Georg; Kienberger, Ferry

    2016-05-01

    In this paper, we present in detail the design, both electromagnetic and mechanical, the fabrication, and the test of the first prototype of a Scanning Microwave Microscope (SMM) suitable for a two-port transmission measurement, recording, and processing the high frequency transmission scattering parameter S21 passing through the investigated sample. The S21 toolbox is composed by a microwave emitter, placed below the sample, which excites an electromagnetic wave passing through the sample under test, and is collected by the cantilever used as the detector, electrically matched for high frequency measurements. This prototype enhances the actual capability of the instrument for a sub-surface imaging at the nanoscale. Moreover, it allows the study of the electromagnetic properties of the material under test obtained through the measurement of the reflection (S11) and transmission (S21) parameters at the same time. The SMM operates between 1 GHz and 20 GHz, current limit for the microwave matching of the cantilever, and the high frequency signal is recorded by means of a two-port Vector Network Analyzer, using both contact and no-contact modes of operation, the latter, especially minded for a fully nondestructive and topography-free characterization. This tool is an upgrade of the already established setup for the reflection mode S11 measurement. Actually, the proposed setup is able to give richer information in terms of scattering parameters, including amplitude and phase measurements, by means of the two-port arrangement.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. An expression tag toolbox for microbial production of membrane bound plant cytochromes P450.

    Science.gov (United States)

    Vazquez-Albacete, Dario; Cavaleiro, Ana Mafalda; Christensen, Ulla; Seppälä, Susanna; Møller, Birger Lindberg; Nørholm, Morten H H

    2017-04-01

    Membrane-associated Cytochromes P450 (P450s) are one of the most important enzyme families for biosynthesis of plant-derived medicinal compounds. However, the hydrophobic nature of P450s makes their use in robust cell factories a challenge. Here, we explore a small library of N-terminal expression 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 homogeneous populations for some of the conditions. Three chimeric designs were chosen for a more complex combinatorial assembly of a multigene pathway consisting of two P450s and a redox partner. Cells expressing these recombinant enzymes catalyzed the conversion of the substrate to highly different ratios of the intermediate and the final product of the pathway. Finally, the effect of a robustly performing expression tag was explored with a library of 49 different P450s from medicinal plants and nearly half of these were improved in expression by more than twofold. The developed toolbox serves as a platform to tune P450 performance in microbial cells, thereby facilitating recombinant production of complex plant P450-derived biochemicals. Biotechnol. Bioeng. 2017;114: 751-760. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  7. 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.

  8. 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.

  9. PRECESSION: Python toolbox for dynamics of spinning black-hole binaries

    Science.gov (United States)

    Gerosa, Davide; Kesden, Michael

    2016-11-01

    PRECESSION is a comprehensive toolbox for exploring the dynamics of precessing black-hole binaries in the post-Newtonian regime. It allows study of the evolution of the black-hole spins along their precession cycles, performs gravitational-wave-driven binary inspirals using both orbit-averaged and precession-averaged integrations, and predicts the properties of the merger remnant through fitting formulas obtained from numerical-relativity simulations. PRECESSION can add the black-hole spin dynamics to larger-scale numerical studies such as gravitational-wave parameter estimation codes, population synthesis models to predict gravitational-wave event rates, galaxy merger trees and cosmological simulations of structure formation, and provides fast and reliable integration methods to propagate statistical samples of black-hole binaries from/to large separations where they form to/from small separations where they become detectable, thus linking gravitational-wave observations of spinning black-hole binaries to their astrophysical formation history. The code is also useful for computing initial parameters for numerical-relativity simulations targeting specific precessing systems.

  10. 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.

  11. 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. PMID:27065841

  12. ObsPy: A Python Toolbox for Seismology

    Science.gov (United States)

    Wassermann, J. M.; Krischer, L.; Megies, T.; Barsch, R.; Beyreuther, M.

    2013-12-01

    Python combines the power of a full-blown programming language with the flexibility and accessibility 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. ObsPy is a community-driven, open-source project extending Python's capabilities to fit the specific needs that arise when working with seismological data. It a) comes with a continuously growing signal processing toolbox that covers most tasks common in seismological analysis, b) provides read and write support for many common waveform, station and event metadata formats and c) enables access to various data centers, webservices and databases to retrieve waveform data and station/event metadata. In combination with mature and free Python packages like NumPy, SciPy, Matplotlib, IPython, Pandas, lxml, and PyQt, ObsPy makes it possible to develop complete workflows in Python, ranging from reading locally stored data or requesting data from one or more different data centers via signal analysis and data processing to visualization in GUI and web applications, output of modified/derived data and the creation of publication-quality figures. All functionality is extensively documented and the ObsPy Tutorial and Gallery give a good impression of the wide range of possible use cases. ObsPy is tested and running on Linux, OS X and Windows and comes with installation routines for these systems. ObsPy is developed in a test-driven approach and is available under the LGPLv3 open source licence. Users are welcome to request help, report bugs, propose enhancements or contribute code via either the user mailing list or the project page on GitHub.

  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......: 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...

  14. The FermiFab Toolbox for Fermionic Many-Particle Quantum Systems

    CERN Document Server

    Mendl, Christian B

    2011-01-01

    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.

  15. VIII. NIH Toolbox Cognition Battery (CB): composite scores of crystallized, fluid, and overall cognition.

    Science.gov (United States)

    Akshoomoff, Natacha; Beaumont, Jennifer L; Bauer, Patricia J; Dikmen, Sureyya S; Gershon, Richard C; Mungas, Dan; Slotkin, Jerry; Tulsky, David; Weintraub, Sandra; Zelazo, Philip David; Heaton, Robert K

    2013-08-01

    The NIH Toolbox Cognition Battery (CB) includes 7 tests covering 6 cognitive abilities. This chapter describes the psychometric characteristics in children ages 3-15 years of a total summary score and composite scores reflecting two major types of cognition: "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 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.

  16. 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

  17. Acrylamide mitigation strategies: critical appraisal of the FoodDrinkEurope toolbox.

    Science.gov (United States)

    Palermo, M; Gökmen, V; De Meulenaer, B; Ciesarová, Z; Zhang, Y; Pedreschi, F; Fogliano, V

    2016-06-15

    FoodDrinkEurope Federation recently released the latest version of the Acrylamide Toolbox to support manufacturers in acrylamide reduction activities giving indication about the possible mitigation strategies. The Toolbox is intended for small and medium size enterprises with limited R&D resources, however no comments about the pro and cons of the different measures were provided to advise the potential users. Experts of the field are aware that not all the strategies proposed have equal value in terms of efficacy and cost/benefit ratio. This consideration prompted us to provide a qualitative science-based ranking of the mitigation strategies proposed in the acrylamide Toolbox, focusing on bakery and fried potato products. Five authors from different geographical areas having a publication record on acrylamide mitigation strategies worked independently ranking the efficacy of the acrylamide mitigation strategies taking into account three key parameters: (i) reduction rate; (ii) side effects; and (iii) applicability and economic impact. On the basis of their own experience and considering selected literature of the last ten years, the authors scored for each key parameter the acrylamide mitigation strategies proposed in the Toolbox. As expected, all strategies selected in the Toolbox turned out to be useful, however, not at the same level. The use of enzyme asparaginase and the selection of low sugar varieties were considered the best mitigation strategies in bakery and in potato products, respectively. According to authors' opinion most of the other mitigation strategies, although effective, either have relevant side effects on the sensory profile of the products, or they are not easy to implement in industrial production. The final outcome was a science based commented ranking which can enrich the acrylamide Toolbox supporting individual manufacturer in taking the best actions to reduce the acrylamide content in their specific production context.

  18. 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. PMID:28275348

  19. 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.

  20. Analysis of Static Synchronous Series Compensators (SSSC, on Congestion Management and Voltage Profile in Power System by PSAT Toolbox

    Directory of Open Access Journals (Sweden)

    Hossein Nasir Aghdam

    2011-07-01

    Full Text Available The maintenance and availability of the power system can be considerd a major aspect of investigation. The encouragement to the planning of HV lines, the valuet of power that transfer per km on HV line and the amount of power transaction as seen from economic side is much responsible for concern towards congestion phenomena in power system. The idea for solving this problem is the use of FACTS devices especially the use of Synchronous Series Compensators (SSSC. In this paper the study of SSSC with its various modes of operation is investigated. Finally by help of modeling of a power system in MATLAB/PSAT toolbox, and by installing SSSC in transmission link, its use as power flow controller and voltage injection is seen. Conclusion is made on different results to see the benefit of SSSC in power system.

  1. MuTE: a MATLAB toolbox to compare established and novel estimators of the multivariate transfer entropy.

    Science.gov (United States)

    Montalto, Alessandro; Faes, Luca; Marinazzo, Daniele

    2014-01-01

    A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different approaches to evaluate transfer entropy, some of them already proposed, some novel, and present their implementation in a freeware MATLAB toolbox. Applications to simulated and real data are presented.

  2. MuTE: a MATLAB toolbox to compare established and novel estimators of the multivariate transfer entropy.

    Directory of Open Access Journals (Sweden)

    Alessandro Montalto

    Full Text Available A challenge for physiologists and neuroscientists is to map information transfer between components of the systems that they study at different scales, in order to derive important knowledge on structure and function from the analysis of the recorded dynamics. The components of physiological networks often interact in a nonlinear way and through mechanisms which are in general not completely known. It is then safer that the method of choice for analyzing these interactions does not rely on any model or assumption on the nature of the data and their interactions. Transfer entropy has emerged as a powerful tool to quantify directed dynamical interactions. In this paper we compare different approaches to evaluate transfer entropy, some of them already proposed, some novel, and present their implementation in a freeware MATLAB toolbox. Applications to simulated and real data are presented.

  3. Phytophthora speelt verstoppertje bij NFT aardbei

    NARCIS (Netherlands)

    Evenhuis, B.; Verhoeven, J.T.W.

    2011-01-01

    Aardbeitelers worden 'blij' gemaakt met Phytophthora cactorum in hun gewas, terwijl ze daar niet op zitten te wachten. Onderzoekers worden teleurgesteld omdat infectie uitblijft terwijl ze er alles aan doen om aantasting te krijgen. Dat hindert ze bij het uitvinden wat het ontsmettingseffect is van

  4. 在 ArcToolbox 中实现用户自定义工具%Implementation of User Defined Tools in ArcToolbox

    Institute of Scientific and Technical Information of China (English)

    徐国庆; 顾钰培; 赵明瑜

    2014-01-01

    简要介绍了ArcToolbox的相关概念以及在ArcToolbox中开发实现用户自定义工具的方法与技巧;并以一个常见的应用场景为例,使用Python脚本语言在ArcToolbox中实现了一个用户自定义工具;最后经实践验证,在ArcToolbox中开发实现用户自定义工具的方法能显著提高测绘生产中地理信息数据处理的效率。%This paper briefly describes the concept of ArcToolbox and the methods and tips of Implementation of User Defined Tools in ArcToolbox , and then using a common user case as an example , developing a user defined tool in ArcToolbox .As practice shows , u-sing user defined tools can notably enhance efficiency of geospatial data processing in survey and mapping .

  5. 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

  6. SIPPI: A Matlab toolbox for sampling the solution to inverse problems with complex prior information. Part 2—Application to crosshole GPR tomography

    Science.gov (United States)

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

    2013-03-01

    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 on the high frequency approximation of the wave-equation and 'fat' ray based forward models relying on finite frequency theory. In order to sample the a posteriori probability density function we make use of both least squares based inversion, for linear Gaussian inverse problems, and the extended Metropolis sampler, for non-linear non-Gaussian inverse problems. To illustrate the applicability of the SIPPI toolbox to a tomographic field data set we use a cross-borehole traveltime data set from Arrenæs, Denmark. Both the computer code and the data are released in the public domain using open source and open data licenses. The code has been developed to facilitate inversion of 2D and 3D travel time tomographic data using a wide range of possible a priori models and choices of forward models.

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

    OpenAIRE

    David M. Zalk; Ton Spee; Matt Gillen; Lentz, Thomas J.; Andrew Garrod; Paul Evans; Paul Swuste

    2011-01-01

    Objectives: This paper presents the framework and protocol design for a construction industry risk management toolbox. The construction industry needs a comprehensive, systematic approach to assess and control occupational risks. These risks span several professional health and safety disciplines, emphasized by multiple international occupational research agenda projects including: falls, electrocution, noise, silica, welding fumes, and musculoskeletal disorders. Yet, the International Social...

  8. 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…

  9. 40 CFR 141.715 - Microbial toolbox options for meeting Cryptosporidium treatment requirements.

    Science.gov (United States)

    2010-07-01

    ... Protection and Management Toolbox Options (1) Watershed control program 0.5-log credit for State-approved.../intake management No prescribed credit. Systems may conduct simultaneous monitoring for treatment bin... criteria are in § 141.717(b). (5) Bank filtration 0.5-log credit for 25-foot setback; 1.0-log credit for...

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

    NARCIS (Netherlands)

    Broek, M. van den; Brederode, E.; Ramírez, A.; Kramers, L.; Kuip, M. van der; Wildenborg, T.; Faaij, A.; Turkenburg, W.

    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 geogra

  11. 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, implemen

  12. A flow cytometer-based whole cell screening toolbox for directed hydrolase evolution through fluorescent hydrogels.

    Science.gov (United States)

    Lülsdorf, Nina; Pitzler, Christian; Biggel, Michael; Martinez, Ronny; Vojcic, Ljubica; Schwaneberg, Ulrich

    2015-05-21

    A high throughput whole cell flow cytometer screening toolbox was developed and validated by identifying improved variants (1.3-7-fold) for three hydrolases (esterase, lipase, cellulase). The screening principle is based on coupled enzymatic reaction using glucose derivatives which yield upon hydrolysis a fluorescent-hydrogel-layer on the surface of E. coli cells.

  13. The triticeae toolbox: combining phenotype and genotype data to advance small-grains breeding

    Science.gov (United States)

    The Triticeae Toolbox (http://triticeaetoolbox.org; 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 speci...

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

    OpenAIRE

    Zalk, David M.; Spee, Ton; Gillen, Matt; Lentz, Thomas J.; Garrod, Andrew; Evans, Paul; Swuste, Paul

    2011-01-01

    Objectives This paper presents the framework and protocol design for a construction industry risk management toolbox. The construction industry needs a comprehensive, systematic approach to assess and control occupational risks. These risks span several professional health and safety disciplines, emphasized by multiple international occupational research agenda projects including: falls, electrocution, noise, silica, welding fumes, and musculoskeletal disorders. Yet, the International Social ...

  15. 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

  16. A toolbox to visually explore cerebellar shape changes in cerebellar disease and dysfunction

    Science.gov (United States)

    Abulnaga, S. Mazdak; Yang, Zhen; Carass, Aaron; Kansal, Kalyani; Jedynak, Bruno M.; Onyike, Chiadi U.; Ying, Sarah H.; Prince, Jerry L.

    2016-03-01

    The cerebellum plays an important role in motor control and is also involved in cognitive processes. Cerebellar function is specialized by location, although the exact topographic functional relationship is not fully understood. The spinocerebellar ataxias are a group of neurodegenerative diseases that cause regional atrophy in the cerebellum, yielding distinct motor and cognitive problems. The ability to study the region-specific atrophy patterns can provide insight into the problem of relating cerebellar function to location. In an effort to study these structural change patterns, we developed a toolbox in MATLAB to provide researchers a unique way to visually explore the correlation between cerebellar lobule shape changes and function loss, with a rich set of visualization and analysis modules. In this paper, we outline the functions and highlight the utility of the toolbox. The toolbox takes as input landmark shape representations of subjects' cerebellar substructures. A principal component analysis is used for dimension reduction. Following this, a linear discriminant analysis and a regression analysis can be performed to find the discriminant direction associated with a specific disease type, or the regression line of a specific functional measure can be generated. The characteristic structural change pattern of a disease type or of a functional score is visualized by sampling points on the discriminant or regression line. The sampled points are used to reconstruct synthetic cerebellar lobule shapes. We showed a few case studies highlighting the utility of the toolbox and we compare the analysis results with the literature.

  17. An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.

    Directory of Open Access Journals (Sweden)

    Sebastián A Romano

    2017-06-01

    Full Text Available The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.

  18. An integrated calcium imaging processing toolbox for the analysis of neuronal population dynamics.

    Science.gov (United States)

    Romano, Sebastián A; Pérez-Schuster, Verónica; Jouary, Adrien; Boulanger-Weill, Jonathan; Candeo, Alessia; Pietri, Thomas; Sumbre, Germán

    2017-06-01

    The development of new imaging and optogenetics techniques to study the dynamics of large neuronal circuits is generating datasets of unprecedented volume and complexity, demanding the development of appropriate analysis tools. We present a comprehensive computational workflow for the analysis of neuronal population calcium dynamics. The toolbox includes newly developed algorithms and interactive tools for image pre-processing and segmentation, estimation of significant single-neuron single-trial signals, mapping event-related neuronal responses, detection of activity-correlated neuronal clusters, exploration of population dynamics, and analysis of clusters' features against surrogate control datasets. The modules are integrated in a modular and versatile processing pipeline, adaptable to different needs. The clustering module is capable of detecting flexible, dynamically activated neuronal assemblies, consistent with the distributed population coding of the brain. We demonstrate the suitability of the toolbox for a variety of calcium imaging datasets. The toolbox open-source code, a step-by-step tutorial and a case study dataset are available at https://github.com/zebrain-lab/Toolbox-Romano-et-al.

  19. 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).

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

    NARCIS (Netherlands)

    Korver, H.P.

    1996-01-01

    In 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 ToolBus whic

  1. GPstuff: Bayesian Modeling with Gaussian Processes

    NARCIS (Netherlands)

    Vanhatalo, J.; Riihimaki, J.; Hartikainen, J.; Jylänki, P.P.; Tolvanen, V.; Vehtari, A.

    2013-01-01

    The GPstuff toolbox is a versatile collection of Gaussian process models and computational tools required for Bayesian inference. The tools include, among others, various inference methods, sparse approximations and model assessment methods.

  2. A generic open-source toolbox to help long term irrigation monitoring for integrated water management in semi-arid Mediterranean areas.

    Science.gov (United States)

    Le Page, Michel; Gosset, Cindy; Oueslati, Ines; Calvez, Roger; Zribi, Mehrez; Lili Chabaane, Zohra

    2016-04-01

    In semi arid areas, irrigated plains are often the major consumer of water well beyond other water demands. Traditionally fed by surface water, irrigation has massively shifted to a more reliable resource: groundwater. This shift occurred in the late thirty years has also provoked an extension and intensification of irrigation, often translated into impressive groundwater table decreases. Integrated water management needs a systematic and robust way to estimate the water demands by the agricultural sector. We propose a generic toolbox based on the FAO-56 method and the Crop Coefficient/NDVI approach used in Remote Sensing. The toolbox can be separated in three main areas: 1) It facilitates the preparation of different input datasets: download, domain extraction, homogenization of formats, or spatial interpolation. 2) A collection of algorithms based on the analysis of NDVI time series is proposed: Separation of irrigated vs non-irrigated area, a simplified annual land cover classification, Crop Coefficient, Fraction Cover and Efficient Rainfall. 3) Synthesis against points or areas produces the output data at the desired spatial and temporal resolution for Integrated Water Modeling or data analysis and comparison. The toolbox has been used in order to build a WEAP21 model of the Merguellil basin in Tunisia for the period of 2000-2014. Different meteorological forcings were easily used and compared: WFDEI, AGRI4CAST, MED-CORDEX. A local rain gauges database was used to produce a daily rainfall gridded dataset. MODIS MOD13Q1 (16 days, 250m) data was used to produce the NDVI derived datasets (Kc, Fc, RainEff). Punctual evapotranspiration was compared to actual measurements obtained by flux towers on wheat and barley showing good agreements on a daily basis (r2=0.77). Finally, the comparison to monthly statistics of three irrigated commands was performed over 4 years. This late comparison showed a bad agreement which led us to suppose two things: First, the simple

  3. DICOM router: an open source toolbox for communication and correction of DICOM objects.

    Science.gov (United States)

    Hackländer, Thomas; Kleber, Klaus; Martin, Jens; Mertens, Heinrich

    2005-03-01

    Today, the exchange of medical images and clinical information is well defined by the digital imaging and communications in medicine (DICOM) and Health Level Seven (ie, HL7) standards. The interoperability among information systems is specified by the integration profiles of IHE (Integrating the Healthcare Enterprise). However, older imaging modalities frequently do not correctly support these interfaces and integration profiles, and some use cases are not yet specified by IHE. Therefore, corrections of DICOM objects are necessary to establish conformity. The aim of this project was to develop a toolbox that can automatically perform these recurrent corrections of the DICOM objects. The toolbox is composed of three main components: 1) a receiver to receive DICOM objects, 2) a processing pipeline to correct each object, and 3) one or more senders to forward each corrected object to predefined addressees. The toolbox is implemented under Java as an open source project. The processing pipeline is realized by means of plug ins. One of the plug ins can be programmed by the user via an external eXtensible Stylesheet Language (ie, XSL) file. Using this plug in, DICOM objects can also be converted into eXtensible Markup Language (ie, XML) documents or other data formats. DICOM storage services, DICOM CD-ROMs, and the local file system are defined as input and output channel. The toolbox is used clinically for different application areas. These are the automatic correction of DICOM objects from non-IHE-conforming modalities, the import of DICOM CD-ROMs into the picture archiving and communication system and the pseudo naming of DICOM images. The toolbox has been accepted by users in a clinical setting. Because of the open programming interfaces, the functionality can easily be adapted to future applications.

  4. 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.

  5. The simulation of a non-linear unstable system of motion, utilising the Solid-Works and Matlab/Simulink extended libraries/toolboxes

    Directory of Open Access Journals (Sweden)

    Zátopek Jiří

    2016-01-01

    Full Text Available This text discusses the use and integration of various support software tools for the purpose of designing the motion control law governing mechanical structures with strongly non-linear behaviour. The detailed mathematical model is derived using Lagrange Equations of the Second Type. The physical model was designed by using SolidWorks 3D CAD software and a SimMechanics library. It extends Simulink with modelling tools for the simulation of mechanical “multi-domain” physical systems. The visualization of Simulink outputs is performed using the 3D Animation toolbox. Control law - designed on the basis of the mathematical model, is tested for both models (i.e. mathematical and physical and the regulatory processes’ results are compared.

  6. Toward a mechanism-based understanding of skeletal formation: Toolbox for biomineralization past, present, and future

    Science.gov (United States)

    Dove, P. M.; Wallace, A. F.; Stephenson, A. E.; Wang, D. E.; Hamm, L.; de Yoreo, J. J.

    2008-05-01

    Since the onset of the Cambrian radiation (~540 Ma), organisms have developed the ability to control the nucleation and growth of amorphous and crystalline earth materials to form skeletal structures. Observations that similar skeletal materials are utilized across multiple branches on the eukaryotic tree of life are cited as evidence that biomineralization strategies evolved independently by similar biochemical pathways that developed early in evolutionary history (A. Knoll). An understanding of these relations is critical to deciphering earth history, yet until recently, studies of biomineral formation were primarily based upon descriptive approaches focused on morphology. Insights into mineralization processes were inferred largely from macroscopic experiments and structural characterizations. Over the last ten years, we have pursued the long-term goal of establishing a mechanistic understanding of biologically controlled mineralization. Through molecular-scale studies of calcium carbonate growth using in situ atomic force microscopy and computational methods, our approach has been to design simple model systems that link direct measurements of growth with the underlying chemical interactions. Recent additions to the toolbox of insights for mineral formation and compositional signatures include: 1) Shape is a kinetic effect of differential energy barriers to solute attachment/detachment and stereochemical relationships between crystal and growth modifier.; 2) From simple amino acids to peptides and full proteins, acidic biomolecules enhance mineralization rate up to 25X by a systematic relation. This suggests a functional role for aspartate- and glutamate-enriched macromolecules long-known to be associated with calcification.; 3) Acidic biomolecules promote uptake of impurities such as magnesium by 2-3 mol%. This enhancement corresponds to a temperature difference of 7- 14°C in proxy models that correlate Mg content with temperature. Anecdotal evidence suggests

  7. 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)

  8. 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.

  9. Improving Awareness, Identification, and Management of Sarcopenic Obesity in Cancer Survivors: An Evidence-Based Toolbox.

    Science.gov (United States)

    Lindsey, Sarah; Astroth, Kim; Kumar, Pankaj

    2016-10-01

    Sarcopenic obesity, the dual condition of decreased muscle mass with increased fat mass, can affect morbidity, mortality, and quality of life in adult cancer survivors. The purpose of this project was to determine the effects of the use of an educational toolbox on advanced practice nurses' (APNs') confidence in identifying and managing adult cancer survivors at risk for sarcopenic obesity. APNs in an outpatient practice who care for adult cancer survivors received an educational toolbox with strategies to identify and manage adult cancer survivors at risk for sarcopenic obesity. APNs reported being more confident in their ability to identify adult patients with cancer at risk for sarcopenic obesity and in their ability to manage these patients compared to prior to the intervention. Educational resources provided an effective tool for identifying and managing patients at risk for sarcopenic obesity.

  10. 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.

  11. 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.

  12. Odefy -- From discrete to continuous models

    Directory of Open Access Journals (Sweden)

    Wittmann Dominik M

    2010-05-01

    Full Text Available Abstract Background Phenomenological information about regulatory interactions is frequently available and can be readily converted to Boolean models. Fully quantitative models, on the other hand, provide detailed insights into the precise dynamics of the underlying system. In order to connect discrete and continuous modeling approaches, methods for the conversion of Boolean systems into systems of ordinary differential equations have been developed recently. As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable. Results We present Odefy, a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations. Models can be created from sets of Boolean equations or graph representations of Boolean networks. Alternatively, the user can import Boolean models from the CellNetAnalyzer toolbox, GINSim and the PBN toolbox. The Boolean models are transformed to systems of ordinary differential equations by multivariate polynomial interpolation and optional application of sigmoidal Hill functions. Our toolbox contains basic simulation and visualization functionalities for both, the Boolean as well as the continuous models. For further analyses, models can be exported to SQUAD, GNA, MATLAB script files, the SB toolbox, SBML and R script files. Odefy contains a user-friendly graphical user interface for convenient access to the simulation and exporting functionalities. We illustrate the validity of our transformation approach as well as the usage and benefit of the Odefy toolbox for two biological systems: a mutual inhibitory switch known from stem cell differentiation and a regulatory network giving rise to a specific spatial expression pattern at the mid-hindbrain boundary. Conclusions Odefy provides an easy-to-use toolbox for the automatic conversion of Boolean models to systems of ordinary

  13. Review of qualitative approaches for the construction industry: designing a risk management toolbox.

    Science.gov (United States)

    Zalk, David M; Spee, Ton; Gillen, Matt; Lentz, Thomas J; Garrod, Andrew; Evans, Paul; Swuste, Paul

    2011-06-01

    This paper presents the framework and protocol design for a construction industry risk management toolbox. The construction industry needs a comprehensive, systematic approach to assess and control occupational risks. These risks span several professional health and safety disciplines, emphasized by multiple international occupational research agenda projects including: falls, electrocution, noise, silica, welding fumes, and musculoskeletal disorders. Yet, the International Social Security Association says, "whereas progress has been made in safety and health, the construction industry is still a high risk sector." Small- and medium-sized enterprises (SMEs) employ about 80% of the world's construction workers. In recent years a strategy for qualitative occupational risk management, known as Control Banding (CB) has gained international attention as a simplified approach for reducing work-related risks. CB groups hazards into stratified risk 'bands', identifying commensurate controls to reduce the level of risk and promote worker health and safety. We review these qualitative solutions-based approaches and identify strengths and weaknesses toward designing a simplified CB 'toolbox' approach for use by SMEs in construction trades. This toolbox design proposal includes international input on multidisciplinary approaches for performing a qualitative risk assessment determining a risk 'band' for a given project. Risk bands are used to identify the appropriate level of training to oversee construction work, leading to commensurate and appropriate control methods to perform the work safely. 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.

  14. BioMet Toolbox 2.0: genome-wide analysis of metabolism and omics data

    OpenAIRE

    Garcia-Albornoz, M.; Thankaswamy-Kosalai, S.; Nilsson, A.; Varemo, L.; Nookaew, I.; Nielsen, J.

    2014-01-01

    Analysis of large data sets using computational and mathematical tools have become a central part of biological sciences. Large amounts of data are being generated each year from different biological research fields leading to a constant development of software and algorithms aimed to deal with the increasing creation of information. The BioMet Toolbox 2.0 integrates a number of functionalities in a user-friendly environment enabling the user to work with biological data in a web interface. T...

  15. 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.

  16. NIH Toolbox Cognitive Battery (NIHTB-CB): The NIHTB Pattern Comparison Processing Speed Test

    OpenAIRE

    2014-01-01

    The NIH Toolbox (NIHTB) Pattern Comparison Processing Speed Test was developed to assess processing speed within the NIHTB for the Assessment of Neurological Behavior and Function Cognition Battery (NIHTB-CB). This study highlights validation data collected in adults ages 18–85 on this measure and reports descriptive data, test–retest reliability, construct validity, and preliminary work creating a composite index of processing speed. Results indicated good test–retest reliability. There was ...

  17. Study on Alzheimer's disease model

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    It is well known that the main brain lesion in Alzheimer's disease (AD) brain is neurofibrillary tangles (NFT) and senile plaques (SP). The amount of NFT is positively correlated with clinical degree of dementia in AD. It is also well studied that the major component of NFT is abnormally hyperphosphorylated microtubule associated protein tau that is caused by an imbalance of protein kinase and protein phosphatase (PP). To reconstitute a specific AD model based on the above hypothesis, we have injected separately calcium calmodulin dependent protein kinase (CaMKKII) activator, bradykinin and PP-2B inhibitor, cyclosporin A into rat hippocampus in the present study. The results showed that the injection of bradykinin caused learning and memory deficient in rats as well as Alzheimer-like tau phosphorylation, including Ser-262/356, Thr-231/235 and Ser-396/404. On the other hand, the injection of cyclosporin A induced the same phosphorylation sites as above except Ser-262/356, however, it did not mimic rat behavior abnormality as bradykinin injection did. The data suggested that activating of CaMKII and the phosphorylation of Ser-262/356 at tau might responsible for the lesion of learning and memory in our model rats. We also incubated PP-2A and PP-1 inhibitor, okadaic acid with human neuroblastoma cell line (SH-SY5Y), and found that (1) inhibition of above PPs induced Alzheimer-like phosphorylation and accumulation of neurofilaments, and Alzheimer-like microtubule disruption, (2) melatonin showed certain protection of the cell from okadaic acid toxicity. The data obtained from this study is significant in AD specific model study.

  18. The determination of residence time distribution for a reactor based on curve fitting toolbox%基于 Curve Fitting Toolbox 反应器停留时间分布的确定

    Institute of Scientific and Technical Information of China (English)

    刘俏; 刘立昕; 金子豪; 赵明举; 齐小辉

    2013-01-01

      反应器停留时间分布的确定是建立反应器流动模型的基础。本文介绍了用 MATLAB 的 Curve Fitting Toolbox 计算反应器停留时间分布的方法。通过在图形界面下导入数据及平滑处理、采用平滑样条拟合数据以及数值积分等操作,确定了反应器停留时间分布的特征值,并且以确定系数 R2、误差平方和以及均方根误差评价拟合模型的精确度。研究表明:计算结果与文献相吻合。该法运行可靠,无需编程、易于掌握。与传统计算方法相比,操作更为便捷,强有力的图形界面也使计算变得更加简单而直观。%  The residence time distribution (RTD) of a chemical reactor is a probability distribution function that describes the amount of time a fluid element could spend inside the reactor. Chemical engineers use the RTD to characterize the mixing and flow within reactors and to compare the behavior of real reactors to their ideal models. This is useful, not only for troubleshooting existing reactors, but in estimating the yield of a given reaction and designing future reactors. The determination of the RTD for a reactor is essential to the reactor flow model. This paper presents a new method to determine the RTD characteristics using MATLAB’s Curve Fitting Toolbox. The acquired data was imported and smoothed via the graphical user interface (GUI). Smoothing spline was used to produce smooth curves to fit to the data, and the RTD characteristics were calculated by numerical integrals. The root-mean-square error (RMSE), error sum of squares (SSE), and determination coefficient (R2) statistics were used to evaluate the model’s accuracy. The study showed that the calculated results are accurate and reliable because they are consistent with those in the literatures. Compared with the traditional calculations, this method provides visualized results, and the GUI simplifies the calculation and makes it intuitive. It can be

  19. TecLines: A MATLAB-Based Toolbox for Tectonic Lineament Analysis from Satellite Images and DEMs, Part 2: Line Segments Linking and Merging

    Directory of Open Access Journals (Sweden)

    Mehdi Rahnama

    2014-11-01

    Full Text Available Extraction and interpretation of tectonic lineaments is one of the routines for mapping large areas using remote sensing data. However, this is a subjective and time-consuming process. It is difficult to choose an optimal lineament extraction method in order to reduce subjectivity and obtain vectors similar to what an analyst would manually extract. The objective of this study is the implementation, evaluation and comparison of Hough transform, segment merging and polynomial fitting methods towards automated tectonic lineament mapping. For this purpose we developed a new MATLAB-based toolbox (TecLines. The proposed toolbox capabilities were validated using a synthetic Digital Elevation Model (DEM and tested along in the Andarab fault zone (Afghanistan where specific fault structures are known. In this study, we used filters in both frequency and spatial domains and the tensor voting framework to produce binary edge maps. We used the Hough transform to extract linear image discontinuities. We used B-spline as a polynomial curve fitting method to eliminate artificial line segments that are out of interest and to link discontinuous segments with similar trends. We performed statistical analyses in order to compare the final image discontinuities maps with existing references map.

  20. DynamicBC: a MATLAB toolbox for dynamic brain connectome analysis.

    Science.gov (United States)

    Liao, Wei; Wu, Guo-Rong; Xu, Qiang; Ji, Gong-Jun; Zhang, Zhiqiang; Zang, Yu-Feng; Lu, Guangming

    2014-12-01

    The brain connectome collects the complex network architectures, looking at both static and dynamic functional connectivity. The former normally requires stationary signals and connections. However, the human brain activity and connections are most likely time dependent and dynamic, and related to ongoing rhythmic activity. We developed an open-source MATLAB toolbox DynamicBC with user-friendly graphical user interfaces, implementing both dynamic functional and effective connectivity for tracking brain dynamics from functional MRI. We provided two strategies for dynamic analysis: (1) the commonly utilized sliding-window analysis and (2) the flexible least squares based time-varying parameter regression strategy. The toolbox also implements multiple functional measures including seed-to-voxel analysis, region of interest (ROI)-to-ROI analysis, and voxel-to-voxel analysis. We describe the principles of the implemented algorithms, and then present representative results from simulations and empirical data applications. We believe that this toolbox will help neuroscientists and neurologists to easily map dynamic brain connectomics.

  1. ARCTIS — A MATLAB® Toolbox for Archaeological Imaging Spectroscopy

    Directory of Open Access Journals (Sweden)

    Clement Atzberger

    2014-09-01

    Full Text Available Imaging spectroscopy acquires imagery in hundreds or more narrow contiguous spectral bands. This offers unprecedented information for archaeological research. To extract the maximum of useful archaeological information from it, however, a number of problems have to be solved. Major problems relate to data redundancy and the visualization of the large amount of data. This makes data mining approaches necessary, as well as efficient data visualization tools. Additional problems relate to data quality. Indeed, the upwelling electromagnetic radiation is recorded in small spectral bands that are only about ten nanometers wide. The signal received by the sensor is, thus quite low compared to sensor noise and possible atmospheric perturbations. The often small, instantaneous field of view (IFOV—essential for archaeologically relevant imaging spectrometer datasets—further limits the useful signal stemming from the ground. The combination of both effects makes radiometric smoothing techniques mandatory. The present study details the functionality of a MATLAB®-based toolbox, called ARCTIS (ARChaeological Toolbox for Imaging Spectroscopy, for filtering, enhancing, analyzing, and visualizing imaging spectrometer datasets. The toolbox addresses the above-mentioned problems. Its Graphical User Interface (GUI is designed to allow non-experts in remote sensing to extract a wealth of information from imaging spectroscopy for archaeological research. ARCTIS will be released under creative commons license, free of charge, via website (http://luftbildarchiv.univie.ac.at.

  2. 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)

  3. 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.

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

    Science.gov (United States)

    Lopez-Calderon, Javier; Luck, Steven J

    2014-01-01

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

  5. 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.

  6. 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.

  7. 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.

  8. The antibody mining toolbox: an open source tool for the rapid analysis of antibody repertoires.

    Science.gov (United States)

    D'Angelo, Sara; Glanville, Jacob; Ferrara, Fortunato; Naranjo, Leslie; Gleasner, Cheryl D; Shen, Xiaohong; Bradbury, Andrew R M; Kiss, Csaba

    2014-01-01

    In vitro selection has been an essential tool in the development of recombinant antibodies against various antigen targets. Deep sequencing has recently been gaining ground as an alternative and valuable method to analyze such antibody selections. The analysis provides a novel and extremely detailed view of selected antibody populations, and allows the identification of specific antibodies using only sequencing data, potentially eliminating the need for expensive and laborious low-throughput screening methods such as enzyme-linked immunosorbant assay. The high cost and the need for bioinformatics experts and powerful computer clusters, however, have limited the general use of deep sequencing in antibody selections. Here, we describe the AbMining ToolBox, an open source software package for the straightforward analysis of antibody libraries sequenced by the three main next generation sequencing platforms (454, Ion Torrent, MiSeq). The ToolBox is able to identify heavy chain CDR3s as effectively as more computationally intense software, and can be easily adapted to analyze other portions of antibody variable genes, as well as the selection outputs of libraries based on different scaffolds. The software runs on all common operating systems (Microsoft Windows, Mac OS X, Linux), on standard personal computers, and sequence analysis of 1-2 million reads can be accomplished in 10-15 min, a fraction of the time of competing software. Use of the ToolBox will allow the average researcher to incorporate deep sequence analysis into routine selections from antibody display libraries.

  9. biomechZoo: An open-source toolbox for the processing, analysis, and visualization of biomechanical movement data.

    Science.gov (United States)

    Dixon, Philippe C; Loh, Jonathan J; Michaud-Paquette, Yannick; Pearsall, David J

    2017-03-01

    It is common for biomechanics data sets to contain numerous dependent variables recorded over time, for many subjects, groups, and/or conditions. These data often require standard sorting, processing, and analysis operations to be performed in order to answer research questions. Visualization of these data is also crucial. This manuscript presents biomechZoo, an open-source toolbox that provides tools and graphical user interfaces to help users achieve these goals. The aims of this manuscript are to (1) introduce the main features of the toolbox, including a virtual three-dimensional environment to animate motion data (Director), a data plotting suite (Ensembler), and functions for the computation of three-dimensional lower-limb joint angles, moments, and power and (2) compare these computations to those of an existing validated system. To these ends, the steps required to process and analyze a sample data set via the toolbox are outlined. The data set comprises three-dimensional marker, ground reaction force (GRF), joint kinematic, and joint kinetic data of subjects performing straight walking and 90° turning manoeuvres. Joint kinematics and kinetics processed within the toolbox were found to be similar to outputs from a commercial system. The biomechZoo toolbox represents the work of several years and multiple contributors to provide a flexible platform to examine time-series data sets typical in the movement sciences. The toolbox has previously been used to process and analyse walking, running, and ice hockey data sets, and can integrate existing routines, such as the KineMat toolbox, for additional analyses. The toolbox can help researchers and clinicians new to programming or biomechanics to process and analyze their data through a customizable workflow, while advanced users are encouraged to contribute additional functionality to the project. Students may benefit from using biomechZoo as a learning and research tool. It is hoped that the toolbox can play a

  10. 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

  11. 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.

  12. 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

  13. A Situation Analysis Toolbox for Course of Action Evaluation

    Science.gov (United States)

    2011-06-01

    This follows a standard intuition about levels 2 and 3 of the standard JDL Information Fusion model where, according to Steinberg and Bowman [4...Revisions to the JDL data fusion model. In D. L. Hall and J. Llinas, editors, Handbook of Multisensor Data Fusion, The Electrical Engineering and Applied

  14. 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

  15. BioMet Toolbox: genome-wide analysis of metabolism

    OpenAIRE

    Cvijovic, M.; R. Olivares-Hernandez; Agren, R.; Dahr, N.; Vongsangnak, W.; Nookaew, I.; K. R. Patil; Nielsen, J.

    2010-01-01

    The rapid progress of molecular biology tools for directed genetic modifications, accurate quantitative experimental approaches, high-throughput measurements, together with development of genome sequencing has made the foundation for a new area of metabolic engineering that is driven by metabolic 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 co...

  16. 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.

  17. GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks.

    Science.gov (United States)

    Taylor, Avigail; Steinberg, Julia; Andrews, Tallulah S; Webber, Caleb

    2015-02-01

    We present GeneNet Toolbox for MATLAB (also available as a set of standalone applications for Linux). The toolbox, available as command-line or with a graphical user interface, enables biologists to assess connectivity among a set of genes of interest ('seed-genes') within a biological network of their choosing. Two methods are implemented for calculating the significance of connectivity among seed-genes: 'seed randomization' and 'network permutation'. Options include restricting analyses to a specified subnetwork of the primary biological network, and calculating connectivity from the seed-genes to a second set of interesting genes. Pre-analysis tools help the user choose the best connectivity-analysis algorithm for their network. The toolbox also enables visualization of the connections among seed-genes. GeneNet Toolbox functions execute in reasonable time for very large networks (∼10 million edges) on a desktop computer. GeneNet Toolbox is open source and freely available from http://avigailtaylor.github.io/gntat14. Supplementary data are available at Bioinformatics online. avigail.taylor@dpag.ox.ac.uk. © The Author 2014. Published by Oxford University Press.

  18. PDB2Graph: A toolbox for identifying critical amino acids map in proteins based on graph theory.

    Science.gov (United States)

    Niknam, Niloofar; Khakzad, Hamed; Arab, Seyed Shahriar; Naderi-Manesh, Hossein

    2016-05-01

    The integrative and cooperative nature of protein structure involves the assessment of topological and global features of constituent parts. Network concept takes complete advantage of both of these properties in the analysis concomitantly. High compatibility to structural concepts or physicochemical properties in addition to exploiting a remarkable simplification in the system has made network an ideal tool to explore biological systems. There are numerous examples in which different protein structural and functional characteristics have been clarified by the network approach. Here, we present an interactive and user-friendly Matlab-based toolbox, PDB2Graph, devoted to protein structure network construction, visualization, and analysis. Moreover, PDB2Graph is an appropriate tool for identifying critical nodes involved in protein structural robustness and function based on centrality indices. It maps critical amino acids in protein networks and can greatly aid structural biologists in selecting proper amino acid candidates for manipulating protein structures in a more reasonable and rational manner. To introduce the capability and efficiency of PDB2Graph in detail, the structural modification of Calmodulin through allosteric binding of Ca(2+) is considered. In addition, a mutational analysis for three well-identified model proteins including Phage T4 lysozyme, Barnase and Ribonuclease HI, was performed to inspect the influence of mutating important central residues on protein activity.

  19. eProS--a database and toolbox for investigating protein sequence-structure-function relationships through energy profiles.

    Science.gov (United States)

    Heinke, Florian; Schildbach, Stefan; Stockmann, Daniel; Labudde, Dirk

    2013-01-01

    Gaining information about structural and functional features of newly identified proteins is often a difficult task. This information is crucial for understanding sequence-structure-function relationships of target proteins and, thus, essential in comprehending the mechanisms and dynamics of the molecular systems of interest. Using protein energy profiles is a novel approach that can contribute in addressing such problems. An energy profile corresponds to the sequence of energy values that are derived from a coarse-grained energy model. Energy profiles can be computed from protein structures or predicted from sequences. As shown, correspondences and dissimilarities in energy profiles can be applied for investigations of protein mechanics and dynamics. We developed eProS (energy profile suite, freely available at http://bioservices.hs-mittweida.de/Epros/), a database that provides ∼76 000 pre-calculated energy profiles as well as a toolbox for addressing numerous problems of structure biology. Energy profiles can be browsed, visualized, calculated from an uploaded structure or predicted from sequence. Furthermore, it is possible to align energy profiles of interest or compare them with all entries in the eProS database to identify significantly similar energy profiles and, thus, possibly relevant structural and functional relationships. Additionally, annotations and cross-links from numerous sources provide a broad view of potential biological correspondences.

  20. PV_LIB Toolbox v. 1.3

    Energy Technology Data Exchange (ETDEWEB)

    2015-12-09

    PV_LIB comprises a library of Matlab? code for modeling photovoltaic (PV) systems. Included are functions to compute solar position and to estimate irradiance in the PV system’s plane of array, cell temperature, PV module electrical output, and conversion from DC to AC power. Also included are functions that aid in determining parameters for module performance models from module characterization testing. PV_LIB is open source code primarily intended for research and academic purposes. All algorithms are documented in openly available literature with the appropriate references included in comments within the code.

  1. Rat traps: filling the toolbox for manipulating the rat genome

    OpenAIRE

    van Boxtel, Ruben; Cuppen, Edwin

    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 and application of these techniques in the rat.

  2. PETPVC: a toolbox for performing partial volume correction techniques in positron emission tomography

    Science.gov (United States)

    Thomas, Benjamin A.; Cuplov, Vesna; Bousse, Alexandre; Mendes, Adriana; Thielemans, Kris; Hutton, Brian F.; Erlandsson, Kjell

    2016-11-01

    Positron emission tomography (PET) images are degraded by a phenomenon known as the partial volume effect (PVE). Approaches have been developed to reduce PVEs, typically through the utilisation of structural information provided by other imaging modalities such as MRI or CT. These methods, known as partial volume correction (PVC) techniques, reduce PVEs by compensating for the effects of the scanner resolution, thereby improving the quantitative accuracy. The PETPVC toolbox described in this paper comprises a suite of methods, both classic and more recent approaches, for the purposes of applying PVC to PET data. Eight core PVC techniques are available. These core methods can be combined to create a total of 22 different PVC techniques. Simulated brain PET data are used to demonstrate the utility of toolbox in idealised conditions, the effects of applying PVC with mismatched point-spread function (PSF) estimates and the potential of novel hybrid PVC methods to improve the quantification of lesions. All anatomy-based PVC techniques achieve complete recovery of the PET signal in cortical grey matter (GM) when performed in idealised conditions. Applying deconvolution-based approaches results in incomplete recovery due to premature termination of the iterative process. PVC techniques are sensitive to PSF mismatch, causing a bias of up to 16.7% in GM recovery when over-estimating the PSF by 3 mm. The recovery of both GM and a simulated lesion was improved by combining two PVC techniques together. The PETPVC toolbox has been written in C++, supports Windows, Mac and Linux operating systems, is open-source and publicly available.

  3. 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.

  4. "FluvialCorridor": A new ArcGIS toolbox package for multiscale riverscape exploration

    Science.gov (United States)

    Roux, Clément; Alber, Adrien; Bertrand, Mélanie; Vaudor, Lise; Piégay, Hervé

    2015-08-01

    Both for scientists and river basin managers, development of automated geographic information system (GIS) tools is essential today to characterize riverscapes and explore biogeomorphologic processes over large channel networks. Since the 1990s, GIS toolboxes and add-in programs have been used to characterize catchments. However, there is currently no equivalent to a planimetric and longitudinal characterization of fluvial corridor networks at multiple scales. This paper describes FluvialCorridor, a new GIS toolbox. This package allows the user: (i) to extract a large set of riverscape features such as the main components of fluvial corridors from DEM and vector layers (e.g. stream network or valley bottom), and (ii) to aggregate spatial features into homogeneous segments and metrics characterizing each of them. The methodological frameworks involved have been previously described by Alber and Piégay (2011), Leviandier et al. (2012) and Bertrand et al. (2013) and this contribution focuses on the GIS tools allowing the user to automatically operate them. A case study on the Drôme River (France) is provided to illustrate the potential of the package both for geomorphologic understanding and target management actions. FluvialCorridor has been developed for ArcGIS with the related native Python library named ArcPy and tested on ArcGIS 10.0 and 10.1. Obviously, each component of the package can be used separately; however, it also provides a complete workflow for fluvial corridor characterization, even as the toolbox is continually under development and revision. Case study database, FluvialCorridor package and guidelines are available online at http://umrevs-isig.fr.

  5. 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.

  6. An educational model for ensemble streamflow simulation and uncertainty analysis

    National Research Council Canada - National Science Library

    AghaKouchak, A; Nakhjiri, N; Habib, E

    2013-01-01

    ...) 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...

  7. Multi-Modal Imaging with a Toolbox of Influenza A Reporter Viruses.

    Science.gov (United States)

    Tran, Vy; Poole, Daniel S; Jeffery, Justin J; Sheahan, Timothy P; Creech, Donald; Yevtodiyenko, Aleksey; Peat, Andrew J; Francis, Kevin P; You, Shihyun; Mehle, Andrew

    2015-10-13

    Reporter viruses are useful probes for studying multiple stages of the viral life cycle. Here we describe an expanded toolbox of fluorescent and bioluminescent influenza A reporter viruses. The enhanced utility of these tools enabled kinetic studies of viral attachment, infection, and co-infection. Multi-modal bioluminescence and positron emission tomography-computed tomography (PET/CT) imaging of infected animals revealed that antiviral treatment reduced viral load, dissemination, and inflammation. These new technologies and applications will dramatically accelerate in vitro and in vivo influenza virus studies.

  8. Basic Radar Altimetry Toolbox: Tools to Use Radar Altimetry for Geodesy

    Science.gov (United States)

    Rosmorduc, V.; Benveniste, J. J.; Bronner, E.; Niejmeier, S.

    2010-12-01

    Radar altimetry is very much a technique expanding its applications and uses. If quite a lot of efforts have been made for oceanography users (including easy-to-use data), the use of those data for geodesy, especially combined witht ESA GOCE mission data is still somehow hard. ESA and CNES thus had the Basic Radar Altimetry Toolbox developed (as well as, on ESA side, the GOCE User Toolbox, both being linked). The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat and the future Saral missions, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. About 1200 people downloaded it (Summer 2010), with many "newcomers" to altimetry among them. Users' feedbacks, developments in altimetry, and practice, showed that new interesting features could be added. Some have been

  9. A Toolbox of Metrology-Based Techniques for Optical System Alignment

    Science.gov (United States)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hetherington, Samuel E.; Kubalak, David A.; McLean, Kyle F.; McMann, Joseph; Redman, Kevin W.; Sampler, Henry P.; Wenzel, Greg W.; Young, Jerrod L.

    2016-01-01

    The NASA Goddard Space Flight Center (GSFC) and its partners have broad experience in the alignment of flight optical instruments and spacecraft structures. Over decades, GSFC developed alignment capabilities and techniques for a variety of optical and aerospace applications. In this paper, we provide an overview of a subset of the capabilities and techniques used on several recent projects in a "toolbox" format. We discuss a range of applications, from small-scale optical alignment of sensors to mirror and bench examples that make use of various large-volume metrology techniques. We also discuss instruments and analytical tools.

  10. A toolbox of metrology-based techniques for optical system alignment

    Science.gov (United States)

    Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Chambers, Victor J.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.; Hetherington, Samuel E.; Kubalak, David A.; Mclean, Kyle F.; McMann, Joseph C.; Redman, Kevin W.; Sampler, Henry P.; Wenzel, Greg W.; Young, Jerrod L.

    2016-10-01

    The NASA Goddard Space Flight Center (GSFC) and its partners have broad experience in the alignment of flight optical instruments and spacecraft structures. Over decades, GSFC developed alignment capabilities and techniques for a variety of optical and aerospace applications. In this paper, we provide an overview of a subset of the capabilities and techniques used on several recent projects in a "toolbox" format. We discuss a range of applications, from small-scale optical alignment of sensors to mirror and bench examples that make use of various large-volume metrology techniques. We also discuss instruments and analytical tools.

  11. 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.

  12. Genetic landscapes GIS Toolbox: tools to map patterns of genetic divergence and diversity.

    Science.gov (United States)

    Vandergast, Amy G.; Perry, William M.; Lugo, Roberto V.; Hathaway, Stacie A.

    2011-01-01

    The Landscape Genetics GIS Toolbox contains tools that run in the Geographic Information System software, ArcGIS, to map genetic landscapes and to summarize multiple genetic landscapes as average and variance surfaces. These tools can be used to visualize the distribution of genetic diversity across geographic space and to study associations between patterns of genetic diversity and geographic features or other geo-referenced environmental data sets. Together, these tools create genetic landscape surfaces directly from tables containing genetic distance or diversity data and sample location coordinates, greatly reducing the complexity of building and analyzing these raster surfaces in a Geographic Information System.

  13. Multi-Modal Imaging with a Toolbox of Influenza AReporter Viruses

    Directory of Open Access Journals (Sweden)

    Vy Tran

    2015-10-01

    Full Text Available Reporter viruses are useful probes for studying multiple stages of the viral life cycle. Here we describe an expanded toolbox of fluorescent and bioluminescent influenza A reporter viruses. The enhanced utility of these tools enabled kinetic studies of viral attachment, infection, and co-infection. Multi-modal bioluminescence and positron emission tomography–computed tomography (PET/CT imaging of infected animals revealed that antiviral treatment reduced viral load, dissemination, and inflammation. These new technologies and applications will dramatically accelerate in vitro and in vivo influenza virus studies.

  14. 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...... 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...

  15. A 3D Printed Toolbox for Opto-Mechanical Components

    Science.gov (United States)

    P. Torres, Juan; Valencia, Alejandra

    2017-01-01

    In this article we present the development of a set of opto-mechanical components (a kinematic mount, a translation stage and an integrating sphere) that can be easily built using a 3D printer based on Fused Filament Fabrication (FFF) and parts that can be found in any hardware store. Here we provide a brief description of the 3D models used and some details on the fabrication process. Moreover, with the help of three simple experimental setups, we evaluate the performance of the opto-mechanical components developed by doing a quantitative comparison with its commercial counterparts. Our results indicate that the components fabricated are highly customizable, low-cost, require a short time to be fabricated and surprisingly, offer a performance that compares favorably with respect to low-end commercial alternatives. PMID:28099494

  16. LESTO: an Open Source GIS-based toolbox for LiDAR analysis

    Science.gov (United States)

    Franceschi, Silvia; Antonello, Andrea; Tonon, Giustino

    2015-04-01

    During the last five years different research institutes and private companies stared to implement new algorithms to analyze and extract features from LiDAR data but only a few of them also created a public available software. In the field of forestry there are different examples of software that can be used to extract the vegetation parameters from LiDAR data, unfortunately most of them are closed source (even if free), which means that the source code is not shared with the public for anyone to look at or make changes to. In 2014 we started the development of the library LESTO (LiDAR Empowered Sciences Toolbox Opensource): a set of modules for the analysis of LiDAR point cloud with an Open Source approach with the aim of improving the performance of the extraction of the volume of biomass and other vegetation parameters on large areas for mixed forest structures. LESTO contains a set of modules for data handling and analysis implemented within the JGrassTools spatial processing library. The main subsections are dedicated to 1) preprocessing of LiDAR raw data mainly in LAS format (utilities and filtering); 2) creation of raster derived products; 3) flight-lines identification and normalization of the intensity values; 4) tools for extraction of vegetation and buildings. The core of the LESTO library is the extraction of the vegetation parameters. We decided to follow the single tree based approach starting with the implementation of some of the most used algorithms in literature. These have been tweaked and applied on LiDAR derived raster datasets (DTM, DSM) as well as point clouds of raw data. The methods range between the simple extraction of tops and crowns from local maxima, the region growing method, the watershed method and individual tree segmentation on point clouds. The validation procedure consists in finding the matching between field and LiDAR-derived measurements at individual tree and plot level. An automatic validation procedure has been developed

  17. 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.

  18. Fungal secretomes--nature's toolbox for white biotechnology.

    Science.gov (United States)

    Bouws, Henning; Wattenberg, Andreas; Zorn, Holger

    2008-09-01

    Adapting their metabolism to varying carbon and nitrogen sources, saprophytic fungi produce an arsenal of extracellular enzymes, the secretome, which allows for an efficient degradation of lignocelluloses and further biopolymers. Based on fundamental advances in electrophoretic, chromatographic, and mass spectrometric techniques on the one hand and the availability of annotated fungal genomes and sophisticated bioinformatic software tools on the other hand, a detailed analysis of fungal secretomes has become feasible. While a number of reports on ascomycetous secretomes of, e.g., Aspergillus, Trichoderma, and Fusarium species are already available, studies on basidiomycetes have been mainly focused on the two model organisms Phanerochaete chrysosporium and Coprinopsis cinerea so far. Though an impressive number and diversity of fungal biocatalysts has been revealed by secretome analyses, the identity and function of many extracellular proteins still remains to be elucidated. A comprehensive understanding of the qualitative and quantitative composition of fungal secretomes, together with their synergistic actions and kinetic expression profiles, will allow for the development of optimized enzyme cocktails for white biotechnology.

  19. 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/.

  20. Toolbox for the Development of Cadastral and Registration Proclamation for Second Level Certification Program in Ethiopia

    Directory of Open Access Journals (Sweden)

    Gebeyehu Belay Shibeshi

    2014-05-01

    Full Text Available Land together with its fixtures is the single most important asset in almost all societies. In Ethiopia land is also playing a pivotal role for sustainable development. Large scale cadastral projects supporting sustainable development and increased investments are planned all over the country as part of the country’s five years growth and transformation plan. But cadastral and registration proclamation is not enacted to facilitate and guide the implementation of cadastral projects. There is a consensus on the importance of cadastral and registration proclamation in Ethiopia, but there is no clear methodology for its development. The purpose of the study was to extend the land administration toolbox RRR edition to guide the development of cadastral and registration proclamation for the implementation of second level certification (mapping of parcels in Ethiopia. Field surveys, focused group discussions, expert panels, and desk work with special emphasis to the review of legal documents and state of the art experiences from other countries, were the major inputs for the study. The toolbox will be used for the development of cadastral and registration proclamation for rural land administration in Ethiopia and may guide the law development in other developing countries with a similar situation.

  1. The Radiology Resident iPad Toolbox: an educational and clinical tool for radiology residents.

    Science.gov (United States)

    Sharpe, Emerson E; Kendrick, Michael; Strickland, Colin; Dodd, Gerald D

    2013-07-01

    Tablet computing and mobile resources are the hot topics in technology today, with that interest spilling into the medical field. To improve resident education, a fully configured iPad, referred to as the "Radiology Resident iPad Toolbox," was created and implemented at the University of Colorado. The goal was to create a portable device with comprehensive educational, clinical, and communication tools that would contain all necessary resources for an entire 4-year radiology residency. The device was distributed to a total of 34 radiology residents (8 first-year residents, 8 second-year residents, 9 third-year residents, and 9 fourth-year residents). This article describes the process used to develop and deploy the device, provides a distillation of useful applications and resources decided upon after extensive evaluation, and assesses the impact this device had on resident education. The Radiology Resident iPad Toolbox is a cost-effective, portable, educational instrument that has increased studying efficiency; improved access to study materials such as books, radiology cases, lectures, and web-based resources; and increased interactivity in educational conferences and lectures through the use of audience-response software, with questions geared toward the new ABR board format. This preconfigured tablet fully embraces the technology shift into mobile computing and represents a paradigm shift in educational strategy.

  2. GEDI: a user-friendly toolbox for analysis of large-scale gene expression data.

    Science.gov (United States)

    Fujita, André; Sato, João R; Ferreira, Carlos E; Sogayar, Mari C

    2007-11-19

    Several mathematical and statistical methods have been proposed in the last few years to analyze microarray data. Most of those methods involve complicated formulas, and software implementations that require advanced computer programming skills. Researchers from other areas may experience difficulties when they attempting to use those methods in their research. Here we present an user-friendly toolbox which allows large-scale gene expression analysis to be carried out by biomedical researchers with limited programming skills. Here, we introduce an user-friendly toolbox called GEDI (Gene Expression Data Interpreter), an extensible, open-source, and freely-available tool that we believe will be useful to a wide range of laboratories, and to researchers with no background in Mathematics and Computer Science, allowing them to analyze their own data by applying both classical and advanced approaches developed and recently published by Fujita et al. GEDI is an integrated user-friendly viewer that combines the state of the art SVR, DVAR and SVAR algorithms, previously developed by us. It facilitates the application of SVR, DVAR and SVAR, further than the mathematical formulas present in the corresponding publications, and allows one to better understand the results by means of available visualizations. Both running the statistical methods and visualizing the results are carried out within the graphical user interface, rendering these algorithms accessible to the broad community of researchers in Molecular Biology.

  3. Probing the cellular effects of bacterial effector proteins with the Yersinia toolbox.

    Science.gov (United States)

    Wölke, Stefan; Heesemann, Jürgen

    2012-04-01

    The type 3 secretion system (T3SS) is a powerful bacterial nanomachine that is able to modify the host cellular immune defense in favor of the pathogen by injection of effector proteins. In this regard, cellular Rho GTPases such as Rac1, RhoA or Cdc42 are targeted by a large group of T3SS effectors by mimicking cellular guanine exchange factors or GTPase-activating proteins. However, functional analysis of one type of T3SS effector that is translocated by bacterial pathogens is challenging because the T3SS effector repertoire can comprise a large number of proteins with redundant or interfering functions. Therefore, we developed the Yersinia toolbox to either analyze singular effector proteins of Yersinia spp. or different bacterial species in the context of bacterial T3SS injection into cells. Here, we focus on the WxxxE guanine exchange factor mimetic proteins IpgB1, IpgB2 and Map, which activate Rac1, RhoA or Cdc42, respectively, as well as the Rho GTPase inactivators YopE (a GTPase-activating mimetic protein) and YopT (cysteine protease), to generate a toolbox module for Rho GTPase manipulation.

  4. Robust correlation analyses: false positive and power validation using a new open source Matlab toolbox

    Directory of Open Access Journals (Sweden)

    Cyril R Pernet

    2013-01-01

    Full Text Available 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.

  5. 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.

  6. 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. PMID:23335907

  7. 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.

  8. PyGaze : An open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments

    NARCIS (Netherlands)

    Dalmaijer, Edwin S.; Mathot, Sebastiaan; Van der Stigchel, Stefan

    2014-01-01

    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 flexi

  9. PyGaze : An open-source, cross-platform toolbox for minimal-effort programming of eyetracking experiments

    NARCIS (Netherlands)

    Dalmaijer, Edwin S.; Mathot, Sebastiaan; Van der Stigchel, Stefan

    2014-01-01

    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 flexi

  10. 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

    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 action research framework, leading to the development of a tailored approach according to Grundfos’ culture...

  11. DETECT: A MATLAB Toolbox for Event Detection and Identification in Time Series, with Applications to Artifact Detection in EEG Signals

    Science.gov (United States)

    2013-04-24

    internal sources such as muscle movements like eye blinks, jaw movements or muscle twitches [1,2]. EEG artifacts often (but not always) have signal...source toolbox for analysis of single -trial EEG dynamics including independent component analysis. Journal of Neuroscience Methods 134: 9–21. doi

  12. 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.

  13. EPA RESPONSE PROTOCOL TOOLBOX TO HELP EVALUATION OF CONTAMINATION THREATS & RESPONDING TO THREATS: MODULE 1-WATER UTILITY PLANNING GUIDE

    Science.gov (United States)

    EPA's Office of Research and Development and Office of Water/Water Security Division have jointly developed a Response Protocol Toolbox (RPTB) to address the complex, multi-faceted challenges of a water utility's planning and response to intentional contamination of drinking wate...

  14. 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...

  15. 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...

  16. A toolbox for the fast information analysis of multiple-site LFP, EEG and spike train recordings

    Directory of Open Access Journals (Sweden)

    Logothetis Nikos K

    2009-07-01

    Full Text Available Abstract Background Information theory is an increasingly popular framework for studying how the brain encodes sensory information. Despite its widespread use for the analysis of spike trains of single neurons and of small neural populations, its application to the analysis of other types of neurophysiological signals (EEGs, LFPs, BOLD has remained relatively limited so far. This is due to the limited-sampling bias which affects calculation of information, to the complexity of the techniques to eliminate the bias, and to the lack of publicly available fast routines for the information analysis of multi-dimensional responses. Results Here we introduce a new C- and Matlab-based information theoretic toolbox, specifically developed for neuroscience data. This toolbox implements a novel computationally-optimized algorithm for estimating many of the main information theoretic quantities and bias correction techniques used in neuroscience applications. We illustrate and test the toolbox in several ways. First, we verify that these algorithms provide accurate and unbiased estimates of the information carried by analog brain signals (i.e. LFPs, EEGs, or BOLD even when using limited amounts of experimental data. This test is important since existing algorithms were so far tested primarily on spike trains. Second, we apply the toolbox to the analysis of EEGs recorded from a subject watching natural movies, and we characterize the electrodes locations, frequencies and signal features carrying the most visual information. Third, we explain how the toolbox can be used to break down the information carried by different features of the neural signal into distinct components reflecting different ways in which correlations between parts of the neural signal contribute to coding. We illustrate this breakdown by analyzing LFPs recorded from primary visual cortex during presentation of naturalistic movies. Conclusion The new toolbox presented here implements fast

  17. Assessment of the applicability of a "toolbox" designed for microbially assisted phytoremediation: the case study at Ingurtosu mining site (Italy).

    Science.gov (United States)

    Sprocati, Anna Rosa; Alisi, Chiara; Pinto, Valentina; Montereali, Maria Rita; Marconi, Paola; Tasso, Flavia; Turnau, Katarzyna; De Giudici, Giovanni; Goralska, Katarzyna; Bevilacqua, Marta; Marini, Federico; Cremisini, Carlo

    2014-01-01

    The paper describes the fieldwork at the Italian test site of the abandoned mine of sphalerite and galena in Ingurtosu (Sardinia), with the aim to assess the applicability of a "toolbox" to establish the optimized techniques for remediation of soils contaminated by mining activities. A preliminary characterization-including (hydro)geochemistry, heavy metal concentration and their mobility in soil, bioprospecting for microbiology and botany-provided a data set for the development of a toolbox to deliver a microbially assisted phytoremediation process. Euphorbia pithyusa was selected as an endemic pioneer plant to be associated with a bacterial consortium, established with ten selected native strains, including metal-tolerant bacteria and producers of plant growth factors. The toolbox was firstly assessed in a greenhouse pot experiment. A positive effect of bacterial inoculum on E. pithyusa germination and total plant survival was observed. E. pithyusa showed to be a well-performing metallophyte species, and only inoculated soil retained a microbial activity with a high functional diversity, expanding metabolic affinity also towards root exudates. These results supported the decision to proceed with a field trial, investigating different treatments used singly or in combination: bioaugmentation with bacterial consortia, mycorrhizal fungi and a commercial mineral amendment. Microbial activity in soil, plant physiological parameters and heavy metal content in plants and in soil were monitored. Five months after the beginning, an early assessment of the toolbox under field conditions was carried out. Despite the cold season (October-March), results suggested the following: (1) the field setup as well as the experimental design proved to be effective; (2) plant survival was satisfactory; (3) soil quality was increased and bioaugmentation improved microbial activity, expanding the metabolic competences towards plant interaction (root exudates); and (4) multivariate

  18. Basic Radar Altimetry Toolbox: Tools and Tutorial To Use Radar Altimetry For Cryosphere

    Science.gov (United States)

    Benveniste, J. J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.

    2010-12-01

    Radar altimetry is very much a technique expanding its applications. If quite a lot of efforts have been made for oceanography users (including easy-to-use data), the use of those data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious, especially for new Altimetry data products users. ESA and CNES thus had the Basic Radar Altimetry Toolbox developed a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat and the future Saral missions, - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available from April 2007, and had been demonstrated during training courses and scientific meetings. About 1200 people downloaded it (Summer 2010), with many "newcomers" to altimetry among them, including teachers

  19. Basic Radar Altimetry Toolbox: Tools and Tutorial to Use Cryosat Data

    Science.gov (United States)

    Benveniste, J.; Bronner, E.; Dinardo, S.; Lucas, B. M.; Rosmorduc, V.; Earith, D.; Niemeijer, S.

    2011-12-01

    Radar altimetry is very much a technique expanding its applications. Even If quite a lot of effort has been invested for oceanography users, the use of Altimetry data for cryosphere application, especially with the new ESA CryoSat-2 mission data is still somehow tedious for new Altimetry data products users. ESA and CNES therfore developed the Basic Radar Altimetry Toolbox a few years ago, and are improving and upgrading it to fit new missions and the growing number of altimetry uses. The Basic Radar Altimetry Toolbox is an "all-altimeter" collection of tools, tutorials and documents designed to facilitate the use of radar altimetry data. The software is able: - to read most distributed radar altimetry data, from ERS-1 & 2, Topex/Poseidon, Geosat Follow-on, Jason-1, Envisat, Jason- 2, CryoSat, the future Saral missions and is ready for adaptation to Sentinel-3 products - to perform some processing, data editing and statistic, - and to visualize the results. It can be used at several levels/several ways: - as a data reading tool, with APIs for C, Fortran, Matlab and IDL - as processing/extraction routines, through the on-line command mode - as an educational and a quick-look tool, with the graphical user interface As part of the Toolbox, a Radar Altimetry Tutorial gives general information about altimetry, the technique involved and its applications, as well as an overview of past, present and future missions, including information on how to access data and additional software and documentation. It also presents a series of data use cases, covering all uses of altimetry over ocean, cryosphere and land, showing the basic methods for some of the most frequent manners of using altimetry data. It is an opportunity to teach remote sensing with practical training. It has been available since April 2007, and had been demonstrated during training courses and scientific meetings. About 2000 people downloaded it (Summer 2011), with many "newcomers" to altimetry among them

  20. 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

  1. A Rapid Aeroelastic/Aeroservoelastic Modeling, Analysis and Optimization System for Advanced Flight Vehicles Project

    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...

  2. 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...

  3. Sliding tethered ligands add topological interactions to the toolbox of ligand-receptor design

    Science.gov (United States)

    Bauer, Martin; Kékicheff, Patrick; Iss, Jean; Fajolles, Christophe; Charitat, Thierry; Daillant, Jean; Marques, Carlos M.

    2015-09-01

    Adhesion in the biological realm is mediated by specific lock-and-key interactions between ligand-receptor pairs. These complementary moieties are ubiquitously anchored to substrates by tethers that control the interaction range and the mobility of the ligands and receptors, thus tuning the kinetics and strength of the binding events. Here we add sliding anchoring to the toolbox of ligand-receptor design by developing a family of tethered ligands for which the spacer can slide at the anchoring point. Our results show that this additional sliding degree of freedom changes the nature of the adhesive contact by extending the spatial range over which binding may sustain a significant force. By introducing sliding tethered ligands with self-regulating length, this work paves the way for the development of versatile and reusable bio-adhesive substrates with potential applications for drug delivery and tissue engineering.

  4. A simple framework (ASF) for behavioral and neuroimaging experiments based on the psychophysics toolbox for MATLAB.

    Science.gov (United States)

    Schwarzbach, Jens

    2011-12-01

    The cognitive neurosciences combine behavioral experiments with acquiring physiological data from different modalities, such as electroencephalography, magnetoencephalography, transcranial magnetic stimulation, and functional magnetic resonance imaging, all of which require excellent timing. A simple framework is proposed in which uni- and multimodal experiments can be conducted with minimal adjustments when one switches between modalities. The framework allows the beginner to quickly become productive and the expert to be flexible and not constrained by the tool by building on existing software such as MATLAB and the Psychophysics Toolbox, which already are serving a large community. The framework allows running standard experiments but also supports and facilitates exciting new possibilities for real-time neuroimaging and state-dependent stimulation.

  5. 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...

  6. A toolbox for computing pebble shape and roundness indexes: experimental tests and recommendations for future applications.

    Science.gov (United States)

    Cassel, M.; Piegay, H.; Lave, J.

    2016-12-01

    Pebble rounding caused by attrition is, beside chemical dissolution, breakage, and grain size segregation, one of the key processes controlling bedload downstream fining in rivers. Downstream changes in pebble geometry is subject of consideration since Aristotle (Krynine, 1960) and its measurement represent a challenge since the end of 19th century, leading to a long standing debate (Blott and Pye, 2008). A toolbox developed by Roussillon et al. (2009) operate on automatic computation of several shape and roundness indexes from images of 2D projection plan of pebbles disposed on a one meter square red board. In order to promote the tool for future applications, we tested the effects of pebble position on board, of picture resolution and treatment on three shape and roundness indexes. We also compared the downstream patterns of these indexes on two pebble samples of the same lithology collected on the Progo River (Indonesia) based on field observations (i) and experimentation (ii). Shape and roundness were measured on (i) 8 sites distributed over a distance of 36 km along the river, and (ii) ten times on a set of particules collected on the Progo spring and transported in an annular flume over the same distance. This travel distance was monitored using passive low frequency RFID system. Results show that pebble position does not have a significant effect on shape and roundness indexes but these indexes are sensible to picture resolutions and treatments so that a clear protocol must be considered for avoiding any observer bias. Downstream changes in roundness indexes are very similar in field and experimental conditions, while abrasion environments are distinct. Discontinuities observed in downstream river pattern but not in experimental one underlined changes in Progo River pebble roundness are probably caused by sediment supplied from tributaries or bank erosion. These results highlight the toolbox potential for diagnosing river systems function.

  7. Reliability and Validity of Composite Scores from the NIH Toolbox Cognition Battery in Adults

    Science.gov (United States)

    Heaton, Robert K.; Akshoomoff, Natacha; Tulsky, David; Mungas, Dan; Weintraub, Sandra; Dikmen, Sureyya; Beaumont, Jennifer; Casaletto, Kaitlin B.; Conway, Kevin; Slotkin, Jerry; Gershon, Richard

    2014-01-01

    This study describes psychometric properties of the NIH Toolbox Cognition Battery (NIHTB-CB) Composite Scores in an adult sample. The NIHTB-CB was designed for use in epidemiologic studies and clinical trials for ages 3 to 85. A total of 268 self-described healthy adults were recruited at four university-based sites, using stratified sampling guidelines to target demographic variability for age (20–85 years), gender, education, and ethnicity. The NIHTB-CB contains seven computer-based instruments assessing five cognitive sub-domains: Language, Executive Function, Episodic Memory, Processing Speed, and Working Memory. Participants completed the NIHTB-CB, corresponding gold standard validation measures selected to tap the same cognitive abilities, and sociodemographic questionnaires. Three Composite Scores were derived for both the NIHTB-CB and gold standard batteries: “Crystallized Cognition Composite,” “Fluid Cognition Composite,” and “Total Cognition Composite” scores. NIHTB Composite Scores showed acceptable internal consistency (Cronbach’s alphas = 0.84 Crystallized, 0.83 Fluid, 0.77 Total), excellent test–retest reliability (r: 0.86–0.92), strong convergent (r: 0.78–0.90) and discriminant (r: 0.19–0.39) validities versus gold standard composites, and expected age effects (r = 0.18 crystallized, r = − 0.68 fluid, r = − 0.26 total). Significant relationships with self-reported prior school difficulties and current health status, employment, and presence of a disability provided evidence of external validity. The NIH Toolbox Cognition Battery Composite Scores have excellent reliability and validity, suggesting they can be used effectively in epidemiologic and clinical studies. PMID:24960398

  8. Reliability and validity of composite scores from the NIH Toolbox Cognition Battery in adults.

    Science.gov (United States)

    Heaton, Robert K; Akshoomoff, Natacha; Tulsky, David; Mungas, Dan; Weintraub, Sandra; Dikmen, Sureyya; Beaumont, Jennifer; Casaletto, Kaitlin B; Conway, Kevin; Slotkin, Jerry; Gershon, Richard

    2014-07-01

    This study describes psychometric properties of the NIH Toolbox Cognition Battery (NIHTB-CB) Composite Scores in an adult sample. The NIHTB-CB was designed for use in epidemiologic studies and clinical trials for ages 3 to 85. A total of 268 self-described healthy adults were recruited at four university-based sites, using stratified sampling guidelines to target demographic variability for age (20-85 years), gender, education, and ethnicity. The NIHTB-CB contains seven computer-based instruments assessing five cognitive sub-domains: Language, Executive Function, Episodic Memory, Processing Speed, and Working Memory. Participants completed the NIHTB-CB, corresponding gold standard validation measures selected to tap the same cognitive abilities, and sociodemographic questionnaires. Three Composite Scores were derived for both the NIHTB-CB and gold standard batteries: "Crystallized Cognition Composite," "Fluid Cognition Composite," and "Total Cognition Composite" scores. NIHTB Composite Scores showed acceptable internal consistency (Cronbach's alphas=0.84 Crystallized, 0.83 Fluid, 0.77 Total), excellent test-retest reliability (r: 0.86-0.92), strong convergent (r: 0.78-0.90) and discriminant (r: 0.19-0.39) validities versus gold standard composites, and expected age effects (r=0.18 crystallized, r=-0.68 fluid, r=-0.26 total). Significant relationships with self-reported prior school difficulties and current health status, employment, and presence of a disability provided evidence of external validity. The NIH Toolbox Cognition Battery Composite Scores have excellent reliability and validity, suggesting they can be used effectively in epidemiologic and clinical studies.

  9. 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.

  10. 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.

  11. GeoPAT: A toolbox for pattern-based information retrieval from large geospatial databases

    Science.gov (United States)

    Jasiewicz, Jarosław; Netzel, Paweł; Stepinski, Tomasz

    2015-07-01

    Geospatial Pattern Analysis Toolbox (GeoPAT) is a collection of GRASS GIS modules for carrying out pattern-based geospatial analysis of images and other spatial datasets. The need for pattern-based analysis arises when images/rasters contain rich spatial information either because of their very high resolution or their very large spatial extent. Elementary units of pattern-based analysis are scenes - patches of surface consisting of a complex arrangement of individual pixels (patterns). GeoPAT modules implement popular GIS algorithms, such as query, overlay, and segmentation, to operate on the grid of scenes. To achieve these capabilities GeoPAT includes a library of scene signatures - compact numerical descriptors of patterns, and a library of distance functions - providing numerical means of assessing dissimilarity between scenes. Ancillary GeoPAT modules use these functions to construct a grid of scenes or to assign signatures to individual scenes having regular or irregular geometries. Thus GeoPAT combines knowledge retrieval from patterns with mapping tasks within a single integrated GIS environment. GeoPAT is designed to identify and analyze complex, highly generalized classes in spatial datasets. Examples include distinguishing between different styles of urban settlements using VHR images, delineating different landscape types in land cover maps, and mapping physiographic units from DEM. The concept of pattern-based spatial analysis is explained and the roles of all modules and functions are described. A case study example pertaining to delineation of landscape types in a subregion of NLCD is given. Performance evaluation is included to highlight GeoPAT's applicability to very large datasets. The GeoPAT toolbox is available for download from

  12. Assessing Social Support, Companionship, and Distress: NIH Toolbox Adult Social Relationship Scales

    Science.gov (United States)

    Cyranowski, Jill M.; Zill, Nicholas; Bode, Rita; Butt, Zeeshan; Kelly, Morgen A. R.; Pilkonis, Paul A.; Salsman, John M.; Cella, David

    2013-01-01

    Objective The quality of our daily social interactions – including perceptions of support, feelings of loneliness, and distress stemming from negative social exchanges – influence physical health and well-being. Despite the importance of social relationships, brief yet precise, unidimensional scales that assess key aspects of social relationship quality are lacking. As part of the NIH Toolbox for the Assessment of Neurological and Behavioral Function, we developed brief self-report scales designed to assess aspects of social support, companionship, and social distress across age cohorts. This report details the development and psychometric testing of the adult NIH Toolbox Social Relationship scales. Methods Social relationship concepts were selected, and item sets were developed and revised based on expert feedback and literature review. Items were then tested across a community-dwelling U.S. internet panel sample of adults aged 18 and above (N=692) using traditional (classic) psychometric methods and item response theory (IRT) approaches to identify items for inclusion in 5–8 item unidimensional scales. Finally, concurrent validity of the newly-developed scales was evaluated with respect to their inter-relationships with classic social relationship validation instruments. Results Results provide support for the internal reliability and concurrent validity of resulting self-report scales assessing Emotional Support, Instrumental Support, Friendship, Loneliness, Perceived Rejection, and Perceived Hostility. Conclusion These brief social relationship scales provide the pragmatic utility and enhanced precision needed to promote future epidemiological and social neuroscience research on the impact of social relationships on physical and emotional health outcomes. PMID:23437856

  13. 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)

  14. From black box to toolbox: Outlining device functionality, engagement activities, and the pervasive information architecture of mHealth interventions

    Science.gov (United States)

    Danaher, Brian G.; Brendryen, Håvar; Seeley, John R.; Tyler, Milagra S.; Woolley, Tim

    2015-01-01

    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 better able to 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. PMID:25750862

  15. 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.

  16. 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....

  17. 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

    is very important when assessing its health status, but tools are currently lacking that could be used at apiary level in field surveys across the EU. Data on ‘beekeeping management practices’ and ‘environmental drivers’ can be collected via questionnaires and available databases, respectively......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....... 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...

  18. Hydroponic lettuce production in different concentrations and flow rates of nutrient solution Produção de cultivares de alface em sistema NFT variando concentração e vazão da solução

    Directory of Open Access Journals (Sweden)

    Gláucio da C Genuncio

    2012-09-01

    Full Text Available The objective of this study was to evaluate the accumulation of fresh weight of hydroponic lettuce in terms of ionic concentrations and flow rates of nutrient solution. This work consisted of three experiments in NFT hydroponic system, conducted between July and September 2006. Lettuce cultivars Lucy Brown, Izabela and Veneza were grown in different ionic concentrations of the 100, 75 and 50% and flow rates of 1.50, 1.00 and 0.75 L min-1. Fresh weight gains were observed for Lucy Brown when grown on 100% of the ion concentration and a flow rate of nutrient solution of 1.0 L min-1. Greater fresh mass was observed for cvs. Izabela and Veneza under the flow rate of 1.5 L min-1. A general analysis of the data allows us to conclude that the application of nutrient solution at a flow rate of 1.5 L min-1, as well as 100% of the ionic concentration is effective to increase the fresh weight of the aerial part of cvs. Lucy Brown, Izabela and Veneza when grown in hydroponics.O objetivo deste trabalho foi avaliar o acúmulo de massa fresca em cultivares de alface hidropônica em função de concentrações iônicas e de vazões de solução nutritiva. O trabalho consistiu em três experimentos em sistema hidropônico NFT, conduzidos entre julho e setembro de 2006. Cultivares de alface Lucy Brown, Izabela e Veneza foram crescidas em concentrações iônicas de 100, 75 e 50% e vazões de 1,50; 1,00 e 0,75 L min-1. Ganhos de massa fresca foram observados para Lucy Brown quando cultivada a 100% da concentração iônica e a uma vazão de solução nutritiva acima de 1,0 L min-1. Para Izabela e Veneza maiores massas frescas foram observadas em vazão de 1,5 L min-1 e 100% de concentração iônica. Uma análise geral dos dados nos permite concluir que a aplicação da solução nutritiva a uma vazão de 1,5 L min-1, assim como 100% da concentração iônica é eficiente para acréscimos de massa fresca de parte aérea para cultivares Lucy Brown, Izabela e Veneza

  19. 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.

  20. 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.

  1. 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.

  2. Introduction of A New Toolbox for Processing Digital Images From Multiple Camera Networks: FMIPROT

    Science.gov (United States)

    Melih Tanis, Cemal; Nadir Arslan, Ali

    2017-04-01

    Webcam networks intended for scientific monitoring of ecosystems is providing digital images and other environmental data for various studies. Also, other types of camera networks can also be used for scientific purposes, e.g. usage of traffic webcams for phenological studies, camera networks for ski tracks and avalanche monitoring over mountains for hydrological studies. To efficiently harness the potential of these camera networks, easy to use software which can obtain and handle images from different networks having different protocols and standards is necessary. For the analyses of the images from webcam networks, numerous software packages are freely available. These software packages have different strong features not only for analyzing but also post processing digital images. But specifically for the ease of use, applicability and scalability, a different set of features could be added. Thus, a more customized approach would be of high value, not only for analyzing images of comprehensive camera networks, but also considering the possibility to create operational data extraction and processing with an easy to use toolbox. At this paper, we introduce a new toolbox, entitled; Finnish Meteorological Institute Image PROcessing Tool (FMIPROT) which a customized approach is followed. FMIPROT has currently following features: • straightforward installation, • no software dependencies that require as extra installations, • communication with multiple camera networks, • automatic downloading and handling images, • user friendly and simple user interface, • data filtering, • visualizing results on customizable plots, • plugins; allows users to add their own algorithms. Current image analyses in FMIPROT include "Color Fraction Extraction" and "Vegetation Indices". The analysis of color fraction extraction is calculating the fractions of the colors in a region of interest, for red, green and blue colors along with brightness and luminance parameters. The

  3. 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.

  4. New portable tool to screen vestibular and visual function--National Institutes of Health Toolbox initiative.

    Science.gov (United States)

    Rine, Rose Marie; Roberts, Dale; Corbin, Bree A; McKean-Cowdin, Roberta; Varma, Rohit; Beaumont, Jennifer; Slotkin, Jerry; Schubert, Michael C

    2012-01-01

    As part of the National Institutes of Health Toolbox initiative, we developed a low-cost, easy-to-administer, and time-efficient test of vestibular and visual function. A computerized test of dynamic visual acuity (cDVA) was used to measure the difference in visual acuity between head still and moving in yaw. Participants included 318 individuals, aged 3 to 85 years (301 without and 17 with vestibular pathology). Adults used Early Treatment of Diabetic Retinopathy Study (ETDRS) optotypes; children used ETDRS, Lea, and HOTV optotypes. Bithermal calorics, rotational chair, and light box testing were used to validate the cDVA. Analysis revealed that the cDVA test is reliable for static (intraclass correlation coefficient [ICC] >/= 0.64) and dynamic (ICC >/= 0.43-0.75) visual acuity. Children younger than 6 years old were more likely to complete cDVA with Lea optotypes, but reliability and correlation with ETDRS was better using HOTV optotypes. The high correlation between static acuity and light box test scores (r = 0.795), significant difference of cDVA scores between those with and without pathology (p visual acuity when the head is still and moving, as well as a good proxy of vestibular function to yaw rotation.

  5. 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.

  6. iElectrodes: A Comprehensive Open-Source Toolbox for Depth and Subdural Grid Electrode Localization

    Science.gov (United States)

    Blenkmann, Alejandro O.; Phillips, Holly N.; Princich, Juan P.; Rowe, James B.; Bekinschtein, Tristan A.; Muravchik, Carlos H.; Kochen, Silvia

    2017-01-01

    The localization of intracranial electrodes is a fundamental step in the analysis of invasive electroencephalography (EEG) recordings in research and clinical practice. The conclusions reached from the analysis of these recordings rely on the accuracy of electrode localization in relationship to brain anatomy. However, currently available techniques for localizing electrodes from magnetic resonance (MR) and/or computerized tomography (CT) images are time consuming and/or limited to particular electrode types or shapes. Here we present iElectrodes, an open-source toolbox that provides robust and accurate semi-automatic localization of both subdural grids and depth electrodes. Using pre- and post-implantation images, the method takes 2–3 min to localize the coordinates in each electrode array and automatically number the electrodes. The proposed pre-processing pipeline allows one to work in a normalized space and to automatically obtain anatomical labels of the localized electrodes without neuroimaging experts. We validated the method with data from 22 patients implanted with a total of 1,242 electrodes. We show that localization distances were within 0.56 mm of those achieved by experienced manual evaluators. iElectrodes provided additional advantages in terms of robustness (even with severe perioperative cerebral distortions), speed (less than half the operator time compared to expert manual localization), simplicity, utility across multiple electrode types (surface and depth electrodes) and all brain regions. PMID:28303098

  7. The aware toolbox for the detection of law infringements on web pages

    Science.gov (United States)

    Shahab, Asif; Kieninger, Thomas; Dengel, Andreas

    2010-01-01

    In the project Aware we aim to develop an automatic assistant for the detection of law infringements on web pages. The motivation for this project is that many authors of web pages are at some points infringing copyrightor other laws, mostly without being aware of that fact, and are more and more often confronted with costly legal warnings. As the legal environment is constantly changing, an important requirement of Aware is that the domain knowledge can be maintained (and initially defined) by numerous legal experts remotely working without further assistance of the computer scientists. Consequently, the software platform was chosen to be a web-based generic toolbox that can be configured to suit individual analysis experts, definitions of analysis flow, information gathering and report generation. The report generated by the system summarizes all critical elements of a given web page and provides case specific hints to the page author and thus forms a new type of service. Regarding the analysis subsystems, Aware mainly builds on existing state-of-the-art technologies. Their usability has been evaluated for each intended task. In order to control the heterogeneous analysis components and to gather the information, a lightweight scripting shell has been developed. This paper describes the analysis technologies, ranging from text based information extraction, over optical character recognition and phonetic fuzzy string matching to a set of image analysis and retrieval tools; as well as the scripting language to define the analysis flow.

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

    Science.gov (United States)

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

    2016-06-15

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

  9. Combined chromatographic and mass spectrometric toolbox for fingerprinting migration from PET tray during microwave heating.

    Science.gov (United States)

    Alin, Jonas; Hakkarainen, Minna

    2013-02-13

    A combined chromatographic and mass spectrometric toolbox was utilized to determine the interactions between poly(ethylene terephthalate) (PET) food packaging and different food simulants during microwave heating. Overall and specific migration was determined by combining weight loss measurements with gas chromatography-mass spectrometry (GC-MS) and electrospray ionization mass spectrometry (ESI-MS). This allowed mapping of low molecular weight migrants in the molecular range up to 2000 g/mol. Microwave heating caused significantly faster migration of cyclic oligomers into ethanol and isooctane as compared to migration during conventional heating at the same temperature. This effect was more significant at lower temperature at which diffusion rates are generally lower. It was also shown that transesterification took place between PET and ethanol during microwave heating, leading to formation of diethyl terephthalate. The detected migrants included cyclic oligomers from dimer to hexamer, in most cases containing extra ethylene glycol units, and oxidized Irgafos 168. ESI-MS combined with CID MS-MS was an excellent tool for structural interpretation of the nonvolatile compounds migrating to the food simulants. The overall migration was below the overall migration limit of 10 mg/dm(2) set by the European commission after 4 h of microwave heating at 100 °C in all studied food simulants.

  10. An av-RGD integrin inhibitor toolbox: drug discovery insight, challenges and opportunities.

    Science.gov (United States)

    Hatley, Richard; Macdonald, Simon; Slack, Robert; Le, Joelle; Ludbrook, Steve; Lukey, Pauline

    2017-09-25

    There is a requirement for efficacious and safe medicines to treat diseases with high unmet need. The resurgence in av RGD integrin inhibitor drug discovery is poised to contribute to this requirement. However, drug discovery in the av integrin space is notoriously difficult due to the receptors being structurally very similar as well as the polar zwitterionic nature of the pharmacophore. This review aims to guide drug discovery research in this field through an av inhibitor toolbox, consisting of small molecules and antibodies. Small molecule av tool compounds with extended profiles in avb1, 3, 5, 6 and 8 cell adhesion assays, with key physicochemical properties, have been collated to assist in the selection of the right tool for the right experiment. This should also facilitate an understanding of partial selectivity profiles of compounds generated in different assays across research institutions. Prospects for further av integrin research and the critical importance of target validation are discussed, where increased knowledge of the selectivity for individual RGD v integrins is key. Insights into the design of small molecule RGD chemotypes for topical or oral administration are provided and clinical findings on advanced molecules are examined. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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. PMID:19184561

  12. Evolutionary process development towards next generation crystalline silicon solar cells : a semiconductor process toolbox application

    Science.gov (United States)

    John, J.; Prajapati, V.; Vermang, B.; Lorenz, A.; Allebe, C.; Rothschild, A.; Tous, L.; Uruena, A.; Baert, K.; Poortmans, J.

    2012-08-01

    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.

  13. 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.

  14. 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

    2017-09-06

    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.

  15. 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.

  16. 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.

  17. PileLine: a toolbox to handle genome position information in next-generation sequencing studies

    Directory of Open Access Journals (Sweden)

    Fdez-Riverola Florentino

    2011-01-01

    Full Text Available Abstract Background Genomic position (GP files currently used in next-generation sequencing (NGS studies are always difficult to manipulate due to their huge size and the lack of appropriate tools to properly manage them. The structure of these flat files is based on representing one line per position that has been covered by at least one aligned read, imposing significant restrictions from a computational performance perspective. Results PileLine implements a flexible command-line toolkit providing specific support to the management, filtering, comparison and annotation of GP files produced by NGS experiments. PileLine tools are coded in Java and run on both UNIX (Linux, Mac OS and Windows platforms. The set of tools comprising PileLine are designed to be memory efficient by performing fast seek on-disk operations over sorted GP files. Conclusions Our novel toolbox has been extensively tested taking into consideration performance issues. It is publicly available at http://sourceforge.net/projects/pilelinetools under the GNU LGPL license. Full documentation including common use cases and guided analysis workflows is available at http://sing.ei.uvigo.es/pileline.

  18. 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.

  19. NIH Toolbox Cognitive Battery (NIHTB-CB): the NIHTB Pattern Comparison Processing Speed Test.

    Science.gov (United States)

    Carlozzi, Noelle E; Tulsky, David S; Chiaravalloti, Nancy D; Beaumont, Jennifer L; Weintraub, Sandra; Conway, Kevin; Gershon, Richard C

    2014-07-01

    The NIH Toolbox (NIHTB) Pattern Comparison Processing Speed Test was developed to assess processing speed within the NIHTB for the Assessment of Neurological Behavior and Function Cognition Battery (NIHTB-CB). This study highlights validation data collected in adults ages 18-85 on this measure and reports descriptive data, test-retest reliability, construct validity, and preliminary work creating a composite index of processing speed. Results indicated good test-retest reliability. There was also evidence for both convergent and discriminant validity; the Pattern Comparison Processing Speed Test demonstrated moderate significant correlations with other processing speed tests (i.e., WAIS-IV Coding, Symbol Search and Processing Speed Index), small significant correlations with measures of working memory (i.e., WAIS-IV Letter-Number Sequencing and PASAT), and non-significant correlations with a test of vocabulary comprehension (i.e., PPVT-IV). Finally, analyses comparing and combining scores on the NIHTB Pattern Comparison Processing Speed Test with other measures of simple reaction time from the NIHTB-CB indicated that a Processing Speed Composite score performed better than any test examined in isolation. The NIHTB Pattern Comparison Processing Speed Test exhibits several strengths: it is appropriate for use across the lifespan (ages, 3-85 years), it is short and easy to administer, and it has high construct validity.

  20. Functional Genomics Assistant (FUGA: a toolbox for the analysis of complex biological networks

    Directory of Open Access Journals (Sweden)

    Ouzounis Christos A

    2011-10-01

    Full Text Available Abstract Background Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context. Findings We present Functional Genomics Assistant (FUGA - an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology. Conclusion FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at http://code.google.com/p/fuga.