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

PubMed

Nuutinen, Mikko; Mustonen, Terhi; Häkkinen, Jukka

2017-09-15

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

The Physics of Cancer

NASA Astrophysics Data System (ADS)

La Porta, Caterina A. M.; Zapperi, Stefano

2017-04-01

Preface; 1. Introduction to the cell; 2. The biology of cancer; 3. A modeling toolbox for cancer growth; 4. Vascular hydrodynamics and tumor angiogenesis; 5. Cancer stem cells and the population dynamics of tumors; 6. Biomechanics of cancer; 7. Cancer cell migration; 8. Chromosome and chromatin dynamics in cancer; 9. Control of tumor growth by the immune system; 10. Pharmacological approaches: old and new; 11. Outlook on the physics of cancer: a new interdisciplinary area; References; Index.

Robust master-slave synchronization for general uncertain delayed dynamical model based on adaptive control scheme.

PubMed

Wang, Tianbo; Zhou, Wuneng; Zhao, Shouwei; Yu, Weiqin

2014-03-01

In this paper, the robust exponential synchronization problem for a class of uncertain delayed master-slave dynamical system is investigated by using the adaptive control method. Different from some existing master-slave models, the considered master-slave system includes bounded unmodeled dynamics. In order to compensate the effect of unmodeled dynamics and effectively achieve synchronization, a novel adaptive controller with simple updated laws is proposed. Moreover, the results are given in terms of LMIs, which can be easily solved by LMI Toolbox in Matlab. A numerical example is given to illustrate the effectiveness of the method. Copyright © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Distributed Aerodynamic Sensing and Processing Toolbox

NASA Technical Reports Server (NTRS)

Brenner, Martin; Jutte, Christine; Mangalam, Arun

2011-01-01

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

Analysis and control of the vibration of doubly fed wind turbine

NASA Astrophysics Data System (ADS)

Yu, Manye; Lin, Ying

2017-01-01

The fault phenomena of the violent vibration of certain doubly-fed wind turbine were researched comprehensively, and the dynamic characteristics, load and fault conditions of the system were discussed. Firstly, the structural dynamics analysis of wind turbine is made, and the dynamics mold is built. Secondly, the vibration testing of wind turbine is done with the German test and analysis systems BBM. Thirdly, signal should be analyzed and dealt with. Based on the experiment, spectrum analysis of the motor dynamic balance can be made by using signal processing toolbox of MATLAB software, and the analysis conclusions show that the vibration of wind turbine is caused by dynamic imbalance. The results show that integrating mechanical system dynamics theory with advanced test technology can solve the vibration problem more successfully, which is important in vibration diagnosis of mechanical equipment.

Wavefront Control Toolbox for James Webb Space Telescope Testbed

NASA Technical Reports Server (NTRS)

Shiri, Ron; Aronstein, David L.; Smith, Jeffery Scott; Dean, Bruce H.; Sabatke, Erin

2007-01-01

We have developed a Matlab toolbox for wavefront control of optical systems. We have applied this toolbox to the optical models of James Webb Space Telescope (JWST) in general and to the JWST Testbed Telescope (TBT) in particular, implementing both unconstrained and constrained wavefront optimization to correct for possible misalignments present on the segmented primary mirror or the monolithic secondary mirror. The optical models implemented in Zemax optical design program and information is exchanged between Matlab and Zemax via the Dynamic Data Exchange (DDE) interface. The model configuration is managed using the XML protocol. The optimization algorithm uses influence functions for each adjustable degree of freedom of the optical mode. The iterative and non-iterative algorithms have been developed to converge to a local minimum of the root-mean-square (rms) of wavefront error using singular value decomposition technique of the control matrix of influence functions. The toolkit is highly modular and allows the user to choose control strategies for the degrees of freedom to be adjusted on a given iteration and wavefront convergence criterion. As the influence functions are nonlinear over the control parameter space, the toolkit also allows for trade-offs between frequency of updating the local influence functions and execution speed. The functionality of the toolbox and the validity of the underlying algorithms have been verified through extensive simulations.

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2012 CFR

2012-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2013 CFR

2013-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

40 CFR 141.716 - Source toolbox components.

Code of Federal Regulations, 2014 CFR

2014-07-01

... for Microbial Toolbox Components § 141.716 Source toolbox components. (a) Watershed control program. Systems receive 0.5-log Cryptosporidium treatment credit for implementing a watershed control program that meets the requirements of this section. (1) Systems that intend to apply for the watershed control...

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

NASA Technical Reports Server (NTRS)

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.

Pointing System Simulation Toolbox with Application to a Balloon Mission Simulator

NASA Technical Reports Server (NTRS)

Maringolo Baldraco, Rosana M.; Aretskin-Hariton, Eliot D.; Swank, Aaron J.

2017-01-01

The development of attitude estimation and pointing-control algorithms is necessary in order to achieve high-fidelity modeling for a Balloon Mission Simulator (BMS). A pointing system simulation toolbox was developed to enable this. The toolbox consists of a star-tracker (ST) and Inertial Measurement Unit (IMU) signal generator, a UDP (User Datagram Protocol) communication le (bridge), and an indirect-multiplicative extended Kalman filter (imEKF). This document describes the Python toolbox developed and the results of its implementation in the imEKF.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Various Solution Methods, Accompanied by Dynamic Investigation, for the Same Problem as a Means for Enriching the Mathematical Toolbox

ERIC Educational Resources Information Center

Oxman, Victor; Stupel, Moshe

2018-01-01

A geometrical task is presented with multiple solutions using different methods, in order to show the connection between various branches of mathematics and to highlight the importance of providing the students with an extensive 'mathematical toolbox'. Investigation of the property that appears in the task was carried out using a computerized tool.

Various solution methods, accompanied by dynamic investigation, for the same problem as a means for enriching the mathematical toolbox

NASA Astrophysics Data System (ADS)

Oxman, Victor; Stupel, Moshe

2018-04-01

A geometrical task is presented with multiple solutions using different methods, in order to show the connection between various branches of mathematics and to highlight the importance of providing the students with an extensive 'mathematical toolbox'. Investigation of the property that appears in the task was carried out using a computerized tool.

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

PubMed

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 and potential ease of implementation depending on the systems of production and their complementary nature, is the future of managing H. contortus in farmed goats internationally and maintaining the remaining efficacy of veterinary anthelmintics. Copyright © 2016 Elsevier B.V. All rights reserved.

Dynamical modeling and multi-experiment fitting with PottersWheel

PubMed Central

Maiwald, Thomas; Timmer, Jens

2008-01-01

Motivation: Modelers in Systems Biology need a flexible framework that allows them to easily create new dynamic models, investigate their properties and fit several experimental datasets simultaneously. Multi-experiment-fitting is a powerful approach to estimate parameter values, to check the validity of a given model, and to discriminate competing model hypotheses. It requires high-performance integration of ordinary differential equations and robust optimization. Results: We here present the comprehensive modeling framework Potters-Wheel (PW) including novel functionalities to satisfy these requirements with strong emphasis on the inverse problem, i.e. data-based modeling of partially observed and noisy systems like signal transduction pathways and metabolic networks. PW is designed as a MATLAB toolbox and includes numerous user interfaces. Deterministic and stochastic optimization routines are combined by fitting in logarithmic parameter space allowing for robust parameter calibration. Model investigation includes statistical tests for model-data-compliance, model discrimination, identifiability analysis and calculation of Hessian- and Monte-Carlo-based parameter confidence limits. A rich application programming interface is available for customization within own MATLAB code. Within an extensive performance analysis, we identified and significantly improved an integrator–optimizer pair which decreases the fitting duration for a realistic benchmark model by a factor over 3000 compared to MATLAB with optimization toolbox. Availability: PottersWheel is freely available for academic usage at http://www.PottersWheel.de/. The website contains a detailed documentation and introductory videos. The program has been intensively used since 2005 on Windows, Linux and Macintosh computers and does not require special MATLAB toolboxes. Contact: maiwald@fdm.uni-freiburg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:18614583

Session 6: Dynamic Modeling and Systems Analysis

NASA Technical Reports Server (NTRS)

Csank, Jeffrey; Chapman, Jeffryes; May, Ryan

2013-01-01

These presentations cover some of the ongoing work in dynamic modeling and dynamic systems analysis. The first presentation discusses dynamic systems analysis and how to integrate dynamic performance information into the systems analysis. The ability to evaluate the dynamic performance of an engine design may allow tradeoffs between the dynamic performance and operability of a design resulting in a more efficient engine design. The second presentation discusses the Toolbox for Modeling and Analysis of Thermodynamic Systems (T-MATS). T-MATS is a Simulation system with a library containing the basic building blocks that can be used to create dynamic Thermodynamic Systems. Some of the key features include Turbo machinery components, such as turbines, compressors, etc., and basic control system blocks. T-MAT is written in the Matlab-Simulink environment and is open source software. The third presentation focuses on getting additional performance from the engine by allowing the limit regulators only to be active when a limit is danger of being violated. Typical aircraft engine control architecture is based on MINMAX scheme, which is designed to keep engine operating within prescribed mechanical/operational safety limits. Using a conditionally active min-max limit regulator scheme, additional performance can be gained by disabling non-relevant limit regulators

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

PubMed Central

2011-01-01

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. PMID:22035155

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

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

PubMed

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.

An Optimization Framework for Dynamic Hybrid Energy Systems

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

Wenbo Du; Humberto E Garcia; Christiaan J.J. Paredis

A computational framework for the efficient analysis and optimization of dynamic hybrid energy systems (HES) is developed. A microgrid system with multiple inputs and multiple outputs (MIMO) is modeled using the Modelica language in the Dymola environment. The optimization loop is implemented in MATLAB, with the FMI Toolbox serving as the interface between the computational platforms. Two characteristic optimization problems are selected to demonstrate the methodology and gain insight into the system performance. The first is an unconstrained optimization problem that optimizes the dynamic properties of the battery, reactor and generator to minimize variability in the HES. The second problemmore » takes operating and capital costs into consideration by imposing linear and nonlinear constraints on the design variables. The preliminary optimization results obtained in this study provide an essential step towards the development of a comprehensive framework for designing HES.« less

A toolbox for discrete modelling of cell signalling dynamics.

PubMed

Paterson, Yasmin Z; Shorthouse, David; Pleijzier, Markus W; Piterman, Nir; Bendtsen, Claus; Hall, Benjamin A; Fisher, Jasmin

2018-06-18

In an age where the volume of data regarding biological systems exceeds our ability to analyse it, many researchers are looking towards systems biology and computational modelling to help unravel the complexities of gene and protein regulatory networks. In particular, the use of discrete modelling allows generation of signalling networks in the absence of full quantitative descriptions of systems, which are necessary for ordinary differential equation (ODE) models. In order to make such techniques more accessible to mainstream researchers, tools such as the BioModelAnalyzer (BMA) have been developed to provide a user-friendly graphical interface for discrete modelling of biological systems. Here we use the BMA to build a library of discrete target functions of known canonical molecular interactions, translated from ordinary differential equations (ODEs). We then show that these BMA target functions can be used to reconstruct complex networks, which can correctly predict many known genetic perturbations. This new library supports the accessibility ethos behind the creation of BMA, providing a toolbox for the construction of complex cell signalling models without the need for extensive experience in computer programming or mathematical modelling, and allows for construction and simulation of complex biological systems with only small amounts of quantitative data.

ROLE OF SOURCE WATER PROTECTION IN PLANNING FOR AND RESPONDING TO CONTAMINATION THREATS TO DRINKING WATER SYSTEMS

EPA Science Inventory

EPA has developed a "Response Protocol Toolbox" to address the complex, multi-faceted challenges of planning and response to intentional contamination of drinking water (http://www.epa.gov/safewater/security/ertools.html#toolbox). The toolbox is designed to be applied by a numbe...

System engineering toolbox for design-oriented engineers

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

An analysis toolbox to explore mesenchymal migration heterogeneity reveals adaptive switching between distinct modes

PubMed Central

Shafqat-Abbasi, Hamdah; Kowalewski, Jacob M; Kiss, Alexa; Gong, Xiaowei; Hernandez-Varas, Pablo; Berge, Ulrich; Jafari-Mamaghani, Mehrdad; Lock, John G; Strömblad, Staffan

2016-01-01

Mesenchymal (lamellipodial) migration is heterogeneous, although whether this reflects progressive variability or discrete, 'switchable' migration modalities, remains unclear. We present an analytical toolbox, based on quantitative single-cell imaging data, to interrogate this heterogeneity. Integrating supervised behavioral classification with multivariate analyses of cell motion, membrane dynamics, cell-matrix adhesion status and F-actin organization, this toolbox here enables the detection and characterization of two quantitatively distinct mesenchymal migration modes, termed 'Continuous' and 'Discontinuous'. Quantitative mode comparisons reveal differences in cell motion, spatiotemporal coordination of membrane protrusion/retraction, and how cells within each mode reorganize with changed cell speed. These modes thus represent distinctive migratory strategies. Additional analyses illuminate the macromolecular- and cellular-scale effects of molecular targeting (fibronectin, talin, ROCK), including 'adaptive switching' between Continuous (favored at high adhesion/full contraction) and Discontinuous (low adhesion/inhibited contraction) modes. Overall, this analytical toolbox now facilitates the exploration of both spontaneous and adaptive heterogeneity in mesenchymal migration. DOI: http://dx.doi.org/10.7554/eLife.11384.001 PMID:26821527

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis.

PubMed

Fayyaz S, S Kiavash; Liu, Xiaoyue Cathy; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George's transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis.

An efficient General Transit Feed Specification (GTFS) enabled algorithm for dynamic transit accessibility analysis

PubMed Central

Fayyaz S., S. Kiavash; Zhang, Guohui

2017-01-01

The social functions of urbanized areas are highly dependent on and supported by the convenient access to public transportation systems, particularly for the less privileged populations who have restrained auto ownership. To accurately evaluate the public transit accessibility, it is critical to capture the spatiotemporal variation of transit services. This can be achieved by measuring the shortest paths or minimum travel time between origin-destination (OD) pairs at each time-of-day (e.g. every minute). In recent years, General Transit Feed Specification (GTFS) data has been gaining popularity for between-station travel time estimation due to its interoperability in spatiotemporal analytics. Many software packages, such as ArcGIS, have developed toolbox to enable the travel time estimation with GTFS. They perform reasonably well in calculating travel time between OD pairs for a specific time-of-day (e.g. 8:00 AM), yet can become computational inefficient and unpractical with the increase of data dimensions (e.g. all times-of-day and large network). In this paper, we introduce a new algorithm that is computationally elegant and mathematically efficient to address this issue. An open-source toolbox written in C++ is developed to implement the algorithm. We implemented the algorithm on City of St. George’s transit network to showcase the accessibility analysis enabled by the toolbox. The experimental evidence shows significant reduction on computational time. The proposed algorithm and toolbox presented is easily transferable to other transit networks to allow transit agencies and researchers perform high resolution transit performance analysis. PMID:28981544

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

NASA Astrophysics Data System (ADS)

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

2018-06-01

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

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

NASA Astrophysics Data System (ADS)

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.

System modelling for LISA Pathfinder

NASA Astrophysics Data System (ADS)

Diaz-Aguiló, Marc; Grynagier, Adrien; Rais, Boutheina

LISA Pathfinder is the technology demonstrator for LISA, a space-borne gravitational waves observatory. The goal of the mission is to characterise the dynamics of the LISA Technology Package (LTP) to prove that on-board experimental conditions are compatible with the de-tection of gravitational waves. The LTP is a drag-free dynamics experiment which includes a control loop with sensors (interferometric and capacitive), actuators (capacitive actuators and thrusters), controlled disturbances (magnetic coils, heaters) and which is subject to various endogenous or exogenous noise sources such as infrared pressure or solar wind. The LTP experiment features new hardware which was never flown in space. The mission has a tight operation timeline as it is constrained to about 100 days. It is therefore vital to have efficient and precise means of investigation and diagnostics to be used during the on-orbit operations. These will be conducted using the LTP Data Analysis toolbox (LTPDA) which allows for simulation, parameter identification and various analyses (covariance analysis, state estimation) given an experimental model. The LTPDA toolbox therefore contains a series of models which are state-space representations of each component in the LTP. The State-Space Models (SSM) are objects of a state-space class within the LTPDA toolbox especially designed to address all the requirements of this tool. The user has access to a set of linear models which represent every satellite subsystem; the models are available in different forms representing 1D, 2D and 3D systems, each with settable symbolic and numeric parameters. To limit the possible errors, the models can be automatically linked to produce composite systems and closed-loops of the LTP. Finally, for the sake of completeness, accuracy and maintainability of the tool, the models contain all the physical information they mimic (i.e. variable units, description of parameters, description of inputs/outputs, etc). Models developed for this work include the fixed-point linearized equations of motion for the LTP and the linear models for sensors and actuators with their noise modelling blocks issued from the analysis of the individual actuators. The drag-free controller model includes the dis-crete delays expected in the hardware. In this work we briefly describe the software architecture, in order to concentrate then on the physical description of the models. This is supported by an overview of different user scenarios and some examples of model analysis that highlight the advantages of this high-level programming engineering toolbox for space mission data analysis and calibration.

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

USGS Publications Warehouse

Price, Curtis

2010-01-01

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 software (versions 9.3 and 9.3.1). The toolbox is composed of a collection of custom tools that implement geographic information system (GIS) techniques used by the NAWQA Program to characterize aquifer areas, drainage basins, and sampled wells.

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

PubMed Central

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.

2012-01-01

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 methods developed since its original release. New functions include: (1) network gap filling, (2) 13C analysis, (3) metabolic engineering, (4) omics-guided analysis, and (5) 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. PMID:21886097

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

NASA Technical Reports Server (NTRS)

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.

40 CFR 141.717 - Pre-filtration treatment toolbox components.

Code of Federal Regulations, 2011 CFR

2011-07-01

... surface water or GWUDI source. (c) Bank filtration. Systems receive Cryptosporidium treatment credit for... paragraph. Systems using bank filtration when they begin source water monitoring under § 141.701(a) must... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Pre-filtration treatment toolbox...

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

PubMed

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

2015-01-01

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

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

PubMed

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 role in advancing research in the movement sciences. The biomechZoo m-files, sample data, and help repositories are available online (http://www.biomechzoo.com) under the Apache 2.0 License. The toolbox is supported for Matlab (r2014b or newer, The Mathworks Inc., Natick, USA) for Windows (Microsoft Corp., Redmond, USA) and Mac OS (Apple Inc., Cupertino, USA). Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Drinking Water Cyanotoxin Risk Communication Toolbox

EPA Pesticide Factsheets

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

A CRISPR-Based Toolbox for Studying T Cell Signal Transduction

PubMed Central

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

National Water-Quality Assessment (NAWQA) area-characterization toolbox

USGS Publications Warehouse

Price, Curtis V.; Nakagaki, Naomi; Hitt, Kerie J.

2010-01-01

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 software (versions 9.3 and 9.3.1). The toolbox is composed of a collection of custom tools that implement geographic information system (GIS) techniques used by the NAWQA Program to characterize aquifer areas, drainage basins, and sampled wells. These tools are built on top of standard functionality included in ArcGIS Desktop running at the ArcInfo license level. Most of the tools require a license for the ArcGIS Spatial Analyst extension. ArcGIS is a commercial GIS software system produced by ESRI, Inc. (http://www.esri.com). The NAWQA Area-Characterization Toolbox is not supported by ESRI, Inc. or its technical support staff. Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

ΔΔPT: a comprehensive toolbox for the analysis of protein motion

PubMed Central

2013-01-01

Background Normal Mode Analysis is one of the most successful techniques for studying motions in proteins and macromolecules. It can provide information on the mechanism of protein functions, used to aid crystallography and NMR data reconstruction, and calculate protein free energies. Results ΔΔPT is a toolbox allowing calculation of elastic network models and principle component analysis. It allows the analysis of pdb files or trajectories taken from; Gromacs, Amber, and DL_POLY. As well as calculation of the normal modes it also allows comparison of the modes with experimental protein motion, variation of modes with mutation or ligand binding, and calculation of molecular dynamic entropies. Conclusions This toolbox makes the respective tools available to a wide community of potential NMA users, and allows them unrivalled ability to analyse normal modes using a variety of techniques and current software. PMID:23758746

An image analysis toolbox for high-throughput C. elegans assays

PubMed Central

Wählby, Carolina; Kamentsky, Lee; Liu, Zihan H.; Riklin-Raviv, Tammy; Conery, Annie L.; O’Rourke, Eyleen J.; Sokolnicki, Katherine L.; Visvikis, Orane; Ljosa, Vebjorn; Irazoqui, Javier E.; Golland, Polina; Ruvkun, Gary; Ausubel, Frederick M.; Carpenter, Anne E.

2012-01-01

We present a toolbox for high-throughput screening of image-based Caenorhabditis elegans phenotypes. The image analysis algorithms measure morphological phenotypes in individual worms and are effective for a variety of assays and imaging systems. This WormToolbox is available via the open-source CellProfiler project and enables objective scoring of whole-animal high-throughput image-based assays of C. elegans for the study of diverse biological pathways relevant to human disease. PMID:22522656

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

PubMed

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

2017-02-01

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

Integrating hidden Markov model and PRAAT: a toolbox for robust automatic speech transcription

NASA Astrophysics Data System (ADS)

Kabir, A.; Barker, J.; Giurgiu, M.

2010-09-01

An automatic time-aligned phone transcription toolbox of English speech corpora has been developed. Especially the toolbox would be very useful to generate robust automatic transcription and able to produce phone level transcription using speaker independent models as well as speaker dependent models without manual intervention. The system is based on standard Hidden Markov Models (HMM) approach and it was successfully experimented over a large audiovisual speech corpus namely GRID corpus. One of the most powerful features of the toolbox is the increased flexibility in speech processing where the speech community would be able to import the automatic transcription generated by HMM Toolkit (HTK) into a popular transcription software, PRAAT, and vice-versa. The toolbox has been evaluated through statistical analysis on GRID data which shows that automatic transcription deviates by an average of 20 ms with respect to manual transcription.

Vestibular function assessment using the NIH Toolbox

PubMed Central

Schubert, Michael C.; Whitney, Susan L.; Roberts, Dale; Redfern, Mark S.; Musolino, Mark C.; Roche, Jennica L.; Steed, Daniel P.; Corbin, Bree; Lin, Chia-Cheng; Marchetti, Greg F.; Beaumont, Jennifer; Carey, John P.; Shepard, Neil P.; Jacobson, Gary P.; Wrisley, Diane M.; Hoffman, Howard J.; Furman, Gabriel; Slotkin, Jerry

2013-01-01

Objective: Development of an easy to administer, low-cost test of vestibular function. Methods: Members of the NIH Toolbox Sensory Domain Vestibular, Vision, and Motor subdomain teams collaborated to identify 2 tests: 1) Dynamic Visual Acuity (DVA), and 2) the Balance Accelerometry Measure (BAM). Extensive work was completed to identify and develop appropriate software and hardware. More than 300 subjects between the ages of 3 and 85 years, with and without vestibular dysfunction, were recruited and tested. Currently accepted gold standard measures of static visual acuity, vestibular function, dynamic visual acuity, and balance were performed to determine validity. Repeat testing was performed to examine reliability. Results: The DVA and BAM tests are affordable and appropriate for use for individuals 3 through 85 years of age. The DVA had fair to good reliability (0.41–0.94) and sensitivity and specificity (50%–73%), depending on age and optotype chosen. The BAM test was moderately correlated with center of pressure (r = 0.42–0.48) and dynamic posturography (r = −0.48), depending on age and test condition. Both tests differentiated those with and without vestibular impairment and the young from the old. Each test was reliable. Conclusion: The newly created DVA test provides a valid measure of visual acuity with the head still and moving quickly. The novel BAM is a valid measure of balance. Both tests are sensitive to age-related changes and are able to screen for impairment of the vestibular system. PMID:23479540

Impact adding bifurcation in an autonomous hybrid dynamical model of church bell

NASA Astrophysics Data System (ADS)

Brzeski, P.; Chong, A. S. E.; Wiercigroch, M.; Perlikowski, P.

2018-05-01

In this paper we present the bifurcation analysis of the yoke-bell-clapper system which corresponds to the biggest bell "Serce Lodzi" mounted in the Cathedral Basilica of St Stanislaus Kostka, Lodz, Poland. The mathematical model of the system considered in this work has been derived and verified based on measurements of dynamics of the real bell. We perform numerical analysis both by direct numerical integration and path-following method using toolbox ABESPOL (Chong, 2016). By introducing the active yoke the position of the bell-clapper system with respect to the yoke axis of rotation can be easily changed and it can be used to probe the system dynamics. We found a wide variety of periodic and non-periodic solutions, and examined the ranges of coexistence of solutions and transitions between them via different types of bifurcations. Finally, a new type of bifurcation induced by a grazing event - an "impact adding bifurcation" has been proposed. When it occurs, the number of impacts between the bell and the clapper is increasing while the period of the system's motion stays the same.

A Process for the Creation of T-MATS Propulsion System Models from NPSS data

NASA Technical Reports Server (NTRS)

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

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink (Math Works, Inc.) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

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

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Trademark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

A Process for the Creation of T-MATS Propulsion System Models from NPSS Data

NASA Technical Reports Server (NTRS)

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

2014-01-01

A modular thermodynamic simulation package called the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) has been developed for the creation of dynamic simulations. The T-MATS software is designed as a plug-in for Simulink(Registered TradeMark) and allows a developer to create system simulations of thermodynamic plants (such as gas turbines) and controllers in a single tool. Creation of such simulations can be accomplished by matching data from actual systems, or by matching data from steady state models and inserting appropriate dynamics, such as the rotor and actuator dynamics for an aircraft engine. This paper summarizes the process for creating T-MATS turbo-machinery simulations using data and input files obtained from a steady state model created in the Numerical Propulsion System Simulation (NPSS). The NPSS is a thermodynamic simulation environment that is commonly used for steady state gas turbine performance analysis. Completion of all the steps involved in the process results in a good match between T-MATS and NPSS at several steady state operating points. Additionally, the T-MATS model extended to run dynamically provides the possibility of simulating and evaluating closed loop responses.

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

PubMed

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.

Study on perception and control layer of mine CPS with mixed logic dynamic approach

NASA Astrophysics Data System (ADS)

Li, Jingzhao; Ren, Ping; Yang, Dayu

2017-01-01

Mine inclined roadway transportation system of mine cyber physical system is a hybrid system consisting of a continuous-time system and a discrete-time system, which can be divided into inclined roadway signal subsystem, error-proofing channel subsystems, anti-car subsystems, and frequency control subsystems. First, to ensure stable operation, improve efficiency and production safety, this hybrid system model with n inputs and m outputs is constructed and analyzed in detail, then its steady schedule state to be solved. Second, on the basis of the formal modeling for real-time systems, we use hybrid toolbox for system security verification. Third, the practical application of mine cyber physical system shows that the method for real-time simulation of mine cyber physical system is effective.

Complete scanpaths analysis toolbox.

PubMed

Augustyniak, Piotr; Mikrut, Zbigniew

2006-01-01

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

Mid-frequency Band Dynamics of Large Space Structures

NASA Technical Reports Server (NTRS)

Coppolino, Robert N.; Adams, Douglas S.

2004-01-01

High and low intensity dynamic environments experienced by a spacecraft during launch and on-orbit operations, respectively, induce structural loads and motions, which are difficult to reliably predict. Structural dynamics in low- and mid-frequency bands are sensitive to component interface uncertainty and non-linearity as evidenced in laboratory testing and flight operations. Analytical tools for prediction of linear system response are not necessarily adequate for reliable prediction of mid-frequency band dynamics and analysis of measured laboratory and flight data. A new MATLAB toolbox, designed to address the key challenges of mid-frequency band dynamics, is introduced in this paper. Finite-element models of major subassemblies are defined following rational frequency-wavelength guidelines. For computational efficiency, these subassemblies are described as linear, component mode models. The complete structural system model is composed of component mode subassemblies and linear or non-linear joint descriptions. Computation and display of structural dynamic responses are accomplished employing well-established, stable numerical methods, modern signal processing procedures and descriptive graphical tools. Parametric sensitivity and Monte-Carlo based system identification tools are used to reconcile models with experimental data and investigate the effects of uncertainties. Models and dynamic responses are exported for employment in applications, such as detailed structural integrity and mechanical-optical-control performance analyses.

System-Events Toolbox--Activating Urban Places for Social Cohesion through Designing a System of Events That Relies on Local Resources

ERIC Educational Resources Information Center

Fassi, Davide; Motter, Roberta

2014-01-01

This paper is a reflection on the use of public spaces in towns and the development of a system-events toolbox to activate them towards social cohesion. It is the result of a 1 year action research developed together with POLIMI DESIS Lab of the Department of Design to develop design solutions to open up the public spaces of the campus to the…

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

NASA Technical Reports Server (NTRS)

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.

RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO CONTAMINATION THREATS TO DRINKING WATER SYSTEMS

EPA Science Inventory

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...

PV_LIB Toolbox

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

2012-09-11

While an organized source of reference information on PV performance modeling is certainly valuable, there is nothing to match the availability of actual examples of modeling algorithms being used in practice. To meet this need, Sandia has developed a PV performance modeling toolbox (PV_LIB) for Matlab. It contains a set of well-documented, open source functions and example scripts showing the functions being used in practical examples. This toolbox is meant to help make the multi-step process of modeling a PV system more transparent and provide the means for model users to validate and understand the models they use and ormore » develop. It is fully integrated into Matlab's help and documentation utilities. The PV_LIB Toolbox provides more than 30 functions that are sorted into four categories« less

Experiments with bosonic atoms for quantum gas assembly

NASA Astrophysics Data System (ADS)

Brown, Mark; Lin, Yiheng; Lester, Brian; Kaufman, Adam; Ball, Randall; Brossard, Ludovic; Isaev, Leonid; Thiele, Tobias; Lewis-Swan, Robert; Schymik, Kai-Niklas; Rey, Ana Maria; Regal, Cindy

2017-04-01

Quantum gas assembly is a promising platform for preparing and observing neutral atom systems on the single-atom level. We have developed a toolbox that includes ground-state laser cooling, high-fidelity loading techniques, addressable spin control, and dynamic spatial control and coupling of atoms. Already, this platform has enabled us to pursue a number of experiments studying entanglement and interference of pairs of bosonic atoms. We discuss our recent work in probabilistically entangling neutral atoms via interference, measurement, and post-selection as well as our future pursuits of interesting spin-motion dynamics of larger arrays of atoms. This work was supported by the David and Lucile Packard Foundation, National Science Foundation Physics Frontier Centers, and the National Defense Science and Engineering Graduate Fellowships program.

U.S. Geological Survey groundwater toolbox, a graphical and mapping interface for analysis of hydrologic data (version 1.0): user guide for estimation of base flow, runoff, and groundwater recharge from streamflow data

USGS Publications Warehouse

Barlow, Paul M.; Cunningham, William L.; Zhai, Tong; Gray, Mark

2015-01-01

This report is a user guide for the streamflow-hydrograph analysis methods provided with version 1.0 of the U.S. Geological Survey (USGS) Groundwater Toolbox computer program. These include six hydrograph-separation methods to determine the groundwater-discharge (base-flow) and surface-runoff components of streamflow—the Base-Flow Index (BFI; Standard and Modified), HYSEP (Fixed Interval, Sliding Interval, and Local Minimum), and PART methods—and the RORA recession-curve displacement method and associated RECESS program to estimate groundwater recharge from streamflow data. The Groundwater Toolbox is a customized interface built on the nonproprietary, open source MapWindow geographic information system software. The program provides graphing, mapping, and analysis capabilities in a Microsoft Windows computing environment. In addition to the four hydrograph-analysis methods, the Groundwater Toolbox allows for the retrieval of hydrologic time-series data (streamflow, groundwater levels, and precipitation) from the USGS National Water Information System, downloading of a suite of preprocessed geographic information system coverages and meteorological data from the National Oceanic and Atmospheric Administration National Climatic Data Center, and analysis of data with several preprocessing and postprocessing utilities. With its data retrieval and analysis tools, the Groundwater Toolbox provides methods to estimate many of the components of the water budget for a hydrologic basin, including precipitation; streamflow; base flow; runoff; groundwater recharge; and total, groundwater, and near-surface evapotranspiration.

Developing a Fluorescent Toolbox To Shed Light on the Mysteries of RNA.

PubMed

Alexander, Seth C; Devaraj, Neal K

2017-10-03

Technologies that detect and image RNA have illuminated the complex roles played by RNA, redefining the traditional and superficial role first outlined by the central dogma of biology. Because there is such a wide diversity of RNA structure arising from an assortment of functions within biology, a toolbox of approaches have emerged for investigation of this important class of biomolecules. These methods are necessary to detect and elucidate the localization and dynamics of specific RNAs and in doing so unlock our understanding of how RNA dysregulation leads to disease. Current methods for detecting and imaging RNA include in situ hybridization techniques, fluorescent aptamers, RNA binding proteins fused to fluorescent reporters, and covalent labeling strategies. Because of the inherent diversity of these methods, each approach comes with a set of strengths and limitations that leave room for future improvement. This perspective seeks to highlight the most recent advances and remaining challenges for the wide-ranging toolbox of technologies that illuminate RNA's contribution to cellular complexity.

Wastewater Collection System Toolbox | Eliminating Sanitary ...

EPA Pesticide Factsheets

2017-04-10

Communities across the United States are working to find cost-effective, long-term approaches to managing their aging wastewater infrastructure and preventing the problems that lead to sanitary sewer overflows. The Toolbox is an effort by EPA New England to provide examples of programs and educational efforts from New England and beyond.

Examining inter-family differences in intra-family (parent-adolescent) dynamics using grid-sequence analysis.

PubMed

Brinberg, Miriam; Fosco, Gregory M; Ram, Nilam

2017-12-01

Family systems theorists have forwarded a set of theoretical principles meant to guide family scientists and practitioners in their conceptualization of patterns of family interaction-intra-family dynamics-that, over time, give rise to family and individual dysfunction and/or adaptation. In this article, we present an analytic approach that merges state space grid methods adapted from the dynamic systems literature with sequence analysis methods adapted from molecular biology into a "grid-sequence" method for studying inter-family differences in intra-family dynamics. Using dyadic data from 86 parent-adolescent dyads who provided up to 21 daily reports about connectedness, we illustrate how grid-sequence analysis can be used to identify a typology of intrafamily dynamics and to inform theory about how specific types of intrafamily dynamics contribute to adolescent behavior problems and family members' mental health. Methodologically, grid-sequence analysis extends the toolbox of techniques for analysis of family experience sampling and daily diary data. Substantively, we identify patterns of family level microdynamics that may serve as new markers of risk/protective factors and potential points for intervention in families. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Toolbox for Research and Exploration (TREX): Investigations of Fine-Grained Materials on Small Bodies

NASA Technical Reports Server (NTRS)

Domingue, D. L.; Allain, J.-P.; Banks, M.; Christoffersen, R.; Cintala, M.; Clark, R.; Cloutis, E.; Graps, A.; Hendrix, A. R.; Hsieh, H.;

PLDAPS: A Hardware Architecture and Software Toolbox for Neurophysiology Requiring Complex Visual Stimuli and Online Behavioral Control.

PubMed

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.

LASSIM-A network inference toolbox for genome-wide mechanistic modeling.

PubMed

Magnusson, Rasmus; Mariotti, Guido Pio; Köpsén, Mattias; Lövfors, William; Gawel, Danuta R; Jörnsten, Rebecka; Linde, Jörg; Nordling, Torbjörn E M; Nyman, Elin; Schulze, Sylvie; Nestor, Colm E; Zhang, Huan; Cedersund, Gunnar; Benson, Mikael; Tjärnberg, Andreas; Gustafsson, Mika

2017-06-01

Recent technological advancements have made time-resolved, quantitative, multi-omics data available for many model systems, which could be integrated for systems pharmacokinetic use. Here, we present large-scale simulation modeling (LASSIM), which is a novel mathematical tool for performing large-scale inference using mechanistically defined ordinary differential equations (ODE) for gene regulatory networks (GRNs). LASSIM integrates structural knowledge about regulatory interactions and non-linear equations with multiple steady state and dynamic response expression datasets. The rationale behind LASSIM is that biological GRNs can be simplified using a limited subset of core genes that are assumed to regulate all other gene transcription events in the network. The LASSIM method is implemented as a general-purpose toolbox using the PyGMO Python package to make the most of multicore computers and high performance clusters, and is available at https://gitlab.com/Gustafsson-lab/lassim. As a method, LASSIM works in two steps, where it first infers a non-linear ODE system of the pre-specified core gene expression. Second, LASSIM in parallel optimizes the parameters that model the regulation of peripheral genes by core system genes. We showed the usefulness of this method by applying LASSIM to infer a large-scale non-linear model of naïve Th2 cell differentiation, made possible by integrating Th2 specific bindings, time-series together with six public and six novel siRNA-mediated knock-down experiments. ChIP-seq showed significant overlap for all tested transcription factors. Next, we performed novel time-series measurements of total T-cells during differentiation towards Th2 and verified that our LASSIM model could monitor those data significantly better than comparable models that used the same Th2 bindings. In summary, the LASSIM toolbox opens the door to a new type of model-based data analysis that combines the strengths of reliable mechanistic models with truly systems-level data. We demonstrate the power of this approach by inferring a mechanistically motivated, genome-wide model of the Th2 transcription regulatory system, which plays an important role in several immune related diseases.

Multirate Flutter Suppression System Design for the Benchmark Active Controls Technology Wing. Part 2; Methodology Application Software Toolbox

NASA Technical Reports Server (NTRS)

Mason, Gregory S.; Berg, Martin C.; Mukhopadhyay, Vivek

2002-01-01

To study the effectiveness of various control system design methodologies, the NASA Langley Research Center initiated the Benchmark Active Controls Project. In this project, the various methodologies were applied to design a flutter suppression system for the Benchmark Active Controls Technology (BACT) Wing. This report describes the user's manual and software toolbox developed at the University of Washington to design a multirate flutter suppression control law for the BACT wing.

A Dynamic Clamp on Every Rig

PubMed Central

2017-01-01

Abstract The dynamic clamp should be a standard part of every cellular electrophysiologist’s toolbox. That it is not, even 25 years after its introduction, comes down to three issues: money, the disruption that adding dynamic clamp to an existing electrophysiology rig entails, and the technical prowess required of experimenters. These have been valid and limiting issues in the past, but no longer. Technological advances associated with the so-called maker movement render them moot. We demonstrate this by implementing a fast (∼100 kHz) dynamic clamp system using an inexpensive microcontroller (Teensy 3.6). The overall cost of the system is less than USD$100, and assembling it requires no prior electronics experience. Modifying it—for example, to add Hodgkin–Huxley-style conductances—requires no prior programming experience. The system works together with existing electrophysiology data acquisition systems (for Macintosh, Windows, and Linux); it does not attempt to supplant them. Moreover, the process of assembling, modifying, and using the system constitutes a useful pedagogical exercise for students and researchers with no background but an interest in electronics and programming. We demonstrate the system’s utility by implementing conductances as fast as a transient sodium conductance and as complex as the Ornstein–Uhlenbeck conductances of the “point conductance” model of synaptic background activity. PMID:29085905

Modeling nuclear processes by Simulink

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

Rashid, Nahrul Khair Alang Md, E-mail: nahrul@iium.edu.my

2015-04-29

Modelling and simulation are essential parts in the study of dynamic systems behaviours. In nuclear engineering, modelling and simulation are important to assess the expected results of an experiment before the actual experiment is conducted or in the design of nuclear facilities. In education, modelling can give insight into the dynamic of systems and processes. Most nuclear processes can be described by ordinary or partial differential equations. Efforts expended to solve the equations using analytical or numerical solutions consume time and distract attention from the objectives of modelling itself. This paper presents the use of Simulink, a MATLAB toolbox softwaremore » that is widely used in control engineering, as a modelling platform for the study of nuclear processes including nuclear reactor behaviours. Starting from the describing equations, Simulink models for heat transfer, radionuclide decay process, delayed neutrons effect, reactor point kinetic equations with delayed neutron groups, and the effect of temperature feedback are used as examples.« less

Rural ITS toolbox and deployment plan for Regions 2, 6, 7 and 9 : ITS toolbox for rural and small urban areas

DOT National Transportation Integrated Search

1998-12-01

As a part of the Small Urban and Rural ITS Study it conducted in 4 of its more rural regions, the New York State Department of Transportation has developed a compendium of systems, devices and strategies that can enhance safety, provide information, ...

RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO DRINKING WATER CONTAMINATION THREATS AND INCIDENTS. OVERVIEW AND APPLICATION. INTERIM FINAL - DECEMBER 2003

EPA Science Inventory

The interim final Response Protocol Toolbox: Planning for and Responding to Contamination Threats to Drinking Water Systems is designed to help the water sector effectively and appropriately respond to intentional contamination threats and incidents. It was produced by EPA, buil...

RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO DRINKING WATER CONTAMINATION THREATS AND INCIDENTS. MODULE 4: ANALYTICAL GUIDE. INTERIM FINAL - DECEMBER 2003

EPA Science Inventory

The interim final Response Protocol Toolbox: Planning for and Responding to Contamination Threats to Drinking Water Systems is designed to help the water sector effectively and appropriately respond to intentional contamination threats and incidents. It was produced by EPA, buil...

Grid Integrated Distributed PV (GridPV) Version 2.

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

Reno, Matthew J.; Coogan, Kyle

2014-12-01

This manual provides the documentation of the MATLAB toolbox of functions for using OpenDSS to simulate the impact of solar energy on the distribution system. The majority of the functio ns are useful for interfacing OpenDSS and MATLAB, and they are of generic use for commanding OpenDSS from MATLAB and retrieving information from simulations. A set of functions is also included for modeling PV plant output and setting up the PV plant in th e OpenDSS simulation. The toolbox contains functions for modeling the OpenDSS distribution feeder on satellite images with GPS coordinates. Finally, example simulations functions are included tomore » show potential uses of the toolbox functions. Each function i n the toolbox is documented with the function use syntax, full description, function input list, function output list, example use, and example output.« less

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

PubMed

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

2012-12-01

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

GUIDANCE DOCUMENT ON IMPLEMENTATION OF THE ...

EPA Pesticide Factsheets

The Agreement in Principle for the Stage 2 M-DBP Federal Advisory Committee contains a list of treatment processes and management practices for water systems to use in meeting additional Cryptosporidium treatment requirements under the LT2ESWTR. This list, termed the microbial toolbox, includes watershed control programs, alternative intake locations, pretreatment processes, additional filtration barriers, inactivation technologies, and enhanced plant performance. The intent of the microbial toolbox is to provide water systems with broad flexibility in selecting cost-effective LT2ESWTR compliance strategies. Moreover, the toolbox allows systems that currently provide additional pathogen barriers or that can demonstrate enhanced performance to receive additional Cryptosporidium treatment credit. Provide guidance to utilities with surface water supplies and to state drinking water programs on the use of different treatment technologies to reduce the level of Cryptosporidium in drinking water. Technologies included in the guidance manual may be used to achieve compliance with the requirements of the LT2ESWTR.

Motor assessment using the NIH Toolbox

PubMed Central

Magasi, Susan; McCreath, Heather E.; Bohannon, Richard W.; Wang, Ying-Chih; Bubela, Deborah J.; Rymer, William Z.; Beaumont, Jennifer; Rine, Rose Marie; Lai, Jin-Shei; Gershon, Richard C.

2013-01-01

Motor function involves complex physiologic processes and requires the integration of multiple systems, including neuromuscular, musculoskeletal, and cardiopulmonary, and neural motor and sensory-perceptual systems. Motor-functional status is indicative of current physical health status, burden of disease, and long-term health outcomes, and is integrally related to daily functioning and quality of life. Given its importance to overall neurologic health and function, motor function was identified as a key domain for inclusion in the NIH Toolbox for Assessment of Neurological and Behavioral Function (NIH Toolbox). We engaged in a 3-stage developmental process to: 1) identify key subdomains and candidate measures for inclusion in the NIH Toolbox, 2) pretest candidate measures for feasibility across the age span of people aged 3 to 85 years, and 3) validate candidate measures against criterion measures in a sample of healthy individuals aged 3 to 85 years (n = 340). Based on extensive literature review and input from content experts, the 5 subdomains of dexterity, strength, balance, locomotion, and endurance were recommended for inclusion in the NIH Toolbox motor battery. Based on our validation testing, valid and reliable measures that are simultaneously low-cost and portable have been recommended to assess each subdomain, including the 9-hole peg board for dexterity, grip dynamometry for upper-extremity strength, standing balance test, 4-m walk test for gait speed, and a 2-minute walk test for endurance. PMID:23479547

Bayesian dynamical systems modelling in the social sciences.

PubMed

Ranganathan, Shyam; Spaiser, Viktoria; Mann, Richard P; Sumpter, David J T

2014-01-01

Data arising from social systems is often highly complex, involving non-linear relationships between the macro-level variables that characterize these systems. We present a method for analyzing this type of longitudinal or panel data using differential equations. We identify the best non-linear functions that capture interactions between variables, employing Bayes factor to decide how many interaction terms should be included in the model. This method punishes overly complicated models and identifies models with the most explanatory power. We illustrate our approach on the classic example of relating democracy and economic growth, identifying non-linear relationships between these two variables. We show how multiple variables and variable lags can be accounted for and provide a toolbox in R to implement our approach.

Early warning signal for interior crises in excitable systems.

PubMed

Karnatak, Rajat; Kantz, Holger; Bialonski, Stephan

2017-10-01

The ability to reliably predict critical transitions in dynamical systems is a long-standing goal of diverse scientific communities. Previous work focused on early warning signals related to local bifurcations (critical slowing down) and nonbifurcation-type transitions. We extend this toolbox and report on a characteristic scaling behavior (critical attractor growth) which is indicative of an impending global bifurcation, an interior crisis in excitable systems. We demonstrate our early warning signal in a conceptual climate model as well as in a model of coupled neurons known to exhibit extreme events. We observed critical attractor growth prior to interior crises of chaotic as well as strange-nonchaotic attractors. These observations promise to extend the classes of transitions that can be predicted via early warning signals.

FISSA: A neuropil decontamination toolbox for calcium imaging signals.

PubMed

Keemink, Sander W; Lowe, Scott C; Pakan, Janelle M P; Dylda, Evelyn; van Rossum, Mark C W; Rochefort, Nathalie L

2018-02-22

In vivo calcium imaging has become a method of choice to image neuronal population activity throughout the nervous system. These experiments generate large sequences of images. Their analysis is computationally intensive and typically involves motion correction, image segmentation into regions of interest (ROIs), and extraction of fluorescence traces from each ROI. Out of focus fluorescence from surrounding neuropil and other cells can strongly contaminate the signal assigned to a given ROI. In this study, we introduce the FISSA toolbox (Fast Image Signal Separation Analysis) for neuropil decontamination. Given pre-defined ROIs, the FISSA toolbox automatically extracts the surrounding local neuropil and performs blind-source separation with non-negative matrix factorization. Using both simulated and in vivo data, we show that this toolbox performs similarly or better than existing published methods. FISSA requires only little RAM, and allows for fast processing of large datasets even on a standard laptop. The FISSA toolbox is available in Python, with an option for MATLAB format outputs, and can easily be integrated into existing workflows. It is available from Github and the standard Python repositories.

The Multivariate Temporal Response Function (mTRF) Toolbox: A MATLAB Toolbox for Relating Neural Signals to Continuous Stimuli.

PubMed

Crosse, Michael J; Di Liberto, Giovanni M; Bednar, Adam; Lalor, Edmund C

2016-01-01

Understanding how brains process sensory signals in natural environments is one of the key goals of twenty-first century neuroscience. While brain imaging and invasive electrophysiology will play key roles in this endeavor, there is also an important role to be played by noninvasive, macroscopic techniques with high temporal resolution such as electro- and magnetoencephalography. But challenges exist in determining how best to analyze such complex, time-varying neural responses to complex, time-varying and multivariate natural sensory stimuli. There has been a long history of applying system identification techniques to relate the firing activity of neurons to complex sensory stimuli and such techniques are now seeing increased application to EEG and MEG data. One particular example involves fitting a filter-often referred to as a temporal response function-that describes a mapping between some feature(s) of a sensory stimulus and the neural response. Here, we first briefly review the history of these system identification approaches and describe a specific technique for deriving temporal response functions known as regularized linear regression. We then introduce a new open-source toolbox for performing this analysis. We describe how it can be used to derive (multivariate) temporal response functions describing a mapping between stimulus and response in both directions. We also explain the importance of regularizing the analysis and how this regularization can be optimized for a particular dataset. We then outline specifically how the toolbox implements these analyses and provide several examples of the types of results that the toolbox can produce. Finally, we consider some of the limitations of the toolbox and opportunities for future development and application.

The Multivariate Temporal Response Function (mTRF) Toolbox: A MATLAB Toolbox for Relating Neural Signals to Continuous Stimuli

PubMed Central

Crosse, Michael J.; Di Liberto, Giovanni M.; Bednar, Adam; Lalor, Edmund C.

2016-01-01

Understanding how brains process sensory signals in natural environments is one of the key goals of twenty-first century neuroscience. While brain imaging and invasive electrophysiology will play key roles in this endeavor, there is also an important role to be played by noninvasive, macroscopic techniques with high temporal resolution such as electro- and magnetoencephalography. But challenges exist in determining how best to analyze such complex, time-varying neural responses to complex, time-varying and multivariate natural sensory stimuli. There has been a long history of applying system identification techniques to relate the firing activity of neurons to complex sensory stimuli and such techniques are now seeing increased application to EEG and MEG data. One particular example involves fitting a filter—often referred to as a temporal response function—that describes a mapping between some feature(s) of a sensory stimulus and the neural response. Here, we first briefly review the history of these system identification approaches and describe a specific technique for deriving temporal response functions known as regularized linear regression. We then introduce a new open-source toolbox for performing this analysis. We describe how it can be used to derive (multivariate) temporal response functions describing a mapping between stimulus and response in both directions. We also explain the importance of regularizing the analysis and how this regularization can be optimized for a particular dataset. We then outline specifically how the toolbox implements these analyses and provide several examples of the types of results that the toolbox can produce. Finally, we consider some of the limitations of the toolbox and opportunities for future development and application. PMID:27965557

RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO DRINKING WATER CONTAMINATION THREATS AND INCIDENTS. MODULE 1: WATER UTILITIES PLANNING GUIDE - INTERIM FINAL - DECEMBER 2003

EPA Science Inventory

The interim final Response Protocol Toolbox: Planning for and Responding to Contamination Threats to Drinking Water Systems is designed to help the water sector effectively and appropriately respond to intentional contamination threats and incidents. It was produced by EPA, buil...

RESPONSE PROTOCOL TOOLBOX: PLANNING FOR AND RESPONDING TO DRINKING WATER CONTAMINATION THREATS AND INCIDENTS, MODULE 3: SITE CHARACTERIZATION AND SAMPLING GUIDE. INTERIM FINAL - DECEMBER 2003

EPA Science Inventory

The interim final Response Protocol Toolbox: Planning for and Responding to Contamination Threats to Drinking Water Systems is designed to help the water sector effectively and appropriately respond to intentional contamination threats and incidents. It was produced by EPA, buil...

NIA outreach to minority and health disparity populations can a toolbox for recruitment and retention be far behind?

PubMed

Harden, J Taylor; Silverberg, Nina

2010-01-01

The ability to locate the right research tool at the right time for recruitment and retention of minority and health disparity populations is a challenge. This article provides an introduction to a number of recruitment and retention tools in a National Institute on Aging Health Disparities Toolbox and to this special edition on challenges and opportunities in recruitment and retention of minority populations in Alzheimer disease and dementia research. The Health Disparities Toolbox and Health Disparities Resource Persons Network are described along with other more established resource tools including the Alzheimer Disease Center Education Cores, Alzheimer Disease Education and Referral Center, and Resource Centers for Minority Aging Research. Nine featured articles are introduced. The articles address a range of concerns including what we know and do not know, conceptual and theoretical perspectives framing issues of diversity and inclusion, success as a result of sustained investment of time and community partnerships, the significant issue of mistrust, willingness to participate in research as a dynamic personal attribute, Helpline Service and the amount of resources required for success, assistance in working with Limited English Proficiency elders, and sage advice from social marketing and investigations of health literacy as a barrier to recruitment and retention. Finally, an appeal is made for scientists to share tools for the National Institute on Aging Health Disparity Toolbox and to join the Health Disparities Resource Persons Network.

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

NASA Technical Reports Server (NTRS)

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.

Predictive Mining of Time Series Data

NASA Astrophysics Data System (ADS)

Java, A.; Perlman, E. S.

2002-05-01

All-sky monitors are a relatively new development in astronomy, and their data represent a largely untapped resource. Proper utilization of this resource could lead to important discoveries not only in the physics of variable objects, but in how one observes such objects. We discuss the development of a Java toolbox for astronomical time series data. Rather than using methods conventional in astronomy (e.g., power spectrum and cross-correlation analysis) we employ rule discovery techniques commonly used in analyzing stock-market data. By clustering patterns found within the data, rule discovery allows one to build predictive models, allowing one to forecast when a given event might occur or whether the occurrence of one event will trigger a second. We have tested the toolbox and accompanying display tool on datasets (representing several classes of objects) from the RXTE All Sky Monitor. We use these datasets to illustrate the methods and functionality of the toolbox. We have found predictive patterns in several ASM datasets. We also discuss problems faced in the development process, particularly the difficulties of dealing with discretized and irregularly sampled data. A possible application would be in scheduling target of opportunity observations where the astronomer wants to observe an object when a certain event or series of events occurs. By combining such a toolbox with an automatic, Java query tool which regularly gathers data on objects of interest, the astronomer or telescope operator could use the real-time datastream to efficiently predict the occurrence of (for example) a flare or other event. By combining the toolbox with dynamic time warping data-mining tools, one could predict events which may happen on variable time scales.

Neural Network based Control of SG based Standalone Generating System with Energy Storage for Power Quality Enhancement

NASA Astrophysics Data System (ADS)

Nayar, Priya; Singh, Bhim; Mishra, Sukumar

2017-08-01

An artificial intelligence based control algorithm is used in solving power quality problems of a diesel engine driven synchronous generator with automatic voltage regulator and governor based standalone system. A voltage source converter integrated with a battery energy storage system is employed to mitigate the power quality problems. An adaptive neural network based signed regressor control algorithm is used for the estimation of the fundamental component of load currents for control of a standalone system with load leveling as an integral feature. The developed model of the system performs accurately under varying load conditions and provides good dynamic response to the step changes in loads. The real time performance is achieved using MATLAB along with simulink/simpower system toolboxes and results adhere to an IEEE-519 standard for power quality enhancement.

SBEToolbox: A Matlab Toolbox for Biological Network Analysis

PubMed Central

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. PMID:24027418

SBEToolbox: A Matlab Toolbox for Biological Network Analysis.

PubMed

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.

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative–quantitative modeling

PubMed Central

Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

2012-01-01

Summary: Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if–then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLabTM-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. Availability: ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/ Contact: stefan.streif@ovgu.de PMID:22451270

ADMIT: a toolbox for guaranteed model invalidation, estimation and qualitative-quantitative modeling.

PubMed

Streif, Stefan; Savchenko, Anton; Rumschinski, Philipp; Borchers, Steffen; Findeisen, Rolf

2012-05-01

Often competing hypotheses for biochemical networks exist in the form of different mathematical models with unknown parameters. Considering available experimental data, it is then desired to reject model hypotheses that are inconsistent with the data, or to estimate the unknown parameters. However, these tasks are complicated because experimental data are typically sparse, uncertain, and are frequently only available in form of qualitative if-then observations. ADMIT (Analysis, Design and Model Invalidation Toolbox) is a MatLab(TM)-based tool for guaranteed model invalidation, state and parameter estimation. The toolbox allows the integration of quantitative measurement data, a priori knowledge of parameters and states, and qualitative information on the dynamic or steady-state behavior. A constraint satisfaction problem is automatically generated and algorithms are implemented for solving the desired estimation, invalidation or analysis tasks. The implemented methods built on convex relaxation and optimization and therefore provide guaranteed estimation results and certificates for invalidity. ADMIT, tutorials and illustrative examples are available free of charge for non-commercial use at http://ifatwww.et.uni-magdeburg.de/syst/ADMIT/

Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) Users' Workshop Presentations

NASA Technical Reports Server (NTRS)

Litt, Jonathan S. (Compiler)

2018-01-01

NASA Glenn Research Center hosted a Users' Workshop on the Toolbox for the Modeling and Analysis of Thermodynamic Systems (T-MATS) on August 21, 2017. The objective of this workshop was to update the user community on the latest features of T-MATS, and to provide a forum to present work performed using T-MATS. Presentations highlighted creative applications and the development of new features and libraries, and emphasized the flexibility and simulation power of T-MATS.

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation

PubMed Central

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

2018-01-01

DynaSim is an open-source MATLAB/GNU Octave toolbox for rapid prototyping of neural models and batch simulation management. It is designed to speed up and simplify the process of generating, sharing, and exploring network models of neurons with one or more compartments. Models can be specified by equations directly (similar to XPP or the Brian simulator) or by lists of predefined or custom model components. The higher-level specification supports arbitrarily complex population models and networks of interconnected populations. DynaSim also includes a large set of features that simplify exploring model dynamics over parameter spaces, running simulations in parallel using both multicore processors and high-performance computer clusters, and analyzing and plotting large numbers of simulated data sets in parallel. It also includes a graphical user interface (DynaSim GUI) that supports full functionality without requiring user programming. The software has been implemented in MATLAB to enable advanced neural modeling using MATLAB, given its popularity and a growing interest in modeling neural systems. The design of DynaSim incorporates a novel schema for model specification to facilitate future interoperability with other specifications (e.g., NeuroML, SBML), simulators (e.g., NEURON, Brian, NEST), and web-based applications (e.g., Geppetto) outside MATLAB. DynaSim is freely available at http://dynasimtoolbox.org. This tool promises to reduce barriers for investigating dynamics in large neural models, facilitate collaborative modeling, and complement other tools being developed in the neuroinformatics community. PMID:29599715

DynaSim: A MATLAB Toolbox for Neural Modeling and Simulation.

PubMed

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

2018-01-01

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

ICT: isotope correction toolbox.

PubMed

Jungreuthmayer, Christian; Neubauer, Stefan; Mairinger, Teresa; Zanghellini, Jürgen; Hann, Stephan

2016-01-01

Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ {christian.jungreuthmayer@boku.ac.at,juergen.zanghellini@boku.ac.at} Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

CEINMS: a toolbox to investigate the influence of different neural control solutions on the prediction of muscle excitation and joint moments during dynamic motor tasks

PubMed Central

Pizzolato, Claudio; Lloyd, David G.; Sartori, Massimo; Ceseracciu, Elena; Besier, Thor F.; Fregly, Benjamin J.; Reggiani, Monica

2015-01-01

Personalized neuromusculoskeletal (NMS) models can represent the neurological, physiological, and anatomical characteristics of an individual and can be used to estimate the forces generated inside the human body. Currently, publicly available software to calculate muscle forces are restricted to static and dynamic optimisation methods, or limited to isometric tasks only. We have created and made freely available for the research community the Calibrated EMG-Informed NMS Modelling Toolbox (CEINMS), an OpenSim plug-in that enables investigators to predict different neural control solutions for the same musculoskeletal geometry and measured movements. CEINMS comprises EMG-driven and EMG-informed algorithms that have been previously published and tested. It operates on dynamic skeletal models possessing any number of degrees of freedom and musculotendon units and can be calibrated to the individual to predict measured joint moments and EMG patterns. In this paper we describe the components of CEINMS and its integration with OpenSim. We then analyse how EMG-driven, EMG-assisted, and static optimisation neural control solutions affect the estimated joint moments, muscle forces, and muscle excitations, including muscle co-contraction. PMID:26522621

Temporal Code-Driven Stimulation: Definition and Application to Electric Fish Signaling

PubMed Central

Lareo, Angel; Forlim, Caroline G.; Pinto, Reynaldo D.; Varona, Pablo; Rodriguez, Francisco de Borja

2016-01-01

Closed-loop activity-dependent stimulation is a powerful methodology to assess information processing in biological systems. In this context, the development of novel protocols, their implementation in bioinformatics toolboxes and their application to different description levels open up a wide range of possibilities in the study of biological systems. We developed a methodology for studying biological signals representing them as temporal sequences of binary events. A specific sequence of these events (code) is chosen to deliver a predefined stimulation in a closed-loop manner. The response to this code-driven stimulation can be used to characterize the system. This methodology was implemented in a real time toolbox and tested in the context of electric fish signaling. We show that while there are codes that evoke a response that cannot be distinguished from a control recording without stimulation, other codes evoke a characteristic distinct response. We also compare the code-driven response to open-loop stimulation. The discussed experiments validate the proposed methodology and the software toolbox. PMID:27766078

Temporal Code-Driven Stimulation: Definition and Application to Electric Fish Signaling.

PubMed

Lareo, Angel; Forlim, Caroline G; Pinto, Reynaldo D; Varona, Pablo; Rodriguez, Francisco de Borja

2016-01-01

Closed-loop activity-dependent stimulation is a powerful methodology to assess information processing in biological systems. In this context, the development of novel protocols, their implementation in bioinformatics toolboxes and their application to different description levels open up a wide range of possibilities in the study of biological systems. We developed a methodology for studying biological signals representing them as temporal sequences of binary events. A specific sequence of these events (code) is chosen to deliver a predefined stimulation in a closed-loop manner. The response to this code-driven stimulation can be used to characterize the system. This methodology was implemented in a real time toolbox and tested in the context of electric fish signaling. We show that while there are codes that evoke a response that cannot be distinguished from a control recording without stimulation, other codes evoke a characteristic distinct response. We also compare the code-driven response to open-loop stimulation. The discussed experiments validate the proposed methodology and the software toolbox.

A molecular engineering toolbox for the structural biologist

PubMed Central

Debelouchina, Galia T.; Muir, Tom W.

2018-01-01

Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease. PMID:29233219

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective.

PubMed

Hu, Xiaotang; Li, Hongbin

2014-10-01

Protein-ligand interactions are ubiquitous and play important roles in almost every biological process. The direct elucidation of the thermodynamic, structural and functional consequences of protein-ligand interactions is thus of critical importance to decipher the mechanism underlying these biological processes. A toolbox containing a variety of powerful techniques has been developed to quantitatively study protein-ligand interactions in vitro as well as in living systems. The development of atomic force microscopy-based single molecule force spectroscopy techniques has expanded this toolbox and made it possible to directly probe the mechanical consequence of ligand binding on proteins. Many recent experiments have revealed how ligand binding affects the mechanical stability and mechanical unfolding dynamics of proteins, and provided mechanistic understanding on these effects. The enhancement effect of mechanical stability by ligand binding has been used to help tune the mechanical stability of proteins in a rational manner and develop novel functional binding assays for protein-ligand interactions. Single molecule force spectroscopy studies have started to shed new lights on the structural and functional consequence of ligand binding on proteins that bear force under their biological settings. Copyright © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

A molecular engineering toolbox for the structural biologist.

PubMed

Debelouchina, Galia T; Muir, Tom W

2017-01-01

Exciting new technological developments have pushed the boundaries of structural biology, and have enabled studies of biological macromolecules and assemblies that would have been unthinkable not long ago. Yet, the enhanced capabilities of structural biologists to pry into the complex molecular world have also placed new demands on the abilities of protein engineers to reproduce this complexity into the test tube. With this challenge in mind, we review the contents of the modern molecular engineering toolbox that allow the manipulation of proteins in a site-specific and chemically well-defined fashion. Thus, we cover concepts related to the modification of cysteines and other natural amino acids, native chemical ligation, intein and sortase-based approaches, amber suppression, as well as chemical and enzymatic bio-conjugation strategies. We also describe how these tools can be used to aid methodology development in X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy and in the studies of dynamic interactions. It is our hope that this monograph will inspire structural biologists and protein engineers alike to apply these tools to novel systems, and to enhance and broaden their scope to meet the outstanding challenges in understanding the molecular basis of cellular processes and disease.

A Monte Carlo-type simulation toolbox for Solar System small body dynamics: Application to the October Draconids

NASA Astrophysics Data System (ADS)

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 1900-2020 and were considered encounters. The simulation reproduces the predictions and observations of the 1933, 1946, 2011 and 2012 October Draconids, including the unexpected but measured deviation of the meteoroid mass index from a power law in 2012 as compared to 2011. We show that when convergence is sufficient in the simulation, the fraction between two encountered mass distributions is independent of the assumed input mass distribution. Finally, we predict an outburst for the 2018 October Draconids with a peak on October 8-9 that could be up to twice as large as the 2011 and 2012 outbursts.

Modern CACSD using the Robust-Control Toolbox

NASA Technical Reports Server (NTRS)

Chiang, Richard Y.; Safonov, Michael G.

1989-01-01

The Robust-Control Toolbox is a collection of 40 M-files which extend the capability of PC/PRO-MATLAB to do modern multivariable robust control system design. Included are robust analysis tools like singular values and structured singular values, robust synthesis tools like continuous/discrete H(exp 2)/H infinity synthesis and Linear Quadratic Gaussian Loop Transfer Recovery methods and a variety of robust model reduction tools such as Hankel approximation, balanced truncation and balanced stochastic truncation, etc. The capabilities of the toolbox are described and illustated with examples to show how easily they can be used in practice. Examples include structured singular value analysis, H infinity loop-shaping and large space structure model reduction.

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

PubMed

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

2014-03-01

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

Engineering emergent multicellular behavior through synthetic adhesion

NASA Astrophysics Data System (ADS)

Glass, David; Riedel-Kruse, Ingmar

In over a decade, synthetic biology has developed increasingly robust gene networks within single cells, but constructed very few systems that demonstrate multicellular spatio-temporal dynamics. We are filling this gap in synthetic biology's toolbox by developing an E. coli self-assembly platform based on modular cell-cell adhesion. We developed a system in which adhesive selectivity is provided by a library of outer membrane-displayed peptides with intra-library specificities, while affinity is provided by consistent expression across the entire library. We further provide a biophysical model to help understand the parameter regimes in which this tool can be used to self-assemble into cellular clusters, filaments, or meshes. The combined platform will enable future development of synthetic multicellular systems for use in consortia-based metabolic engineering, in living materials, and in controlled study of minimal multicellular systems. Stanford Bio-X Bowes Fellowship.

GMDPtoolbox: A Matlab library for designing spatial management policies. Application to the long-term collective management of an airborne disease

PubMed Central

Aubertot, Jean-Noël; Peyrard, Nathalie; Sabbadin, Régis

2017-01-01

Designing management policies in ecology and agroecology is complex. Several components must be managed together while they strongly interact spatially. Decision choices must be made under uncertainty on the results of the actions and on the system dynamics. Furthermore, the objectives pursued when managing ecological systems or agroecosystems are usually long term objectives, such as biodiversity conservation or sustainable crop production. The framework of Graph-Based Markov Decision Processes (GMDP) is well adapted to the qualitative modeling of such problems of sequential decision under uncertainty. Spatial interactions are easily modeled and integrated control policies (combining several action levers) can be designed through optimization. The provided policies are adaptive, meaning that management actions are decided at each time step (for instance yearly) and the chosen actions depend on the current system state. This framework has already been successfully applied to forest management and invasive species management. However, up to now, no “easy-to-use” implementation of this framework was available. We present GMDPtoolbox, a Matlab toolbox which can be used both for the design of new management policies and for comparing policies by simulation. We provide an illustration of the use of the toolbox on a realistic crop disease management problem: the design of long term management policy of blackleg of canola using an optimal combination of three possible cultural levers. This example shows how GMDPtoolbox can be used as a tool to support expert thinking. PMID:28982151

GMDPtoolbox: A Matlab library for designing spatial management policies. Application to the long-term collective management of an airborne disease.

PubMed

Cros, Marie-Josée; Aubertot, Jean-Noël; Peyrard, Nathalie; Sabbadin, Régis

2017-01-01

Designing management policies in ecology and agroecology is complex. Several components must be managed together while they strongly interact spatially. Decision choices must be made under uncertainty on the results of the actions and on the system dynamics. Furthermore, the objectives pursued when managing ecological systems or agroecosystems are usually long term objectives, such as biodiversity conservation or sustainable crop production. The framework of Graph-Based Markov Decision Processes (GMDP) is well adapted to the qualitative modeling of such problems of sequential decision under uncertainty. Spatial interactions are easily modeled and integrated control policies (combining several action levers) can be designed through optimization. The provided policies are adaptive, meaning that management actions are decided at each time step (for instance yearly) and the chosen actions depend on the current system state. This framework has already been successfully applied to forest management and invasive species management. However, up to now, no "easy-to-use" implementation of this framework was available. We present GMDPtoolbox, a Matlab toolbox which can be used both for the design of new management policies and for comparing policies by simulation. We provide an illustration of the use of the toolbox on a realistic crop disease management problem: the design of long term management policy of blackleg of canola using an optimal combination of three possible cultural levers. This example shows how GMDPtoolbox can be used as a tool to support expert thinking.

Programmable oligonucleotide probes design and applications for in situ and in vivo RNA imaging in cells

NASA Astrophysics Data System (ADS)

Cheglakov, Zoya

Unequal spreading of mRNA is a frequent experience observed in varied cell lines. The study of cellular processes dynamics and precise localization of mRNAs offers a vital toolbox to target specific proteins in precise cytoplasmic areas and provides a convenient instrument to uncover their mechanisms and functions. Latest methodological innovations have allowed imaging of a single mRNA molecule in situ and in vivo. Today, Fluorescent In Situ Hybridization (FISH) methods allow the studying of mRNA expression and offer a vital toolbox for accurate biological models. Studies enable analysis of the dynamics of an individual mRNA, have uncovered the multiplex RNA transport systems. With all current approaches, a single mRNA tracking in the mammalian cells is still challenging. This thesis describes mRNA detection methods based on programmable fluorophore-labeled DNA structures complimentary to native targets providing an accurate mRNA imaging in mammalian cells. First method represents beta-actin (ACTB) transcripts in situ detection in human cells, the technique strategy is based on programmable DNA probes, amplified by rolling circle amplification (RCA). The method reports precise localization of molecule of interest with an accuracy of a single-cell. Visualization and localization of specific endogenous mRNA molecules in real-time in vivo has the promising to innovate cellular biology studies, medical analysis and to provide a vital toolbox in drugs invention area. Second method described in this thesis represents miR-21 miRNA detection within a single live-cell resolution. The method using fluorophore-labeled short synthetic DNAs probes forming a stem-loop shape and generating Fluorescent Resonance Energy Transfer (FRET) as a result of target-probes hybridization. Catalytic nucleic acid (DNAzymes) probes are cooperative tool for precise detection of different mRNA targets. With assistance of a complementary fluorophore-quencher labeled substrate, the DNAzymes provide a beneficial strategy for simultaneous tracking readily accomplished by multicolor imaging with diverse fluorescent tags. The third method in this thesis will demonstrate the advantage of DNAzymes probes amplification, and offers potential strategy to monitor miRNAs in mammalian live cells.

Evol and ProDy for bridging protein sequence evolution and structural dynamics

PubMed Central

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

2014-01-01

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

Toolbox for Research, or how to facilitate a central data management in small-scale research projects.

PubMed

Bialke, Martin; Rau, Henriette; Thamm, Oliver C; Schuldt, Ronny; Penndorf, Peter; Blumentritt, Arne; Gött, Robert; Piegsa, Jens; Bahls, Thomas; Hoffmann, Wolfgang

2018-01-25

In most research projects budget, staff and IT infrastructures are limiting resources. Especially for small-scale registries and cohort studies professional IT support and commercial electronic data capture systems are too expensive. Consequently, these projects use simple local approaches (e.g. Excel) for data capture instead of a central data management including web-based data capture and proper research databases. This leads to manual processes to merge, analyze and, if possible, pseudonymize research data of different study sites. To support multi-site data capture, storage and analyses in small-scall research projects, corresponding requirements were analyzed within the MOSAIC project. Based on the identified requirements, the Toolbox for Research was developed as a flexible software solution for various research scenarios. Additionally, the Toolbox facilitates data integration of research data as well as metadata by performing necessary procedures automatically. Also, Toolbox modules allow the integration of device data. Moreover, separation of personally identifiable information and medical data by using only pseudonyms for storing medical data ensures the compliance to data protection regulations. This pseudonymized data can then be exported in SPSS format in order to enable scientists to prepare reports and analyses. The Toolbox for Research was successfully piloted in the German Burn Registry in 2016 facilitating the documentation of 4350 burn cases at 54 study sites. The Toolbox for Research can be downloaded free of charge from the project website and automatically installed due to the use of Docker technology.

A Toolbox to Improve Algorithms for Insulin-Dosing Decision Support

PubMed Central

Donsa, K.; Plank, J.; Schaupp, L.; Mader, J. K.; Truskaller, T.; Tschapeller, B.; Höll, B.; Spat, S.; Pieber, T. R.

2014-01-01

Summary Background Standardized insulin order sets for subcutaneous basal-bolus insulin therapy are recommended by clinical guidelines for the inpatient management of diabetes. The algorithm based GlucoTab system electronically assists health care personnel by supporting clinical workflow and providing insulin-dose suggestions. Objective To develop a toolbox for improving clinical decision-support algorithms. Methods The toolbox has three main components. 1) Data preparation: Data from several heterogeneous sources is extracted, cleaned and stored in a uniform data format. 2) Simulation: The effects of algorithm modifications are estimated by simulating treatment workflows based on real data from clinical trials. 3) Analysis: Algorithm performance is measured, analyzed and simulated by using data from three clinical trials with a total of 166 patients. Results Use of the toolbox led to algorithm improvements as well as the detection of potential individualized subgroup-specific algorithms. Conclusion These results are a first step towards individualized algorithm modifications for specific patient subgroups. PMID:25024768

A House Full of Trap Doors. Identifying barriers to resilient drylands in the toolbox of pastoral development

NASA Astrophysics Data System (ADS)

Krätli, Saverio; Kaufmann, Brigitte; Roba, Hassan; Hiernaux, Pierre; Li, Wenjun; Easdale, Marcos H.; Huelsebusch, Christian

2016-04-01

The theoretical understanding of drylands and pastoral systems has long undergone a U-turn from the initial perspective rooted in classical ecology. The shift has hinged on the way to represent asymmetric variability, from a disturbance in an ecosystem that naturally tends towards uniformity and stability, to a constitutive part of a dynamic ecosystem. Operationalising the new reversed perspective, including the need to update the methodological infrastructure to plan around drylands and pastoral development, remains a challenge. Underlying assumptions about stability and uniformity, that are a legacy of equilibrium thinking, remain embedded in the toolbox of pastoral development, starting from the technical language to talk about the subject. This effectively gets in the way of operationalizing state of the art understanding of pastoral systems and the drylands. Unless these barriers are identified, unpacked and managed, even the present calls for increasing the rigour and intensity of data collection - for example as part of the ongoing global process to revise and improve agricultural data - cannot deliver a realistic representation of pastoral systems in statistics and policy making. This contribution presents the case for understanding variability as an asset, and provides a range of examples of methodological barriers, including classifications of livestock systems, scale of observation, key parameters in animal production, indicators in the measurement of ecological efficiency, concepts of ecological fragility, natural resources, and pastoral risk. The need to update this legacy is a pressing challenge for policy makers concerned with both modernisation and resilience in the drylands.

Wyrm: A Brain-Computer Interface Toolbox in Python.

PubMed

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.

Visual NNet: An Educational ANN's Simulation Environment Reusing Matlab Neural Networks Toolbox

ERIC Educational Resources Information Center

Garcia-Roselló, Emilio; González-Dacosta, Jacinto; Lado, Maria J.; Méndez, Arturo J.; Garcia Pérez-Schofield, Baltasar; Ferrer, Fátima

2011-01-01

Artificial Neural Networks (ANN's) are nowadays a common subject in different curricula of graduate and postgraduate studies. Due to the complex algorithms involved and the dynamic nature of ANN's, simulation software has been commonly used to teach this subject. This software has usually been developed specifically for learning purposes, because…

Optimising the Parallelisation of OpenFOAM Simulations

DTIC Science & Technology

2014-06-01

UNCLASSIFIED UNCLASSIFIED Optimising the Parallelisation of OpenFOAM Simulations Shannon Keough Maritime Division Defence...Science and Technology Organisation DSTO-TR-2987 ABSTRACT The OpenFOAM computational fluid dynamics toolbox allows parallel computation of...performance of a given high performance computing cluster with several OpenFOAM cases, running using a combination of MPI libraries and corresponding MPI

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

PubMed

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.

CEINMS: A toolbox to investigate the influence of different neural control solutions on the prediction of muscle excitation and joint moments during dynamic motor tasks.

PubMed

Pizzolato, Claudio; Lloyd, David G; Sartori, Massimo; Ceseracciu, Elena; Besier, Thor F; Fregly, Benjamin J; Reggiani, Monica

2015-11-05

Personalized neuromusculoskeletal (NMS) models can represent the neurological, physiological, and anatomical characteristics of an individual and can be used to estimate the forces generated inside the human body. Currently, publicly available software to calculate muscle forces are restricted to static and dynamic optimisation methods, or limited to isometric tasks only. We have created and made freely available for the research community the Calibrated EMG-Informed NMS Modelling Toolbox (CEINMS), an OpenSim plug-in that enables investigators to predict different neural control solutions for the same musculoskeletal geometry and measured movements. CEINMS comprises EMG-driven and EMG-informed algorithms that have been previously published and tested. It operates on dynamic skeletal models possessing any number of degrees of freedom and musculotendon units and can be calibrated to the individual to predict measured joint moments and EMG patterns. In this paper we describe the components of CEINMS and its integration with OpenSim. We then analyse how EMG-driven, EMG-assisted, and static optimisation neural control solutions affect the estimated joint moments, muscle forces, and muscle excitations, including muscle co-contraction. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

NASA Technical Reports Server (NTRS)

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(Registered TradeMark) (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.

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

NASA Technical Reports Server (NTRS)

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.

Multimodal Imaging of Brain Connectivity Using the MIBCA Toolbox: Preliminary Application to Alzheimer's Disease

NASA Astrophysics Data System (ADS)

Ribeiro, André Santos; Lacerda, Luís Miguel; Silva, Nuno André da; Ferreira, Hugo Alexandre

2015-06-01

The Multimodal Imaging Brain Connectivity Analysis (MIBCA) toolbox is a fully automated all-in-one connectivity analysis toolbox that offers both pre-processing, connectivity, and graph theory analysis of multimodal images such as anatomical, diffusion, and functional MRI, and PET. In this work, the MIBCA functionalities were used to study Alzheimer's Disease (AD) in a multimodal MR/PET approach. Materials and Methods: Data from 12 healthy controls, and 36 patients with EMCI, LMCI and AD (12 patients for each group) were obtained from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database (adni.loni.usc.edu), including T1-weighted (T1-w), Diffusion Tensor Imaging (DTI) data, and 18F-AV-45 (florbetapir) dynamic PET data from 40-60 min post injection (4x5 min). Both MR and PET data were automatically pre-processed for all subjects using MIBCA. T1-w data was parcellated into cortical and subcortical regions-of-interest (ROIs), and the corresponding thicknesses and volumes were calculated. DTI data was used to compute structural connectivity matrices based on fibers connecting pairs of ROIs. Lastly, dynamic PET images were summed, and the relative Standard Uptake Values calculated for each ROI. Results: An overall higher uptake of 18F-AV-45, consistent with an increased deposition of beta-amyloid, was observed for the AD group. Additionally, patients showed significant cortical atrophy (thickness and volume) especially in the entorhinal cortex and temporal areas, and a significant increase in Mean Diffusivity (MD) in the hippocampus, amygdala and temporal areas. Furthermore, patients showed a reduction of fiber connectivity with the progression of the disease, especially for intra-hemispherical connections. Conclusion: This work shows the potential of the MIBCA toolbox for the study of AD, as findings were shown to be in agreement with the literature. Here, only structural changes and beta-amyloid accumulation were considered. Yet, MIBCA is further able to process fMRI and different radiotracers, thus leading to integration of functional information, and supporting the research for new multimodal biomarkers for AD and other neurodegenerative diseases.

Virtual acoustic environments for comprehensive evaluation of model-based hearing devices.

PubMed

Grimm, Giso; Luberadzka, Joanna; Hohmann, Volker

2018-06-01

Create virtual acoustic environments (VAEs) with interactive dynamic rendering for applications in audiology. A toolbox for creation and rendering of dynamic virtual acoustic environments (TASCAR) that allows direct user interaction was developed for application in hearing aid research and audiology. The software architecture and the simulation methods used to produce VAEs are outlined. Example environments are described and analysed. With the proposed software, a tool for simulation of VAEs is available. A set of VAEs rendered with the proposed software was described.

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

PubMed

Rose, Jonas; Otto, Tobias; Dittrich, Lars

2008-10-30

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

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

PubMed Central

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

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

PubMed

Zhang, Bo; Dai, Ji; Zhang, Tao

2017-11-13

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

FALCON: a toolbox for the fast contextualization of logical networks

PubMed Central

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

2017-01-01

Abstract Motivation Mathematical modelling of regulatory networks allows for the discovery of knowledge at the system level. However, existing modelling tools are often computation-heavy and do not offer intuitive ways to explore the model, to test hypotheses or to interpret the results biologically. Results We have developed a computational approach to contextualize logical models of regulatory networks with biological measurements based on a probabilistic description of rule-based interactions between the different molecules. Here, we propose a Matlab toolbox, FALCON, to automatically and efficiently build and contextualize networks, which includes a pipeline for conducting parameter analysis, knockouts and easy and fast model investigation. The contextualized models could then provide qualitative and quantitative information about the network and suggest hypotheses about biological processes. Availability and implementation FALCON is freely available for non-commercial users on GitHub under the GPLv3 licence. The toolbox, installation instructions, full documentation and test datasets are available at https://github.com/sysbiolux/FALCON. FALCON runs under Matlab (MathWorks) and requires the Optimization Toolbox. Contact thomas.sauter@uni.lu Supplementary information Supplementary data are available at Bioinformatics online. PMID:28673016

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

PubMed

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

2017-11-01

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

Structured Uncertainty Bound Determination From Data for Control and Performance Validation

NASA Technical Reports Server (NTRS)

Lim, Kyong B.

2003-01-01

This report attempts to document the broad scope of issues that must be satisfactorily resolved before one can expect to methodically obtain, with a reasonable confidence, a near-optimal robust closed loop performance in physical applications. These include elements of signal processing, noise identification, system identification, model validation, and uncertainty modeling. Based on a recently developed methodology involving a parameterization of all model validating uncertainty sets for a given linear fractional transformation (LFT) structure and noise allowance, a new software, Uncertainty Bound Identification (UBID) toolbox, which conveniently executes model validation tests and determine uncertainty bounds from data, has been designed and is currently available. This toolbox also serves to benchmark the current state-of-the-art in uncertainty bound determination and in turn facilitate benchmarking of robust control technology. To help clarify the methodology and use of the new software, two tutorial examples are provided. The first involves the uncertainty characterization of a flexible structure dynamics, and the second example involves a closed loop performance validation of a ducted fan based on an uncertainty bound from data. These examples, along with other simulation and experimental results, also help describe the many factors and assumptions that determine the degree of success in applying robust control theory to practical problems.

The Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT): An Open-source Tool for Efficient Fitting of Astrometric and Radial Velocity Data

NASA Astrophysics Data System (ADS)

Mede, Kyle; Brandt, Timothy D.

2017-03-01

We present the Exoplanet Simple Orbit Fitting Toolbox (ExoSOFT), a new, open-source suite to fit the orbital elements of planetary or stellar-mass companions to any combination of radial velocity and astrometric data. To explore the parameter space of Keplerian models, ExoSOFT may be operated with its own multistage sampling approach or interfaced with third-party tools such as emcee. In addition, ExoSOFT is packaged with a collection of post-processing tools to analyze and summarize the results. Although only a few systems have been observed with both radial velocity and direct imaging techniques, this number will increase, thanks to upcoming spacecraft and ground-based surveys. Providing both forms of data enables simultaneous fitting that can help break degeneracies in the orbital elements that arise when only one data type is available. The dynamical mass estimates this approach can produce are important when investigating the formation mechanisms and subsequent evolution of substellar companions. ExoSOFT was verified through fitting to artificial data and was implemented using the Python and Cython programming languages; it is available for public download at https://github.com/kylemede/ExoSOFT under GNU General Public License v3.

Class and Home Problems: Humidification, a True "Home" Problem for p. Chemical Engineer

ERIC Educational Resources Information Center

Condoret, Jean-Stephane

2012-01-01

The problem of maintaining hygrothermal comfort in a house is addressed using the chemical engineer's toolbox. A simple dynamic modelling proved to give a good description of the humidification of the house in winter, using a domestic humidifier. Parameters of the model were identified from a simple experiment. Surprising results, especially…

MatTAP: A MATLAB toolbox for the control and analysis of movement synchronisation experiments.

PubMed

Elliott, Mark T; Welchman, Andrew E; Wing, Alan M

2009-02-15

Investigating movement timing and synchronisation at the sub-second range relies on an experimental setup that has high temporal fidelity, is able to deliver output cues and can capture corresponding responses. Modern, multi-tasking operating systems make this increasingly challenging when using standard PC hardware and programming languages. This paper describes a new free suite of tools (available from http://www.snipurl.com/mattap) for use within the MATLAB programming environment, compatible with Microsoft Windows and a range of data acquisition hardware. The toolbox allows flexible generation of timing cues with high temporal accuracy, the capture and automatic storage of corresponding participant responses and an integrated analysis module for the rapid processing of results. A simple graphical user interface is used to navigate the toolbox and so can be operated easily by users not familiar with programming languages. However, it is also fully extensible and customisable, allowing adaptation for individual experiments and facilitating the addition of new modules in future releases. Here we discuss the relevance of the MatTAP (MATLAB Timing Analysis Package) toolbox to current timing experiments and compare its use to alternative methods. We validate the accuracy of the analysis module through comparison to manual observation methods and replicate a previous sensorimotor synchronisation experiment to demonstrate the versatility of the toolbox features demanded by such movement synchronisation paradigms.

Testing adaptive toolbox models: a Bayesian hierarchical approach.

PubMed

Scheibehenne, Benjamin; Rieskamp, Jörg; Wagenmakers, Eric-Jan

2013-01-01

Many theories of human cognition postulate that people are equipped with a repertoire of strategies to solve the tasks they face. This theoretical framework of a cognitive toolbox provides a plausible account of intra- and interindividual differences in human behavior. Unfortunately, it is often unclear how to rigorously test the toolbox framework. How can a toolbox model be quantitatively specified? How can the number of toolbox strategies be limited to prevent uncontrolled strategy sprawl? How can a toolbox model be formally tested against alternative theories? The authors show how these challenges can be met by using Bayesian inference techniques. By means of parameter recovery simulations and the analysis of empirical data across a variety of domains (i.e., judgment and decision making, children's cognitive development, function learning, and perceptual categorization), the authors illustrate how Bayesian inference techniques allow toolbox models to be quantitatively specified, strategy sprawl to be contained, and toolbox models to be rigorously tested against competing theories. The authors demonstrate that their approach applies at the individual level but can also be generalized to the group level with hierarchical Bayesian procedures. The suggested Bayesian inference techniques represent a theoretical and methodological advancement for toolbox theories of cognition and behavior.

Reliable fuzzy H∞ control for active suspension of in-wheel motor driven electric vehicles with dynamic damping

NASA Astrophysics Data System (ADS)

Shao, Xinxin; Naghdy, Fazel; Du, Haiping

2017-03-01

A fault-tolerant fuzzy H∞ control design approach for active suspension of in-wheel motor driven electric vehicles in the presence of sprung mass variation, actuator faults and control input constraints is proposed. The controller is designed based on the quarter-car active suspension model with a dynamic-damping-in-wheel-motor-driven-system, in which the suspended motor is operated as a dynamic absorber. The Takagi-Sugeno (T-S) fuzzy model is used to model this suspension with possible sprung mass variation. The parallel-distributed compensation (PDC) scheme is deployed to derive a fault-tolerant fuzzy controller for the T-S fuzzy suspension model. In order to reduce the motor wear caused by the dynamic force transmitted to the in-wheel motor, the dynamic force is taken as an additional controlled output besides the traditional optimization objectives such as sprung mass acceleration, suspension deflection and actuator saturation. The H∞ performance of the proposed controller is derived as linear matrix inequalities (LMIs) comprising three equality constraints which are solved efficiently by means of MATLAB LMI Toolbox. The proposed controller is applied to an electric vehicle suspension and its effectiveness is demonstrated through computer simulation.

Aerospace Toolbox--a flight vehicle design, analysis, simulation, and software development environment II: an in-depth overview

NASA Astrophysics Data System (ADS)

Christian, Paul M.

2002-07-01

This paper presents a demonstrated approach to significantly reduce the cost and schedule of non real-time modeling and simulation, real-time HWIL simulation, and embedded code development. The tool and the methodology presented capitalize on a paradigm that has become a standard operating procedure in the automotive industry. The tool described is known as the Aerospace Toolbox, and it is based on the MathWorks Matlab/Simulink framework, which is a COTS application. Extrapolation of automotive industry data and initial applications in the aerospace industry show that the use of the Aerospace Toolbox can make significant contributions in the quest by NASA and other government agencies to meet aggressive cost reduction goals in development programs. The part I of this paper provided a detailed description of the GUI based Aerospace Toolbox and how it is used in every step of a development program; from quick prototyping of concept developments that leverage built-in point of departure simulations through to detailed design, analysis, and testing. Some of the attributes addressed included its versatility in modeling 3 to 6 degrees of freedom, its library of flight test validated library of models (including physics, environments, hardware, and error sources), and its built-in Monte Carlo capability. Other topics that were covered in part I included flight vehicle models and algorithms, and the covariance analysis package, Navigation System Covariance Analysis Tools (NavSCAT). Part II of this series will cover a more in-depth look at the analysis and simulation capability and provide an update on the toolbox enhancements. It will also address how the Toolbox can be used as a design hub for Internet based collaborative engineering tools such as NASA's Intelligent Synthesis Environment (ISE) and Lockheed Martin's Interactive Missile Design Environment (IMD).

System/observer/controller identification toolbox

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan; Horta, Lucas G.; Phan, Minh

1992-01-01

System Identification is the process of constructing a mathematical model from input and output data for a system under testing, and characterizing the system uncertainties and measurement noises. The mathematical model structure can take various forms depending upon the intended use. The SYSTEM/OBSERVER/CONTROLLER IDENTIFICATION TOOLBOX (SOCIT) is a collection of functions, written in MATLAB language and expressed in M-files, that implements a variety of modern system identification techniques. For an open loop system, the central features of the SOCIT are functions for identification of a system model and its corresponding forward and backward observers directly from input and output data. The system and observers are represented by a discrete model. The identified model and observers may be used for controller design of linear systems as well as identification of modal parameters such as dampings, frequencies, and mode shapes. For a closed-loop system, an observer and its corresponding controller gain directly from input and output data.

Towards a Comprehensive Computational Simulation System for Turbomachinery

NASA Technical Reports Server (NTRS)

Shih, Ming-Hsin

1994-01-01

The objective of this work is to develop algorithms associated with a comprehensive computational simulation system for turbomachinery flow fields. This development is accomplished in a modular fashion. These modules includes grid generation, visualization, network, simulation, toolbox, and flow modules. An interactive grid generation module is customized to facilitate the grid generation process associated with complicated turbomachinery configurations. With its user-friendly graphical user interface, the user may interactively manipulate the default settings to obtain a quality grid within a fraction of time that is usually required for building a grid about the same geometry with a general-purpose grid generation code. Non-Uniform Rational B-Spline formulations are utilized in the algorithm to maintain geometry fidelity while redistributing grid points on the solid surfaces. Bezier curve formulation is used to allow interactive construction of inner boundaries. It is also utilized to allow interactive point distribution. Cascade surfaces are transformed from three-dimensional surfaces of revolution into two-dimensional parametric planes for easy manipulation. Such a transformation allows these manipulated plane grids to be mapped to surfaces of revolution by any generatrix definition. A sophisticated visualization module is developed to al-low visualization for both grid and flow solution, steady or unsteady. A network module is built to allow data transferring in the heterogeneous environment. A flow module is integrated into this system, using an existing turbomachinery flow code. A simulation module is developed to combine the network, flow, and visualization module to achieve near real-time flow simulation about turbomachinery geometries. A toolbox module is developed to support the overall task. A batch version of the grid generation module is developed to allow portability and has been extended to allow dynamic grid generation for pitch changing turbomachinery configurations. Various applications with different characteristics are presented to demonstrate the success of this system.

Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data

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

Pelt, Daniël M.; Gürsoy, Dogˇa; Palenstijn, Willem Jan

2016-04-28

The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it ismore » shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy's standard reconstruction method.« less

Integration of TomoPy and the ASTRA toolbox for advanced processing and reconstruction of tomographic synchrotron data

PubMed Central

Pelt, Daniël M.; Gürsoy, Doǧa; Palenstijn, Willem Jan; Sijbers, Jan; De Carlo, Francesco; Batenburg, Kees Joost

2016-01-01

The processing of tomographic synchrotron data requires advanced and efficient software to be able to produce accurate results in reasonable time. In this paper, the integration of two software toolboxes, TomoPy and the ASTRA toolbox, which, together, provide a powerful framework for processing tomographic data, is presented. The integration combines the advantages of both toolboxes, such as the user-friendliness and CPU-efficient methods of TomoPy and the flexibility and optimized GPU-based reconstruction methods of the ASTRA toolbox. It is shown that both toolboxes can be easily installed and used together, requiring only minor changes to existing TomoPy scripts. Furthermore, it is shown that the efficient GPU-based reconstruction methods of the ASTRA toolbox can significantly decrease the time needed to reconstruct large datasets, and that advanced reconstruction methods can improve reconstruction quality compared with TomoPy’s standard reconstruction method. PMID:27140167

Arc_Mat: a Matlab-based spatial data analysis toolbox

NASA Astrophysics Data System (ADS)

Liu, Xingjian; Lesage, James

2010-03-01

This article presents an overview of Arc_Mat, a Matlab-based spatial data analysis software package whose source code has been placed in the public domain. An earlier version of the Arc_Mat toolbox was developed to extract map polygon and database information from ESRI shapefiles and provide high quality mapping in the Matlab software environment. We discuss revisions to the toolbox that: utilize enhanced computing and graphing capabilities of more recent versions of Matlab, restructure the toolbox with object-oriented programming features, and provide more comprehensive functions for spatial data analysis. The Arc_Mat toolbox functionality includes basic choropleth mapping; exploratory spatial data analysis that provides exploratory views of spatial data through various graphs, for example, histogram, Moran scatterplot, three-dimensional scatterplot, density distribution plot, and parallel coordinate plots; and more formal spatial data modeling that draws on the extensive Spatial Econometrics Toolbox functions. A brief review of the design aspects of the revised Arc_Mat is described, and we provide some illustrative examples that highlight representative uses of the toolbox. Finally, we discuss programming with and customizing the Arc_Mat toolbox functionalities.

ESA's Multi-mission Sentinel-1 Toolbox

NASA Astrophysics Data System (ADS)

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 exploitation of polarimetric data including speckle filters, decompositions, and classifiers. The Toolbox will also include tools for large data stacks, supervised and unsupervised classification, improved vector handling and change detection. Architectural improvements such as smart memory configuration, task queuing, and optimizations for complex data will provide better support and performance for very large products and stacks.In addition, a Cloud Exploitation Platform Extension (CEP) has been developed to add the capability to smoothly utilize a cloud computing platform where EO data repositories and high performance processing capabilities are available. The extension to the SENTINEL Application Platform would facilitate entry into cloud processing services for supporting bulk processing on high performance clusters. Since December 2016, the COMET-LiCS InSAR portal (http://comet.nerc.ac.uk/COMET-LiCS-portal/) has been live, delivering interferograms and coherence estimates over the entire Alpine-Himalayan belt. The portal already contains tens of thousands of products, which can be browsed in a user-friendly portal, and downloaded for free by the general public. For our processing, we use the facilities at the Climate and Environmental Monitoring from Space (CEMS). Here we have large storage and processing facilities to our disposal, and a complete duplicate of the Sentinel-1 archive is maintained. This greatly simplifies the infrastructure we had to develop for automated processing of large areas. Here we will give an overview of the current status of the processing system, as well as discuss future plans. We will cover the infrastructure we developed to automatically produce interferograms and its challenges, and the processing strategy for time series analysis. We will outline the objectives of the system in the near and distant future, and a roadmap for its continued development. Finally, we will highlight some of the scientific results and projects linked to the system.

The CatchMod toolbox: easy and guided access to ICT tools for Water Framework Directive implementation.

PubMed

van Griensven, A; Vanrolleghem, P A

2006-01-01

Web-based toolboxes are handy tools to inform experienced users of existing software in their disciplines. However, for the implementation of the Water Framework Directive, a much more diverse public (water managers, consultancy firms, scientists, etc.) will ask for a very wide diversity of Information and Communication Technology (ICT) tools. It is obvious that the users of a web-based ICT-toolbox providing all this will not be experts in all of the disciplines and that a toolbox for ICT tools for Water Framework Directive implementation should thus go beyond just making interesting web-links. To deal with this issue, expert knowledge is brought to the users through the incorporation of visitor-geared guidance (materials) in the Harmoni-CA toolbox. Small workshops of expert teams were organized to deliver documents explaining why the tools are important, when they are required and what activity they support/perform, as well as a categorization of the multitude of available tools. An integration of this information in the web-based toolbox helps the users to browse through a toolbox containing tools, reports, guidance documents and interesting links. The Harmoni-CA toolbox thus provides not only a virtual toolbox, but incorporates a virtual expert as well.

Evol and ProDy for bridging protein sequence evolution and structural dynamics.

PubMed

Bakan, Ahmet; Dutta, Anindita; Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R; Bahar, Ivet

2014-09-15

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

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

USGS Publications Warehouse

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.

Genetic and Genomic Toolbox of Zea mays

PubMed Central

Nannas, Natalie J.; Dawe, R. Kelly

2015-01-01

Maize has a long history of genetic and genomic tool development and is considered one of the most accessible higher plant systems. With a fully sequenced genome, a suite of cytogenetic tools, methods for both forward and reverse genetics, and characterized phenotype markers, maize is amenable to studying questions beyond plant biology. Major discoveries in the areas of transposons, imprinting, and chromosome biology came from work in maize. Moving forward in the post-genomic era, this classic model system will continue to be at the forefront of basic biological study. In this review, we outline the basics of working with maize and describe its rich genetic toolbox. PMID:25740912

A part toolbox to tune genetic expression in Bacillus subtilis

PubMed Central

Guiziou, Sarah; Sauveplane, Vincent; Chang, Hung-Ju; Clerté, Caroline; Declerck, Nathalie; Jules, Matthieu; Bonnet, Jerome

2016-01-01

Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli, such libraries are lacking for the Gram-positive model Bacillus subtilis, a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis. We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ∼14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis. PMID:27402159

GridPV Toolbox

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

Broderick, Robert; Quiroz, Jimmy; Grijalva, Santiago

2014-07-15

Matlab Toolbox for simulating the impact of solar energy on the distribution grid. The majority of the functions are useful for interfacing OpenDSS and MATLAB, and they are of generic use for commanding OpenDSS from MATLAB and retrieving GridPV Toolbox information from simulations. A set of functions is also included for modeling PV plant output and setting up the PV plant in the OpenDSS simulation. The toolbox contains functions for modeling the OpenDSS distribution feeder on satellite images with GPS coordinates. Finally, example simulations functions are included to show potential uses of the toolbox functions.

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

NASA Astrophysics Data System (ADS)

Ozkaya, Sait I.

2018-03-01

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

Modular-based multiscale modeling on viscoelasticity of polymer nanocomposites

NASA Astrophysics Data System (ADS)

Li, Ying; Liu, Zeliang; Jia, Zheng; Liu, Wing Kam; Aldousari, Saad M.; Hedia, Hassan S.; Asiri, Saeed A.

2017-02-01

Polymer nanocomposites have been envisioned as advanced materials for improving the mechanical performance of neat polymers used in aerospace, petrochemical, environment and energy industries. With the filler size approaching the nanoscale, composite materials tend to demonstrate remarkable thermomechanical properties, even with addition of a small amount of fillers. These observations confront the classical composite theories and are usually attributed to the high surface-area-to-volume-ratio of the fillers, which can introduce strong nanoscale interfacial effect and relevant long-range perturbation on polymer chain dynamics. Despite decades of research aimed at understanding interfacial effect and improving the mechanical performance of composite materials, it is not currently possible to accurately predict the mechanical properties of polymer nanocomposites directly from their molecular constituents. To overcome this challenge, different theoretical, experimental and computational schemes will be used to uncover the key physical mechanisms at the relevant spatial and temporal scales for predicting and tuning constitutive behaviors in silico, thereby establishing a bottom-up virtual design principle to achieve unprecedented mechanical performance of nanocomposites. A modular-based multiscale modeling approach for viscoelasticity of polymer nanocomposites has been proposed and discussed in this study, including four modules: (A) neat polymer toolbox; (B) interphase toolbox; (C) microstructural toolbox and (D) homogenization toolbox. Integrating these modules together, macroscopic viscoelasticity of polymer nanocomposites could be directly predicted from their molecular constituents. This will maximize the computational ability to design novel polymer composites with advanced performance. More importantly, elucidating the viscoelasticity of polymer nanocomposites through fundamental studies is a critical step to generate an integrated computational material engineering principle for discovering and manufacturing new composites with transformative impact on aerospace, automobile, petrochemical industries.

UQTools: The Uncertainty Quantification Toolbox - Introduction and Tutorial

NASA Technical Reports Server (NTRS)

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

2012-01-01

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

A toolbox for determining subdiffusive mechanisms

NASA Astrophysics Data System (ADS)

Meroz, Yasmine; Sokolov, Igor M.

2015-04-01

Subdiffusive processes have become a field of great interest in the last decades, due to amounting experimental evidence of subdiffusive behavior in complex systems, and especially in biological systems. Different physical scenarios leading to subdiffusion differ in the details of the dynamics. These differences are what allow to theoretically reconstruct the underlying physics from the results of observations, and will be the topic of this review. We review the main statistical analyses available today to distinguish between these scenarios, categorizing them according to the relevant characteristics. We collect the available tools and statistical tests, presenting them within a broader perspective. We also consider possible complications such as the subordination of subdiffusive mechanisms. Due to the advances in single particle tracking experiments in recent years, we focus on the relevant case of where the available experimental data is scant, at the level of single trajectories.

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

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

Brown, K.G.; Kosson, D.S.; Garrabrants, A.C.

2013-07-01

The Cementitious Barriers Partnership (CBP) Project is a multi-disciplinary, multi-institutional collaboration supported by the Office of Tank Waste Management within the Office of Environmental Management of U.S. Department of Energy (US DOE). The CBP program has developed a set of integrated tools (based on state-of-the-art models and leaching test methods) that improve understanding and predictions of the long-term hydraulic and chemical performance of cementitious barriers used in nuclear applications. Tools selected for and developed under this program are intended to evaluate and predict the behavior of cementitious barriers used in near-surface engineered waste disposal systems for periods of performance upmore » to or longer than 100 years for operating facilities and longer than 1,000 years for waste management purposes. CBP software tools were made available to selected DOE Office of Environmental Management and field site users for training and evaluation based on a set of important degradation scenarios, including sulfate ingress/attack and carbonation of cementitious materials. The tools were presented at two-day training workshops held at U.S. National Institute of Standards and Technology (NIST), Savannah River, and Hanford included LeachXS{sup TM}/ORCHESTRA, STADIUM{sup R}, and a CBP-developed GoldSim Dashboard interface. Collectively, these components form the CBP Software Toolbox. The new U.S. Environmental Protection Agency leaching test methods based on the Leaching Environmental Assessment Framework (LEAF) were also presented. The CBP Dashboard uses a custom Dynamic-link library developed by CBP to couple to the LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} codes to simulate reactive transport and degradation in cementitious materials for selected performance assessment scenarios. The first day of the workshop introduced participants to the software components via presentation materials, and the second day included hands-on tutorial exercises followed by discussions of enhancements desired by participants. Tools were revised based on feedback obtained during the workshops held from April through June 2012. The resulting improved CBP Software Toolbox, including evaluation versions of and LeachXS{sup TM}/ORCHESTRA and STADIUM{sup R} has been made available to workshop and selected other participants for further assessment. Inquiries about future workshops and requests for access to the Toolbox software can be made via the CBP web site [1]. (authors)« less

The first object oriented monitor for intravenous anesthesia.

PubMed

Cantraine, F R; Coussaert, E J

2000-01-01

To describe the design and implementation of "INFUSION TOOLBOX," a software tool to control and monitor multiple intravenous drug infusions simultaneously using pharmacokinetic and pharmacodynamic principles. INFUSION TOOLBOX has been designed to present a graphical interface. Object Oriented design was used and the software was implemented using Smalltalk, to run on a PC. Basic tools are available to manage patient, drugs, pumps and reports. These tools are the PatientPanel, the DrugPanel, the PumpPanel and the HistoryPanel. The screen is built dynamically. The panels may be collapsed or closed to avoid a crowded display. We also built control panels such as the Target ControlPanel which calculates the best infusion sequence to bring the drug concentration in the plasma compartment to a preset value. Before drug delivery, the user enters the patient's data, selects a drug, enters its dilution factor and chooses a pharmacokinetic model. The calculated plasma concentration is continually displayed and updated. The anesthetist may ask for the history of the delivery to obtain a graphic report or to add events to the logbook. A panel targeting the effect is used when a pharmacodynamic model is known. Data files for drugs, pumps and surgery are upgradable. By creating a resizeable ControlPanel we enable the anesthetist to display the information he wishes, when he wishes it. The available panels are diverse enough to meet the anesthetist needs; they may be adapted to the drug used, pumps used and surgery. It is the anesthetist who builds dynamically its different control screens. By adopting an evolutionary solution model we have achieved considerable success in building our drug delivery monitor. In addition we have gained valuable insight into the anesthesia information domain that will allow us to further enhance and expand the system.

Towards a Web-Enabled Geovisualization and Analytics Platform for the Energy and Water Nexus

NASA Astrophysics Data System (ADS)

Sanyal, J.; Chandola, V.; Sorokine, A.; Allen, M.; Berres, A.; Pang, H.; Karthik, R.; Nugent, P.; McManamay, R.; Stewart, R.; Bhaduri, B. L.

2017-12-01

Interactive data analytics are playing an increasingly vital role in the generation of new, critical insights regarding the complex dynamics of the energy/water nexus (EWN) and its interactions with climate variability and change. Integration of impacts, adaptation, and vulnerability (IAV) science with emerging, and increasingly critical, data science capabilities offers a promising potential to meet the needs of the EWN community. To enable the exploration of pertinent research questions, a web-based geospatial visualization platform is being built that integrates a data analysis toolbox with advanced data fusion and data visualization capabilities to create a knowledge discovery framework for the EWN. The system, when fully built out, will offer several geospatial visualization capabilities including statistical visual analytics, clustering, principal-component analysis, dynamic time warping, support uncertainty visualization and the exploration of data provenance, as well as support machine learning discoveries to render diverse types of geospatial data and facilitate interactive analysis. Key components in the system architecture includes NASA's WebWorldWind, the Globus toolkit, postgresql, as well as other custom built software modules.

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

PubMed

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.

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

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

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.

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

PubMed

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.

SacLab: A toolbox for saccade analysis to increase usability of eye tracking systems in clinical ophthalmology practice.

PubMed

Cercenelli, Laura; Tiberi, Guido; Corazza, Ivan; Giannaccare, Giuseppe; Fresina, Michela; Marcelli, Emanuela

2017-01-01

Many open source software packages have been recently developed to expand the usability of eye tracking systems to study oculomotor behavior, but none of these is specifically designed to encompass all the main functions required for creating eye tracking tests and for providing the automatic analysis of saccadic eye movements. The aim of this study is to introduce SacLab, an intuitive, freely-available MATLAB toolbox based on Graphical User Interfaces (GUIs) that we have developed to increase the usability of the ViewPoint EyeTracker (Arrington Research, Scottsdale, AZ, USA) in clinical ophthalmology practice. SacLab consists of four processing modules that enable the user to easily create visual stimuli tests (Test Designer), record saccadic eye movements (Data Recorder), analyze the recorded data to automatically extract saccadic parameters of clinical interest (Data Analyzer) and provide an aggregate analysis from multiple eye movements recordings (Saccade Analyzer), without requiring any programming effort by the user. A demo application of SacLab to carry out eye tracking tests for the analysis of horizontal saccades was reported. We tested the usability of SacLab toolbox with three ophthalmologists who had no programming experience; the ophthalmologists were briefly trained in the use of SacLab GUIs and were asked to perform the demo application. The toolbox gained an enthusiastic feedback from all the clinicians in terms of intuitiveness, ease of use and flexibility. Test creation and data processing were accomplished in 52±21s and 46±19s, respectively, using the SacLab GUIs. SacLab may represent a useful tool to ease the application of the ViewPoint EyeTracker system in clinical routine in ophthalmology. Copyright © 2016 Elsevier Ltd. All rights reserved.

MASER: A Tool Box for Solar System Low Frequency Radio Astronomy

NASA Astrophysics Data System (ADS)

Cecconi, B.; Le Sidaner, P.; Savalle, R.; Bonnin, X.; Zarka, P.; Louis, C.; Coffre, A.; Lamy, L.; Denis, L.; Griessmeier, J.-M.; Faden, J.; Piker, C.; André, N.; Génot, V.; Erard, S.; King, T. A.; Mafi, J. N.; Sharlow, M.; Sky, J.; Demleitner, M.

2018-04-01

MASER (Measuring, Analysing, and Simulating Radio Emissions) is a toolbox for solar system radio astronomy. It provides tools for reading, displaying, finding, and modeling low frequency radio datasets.

Speed management toolbox for rural communities.

DOT National Transportation Integrated Search

2013-04-01

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

Why Heuristics Work.

PubMed

Gigerenzer, Gerd

2008-01-01

The adaptive toolbox is a Darwinian-inspired theory that conceives of the mind as a modular system that is composed of heuristics, their building blocks, and evolved capacities. The study of the adaptive toolbox is descriptive and analyzes the selection and structure of heuristics in social and physical environments. The study of ecological rationality is prescriptive and identifies the structure of environments in which specific heuristics either succeed or fail. Results have been used for designing heuristics and environments to improve professional decision making in the real world. © 2008 Association for Psychological Science.

Aerospace Toolbox---a flight vehicle design, analysis, simulation ,and software development environment: I. An introduction and tutorial

NASA Astrophysics Data System (ADS)

Christian, Paul M.; Wells, Randy

2001-09-01

This paper presents a demonstrated approach to significantly reduce the cost and schedule of non real-time modeling and simulation, real-time HWIL simulation, and embedded code development. The tool and the methodology presented capitalize on a paradigm that has become a standard operating procedure in the automotive industry. The tool described is known as the Aerospace Toolbox, and it is based on the MathWorks Matlab/Simulink framework, which is a COTS application. Extrapolation of automotive industry data and initial applications in the aerospace industry show that the use of the Aerospace Toolbox can make significant contributions in the quest by NASA and other government agencies to meet aggressive cost reduction goals in development programs. The part I of this paper provides a detailed description of the GUI based Aerospace Toolbox and how it is used in every step of a development program; from quick prototyping of concept developments that leverage built-in point of departure simulations through to detailed design, analysis, and testing. Some of the attributes addressed include its versatility in modeling 3 to 6 degrees of freedom, its library of flight test validated library of models (including physics, environments, hardware, and error sources), and its built-in Monte Carlo capability. Other topics to be covered in this part include flight vehicle models and algorithms, and the covariance analysis package, Navigation System Covariance Analysis Tools (NavSCAT). Part II of this paper, to be published at a later date, will conclude with a description of how the Aerospace Toolbox is an integral part of developing embedded code directly from the simulation models by using the Mathworks Real Time Workshop and optimization tools. It will also address how the Toolbox can be used as a design hub for Internet based collaborative engineering tools such as NASA's Intelligent Synthesis Environment (ISE) and Lockheed Martin's Interactive Missile Design Environment (IMD).

An adaptable, low cost test-bed for unmanned vehicle systems research

NASA Astrophysics Data System (ADS)

Goppert, James M.

2011-12-01

An unmanned vehicle systems test-bed has been developed. The test-bed has been designed to accommodate hardware changes and various vehicle types and algorithms. The creation of this test-bed allows research teams to focus on algorithm development and employ a common well-tested experimental framework. The ArduPilotOne autopilot was developed to provide the necessary level of abstraction for multiple vehicle types. The autopilot was also designed to be highly integrated with the Mavlink protocol for Micro Air Vehicle (MAV) communication. Mavlink is the native protocol for QGroundControl, a MAV ground control program. Features were added to QGroundControl to accommodate outdoor usage. Next, the Mavsim toolbox was developed for Scicoslab to allow hardware-in-the-loop testing, control design and analysis, and estimation algorithm testing and verification. In order to obtain linear models of aircraft dynamics, the JSBSim flight dynamics engine was extended to use a probabilistic Nelder-Mead simplex method. The JSBSim aircraft dynamics were compared with wind-tunnel data collected. Finally, a structured methodology for successive loop closure control design is proposed. This methodology is demonstrated along with the rest of the test-bed tools on a quadrotor, a fixed wing RC plane, and a ground vehicle. Test results for the ground vehicle are presented.

MTpy: A Python toolbox for magnetotellurics

NASA Astrophysics Data System (ADS)

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.

Vectorized data acquisition and fast triple-correlation integrals for Fluorescence Triple Correlation Spectroscopy

PubMed Central

Ridgeway, William K; Millar, David P; Williamson, James R

2013-01-01

Fluorescence Correlation Spectroscopy (FCS) is widely used to quantitate reaction rates and concentrations of molecules in vitro and in vivo. We recently reported Fluorescence Triple Correlation Spectroscopy (F3CS), which correlates three signals together instead of two. F3CS can analyze the stoichiometries of complex mixtures and detect irreversible processes by identifying time-reversal asymmetries. Here we report the computational developments that were required for the realization of F3CS and present the results as the Triple Correlation Toolbox suite of programs. Triple Correlation Toolbox is a complete data analysis pipeline capable of acquiring, correlating and fitting large data sets. Each segment of the pipeline handles error estimates for accurate error-weighted global fitting. Data acquisition was accelerated with a combination of off-the-shelf counter-timer chips and vectorized operations on 128-bit registers. This allows desktop computers with inexpensive data acquisition cards to acquire hours of multiple-channel data with sub-microsecond time resolution. Off-line correlation integrals were implemented as a two delay time multiple-tau scheme that scales efficiently with multiple processors and provides an unprecedented view of linked dynamics. Global fitting routines are provided to fit FCS and F3CS data to models containing up to ten species. Triple Correlation Toolbox is a complete package that enables F3CS to be performed on existing microscopes. PMID:23525193

Report on the Current Inventory of the Toolbox for Plant Cell Wall Analysis: Proteinaceous and Small Molecular Probes

PubMed Central

Rydahl, Maja G.; Hansen, Aleksander R.; Kračun, Stjepan K.; Mravec, Jozef

2018-01-01

Plant cell walls are highly complex structures composed of diverse classes of polysaccharides, proteoglycans, and polyphenolics, which have numerous roles throughout the life of a plant. Significant research efforts aim to understand the biology of this cellular organelle and to facilitate cell-wall-based industrial applications. To accomplish this, researchers need to be provided with a variety of sensitive and specific detection methods for separate cell wall components, and their various molecular characteristics in vitro as well as in situ. Cell wall component-directed molecular detection probes (in short: cell wall probes, CWPs) are an essential asset to the plant glycobiology toolbox. To date, a relatively large set of CWPs has been produced—mainly consisting of monoclonal antibodies, carbohydrate-binding modules, synthetic antibodies produced by phage display, and small molecular probes. In this review, we summarize the state-of-the-art knowledge about these CWPs; their classification and their advantages and disadvantages in different applications. In particular, we elaborate on the recent advances in non-conventional approaches to the generation of novel CWPs, and identify the remaining gaps in terms of target recognition. This report also highlights the addition of new “compartments” to the probing toolbox, which is filled with novel chemical biology tools, such as metabolic labeling reagents and oligosaccharide conjugates. In the end, we also forecast future developments in this dynamic field. PMID:29774041

The ROC Toolbox: A toolbox for analyzing receiver-operating characteristics derived from confidence ratings.

PubMed

Koen, Joshua D; Barrett, Frederick S; Harlow, Iain M; Yonelinas, Andrew P

2017-08-01

Signal-detection theory, and the analysis of receiver-operating characteristics (ROCs), has played a critical role in the development of theories of episodic memory and perception. The purpose of the current paper is to present the ROC Toolbox. This toolbox is a set of functions written in the Matlab programming language that can be used to fit various common signal detection models to ROC data obtained from confidence rating experiments. The goals for developing the ROC Toolbox were to create a tool (1) that is easy to use and easy for researchers to implement with their own data, (2) that can flexibly define models based on varying study parameters, such as the number of response options (e.g., confidence ratings) and experimental conditions, and (3) that provides optimal routines (e.g., Maximum Likelihood estimation) to obtain parameter estimates and numerous goodness-of-fit measures.The ROC toolbox allows for various different confidence scales and currently includes the models commonly used in recognition memory and perception: (1) the unequal variance signal detection (UVSD) model, (2) the dual process signal detection (DPSD) model, and (3) the mixture signal detection (MSD) model. For each model fit to a given data set the ROC toolbox plots summary information about the best fitting model parameters and various goodness-of-fit measures. Here, we present an overview of the ROC Toolbox, illustrate how it can be used to input and analyse real data, and finish with a brief discussion on features that can be added to the toolbox.

What precision-protein-tuning and nano-resolved single molecule sciences can do for each other.

PubMed

Milles, Sigrid; Lemke, Edward A

2013-01-01

While innovations in modern microscopy, spectroscopy, and nanoscopy techniques have made single molecule observation a standard in many laboratories, the actual design of meaningful fluorescence reporter systems now hinders major scientific breakthroughs. Even though the field of chemical biology is supercharging the fluorescence toolbox, surprisingly few strategies exist that make the transition from model systems to biologically relevant applications. At the same time, the number of microscopy techniques is growing dramatically. We explain our view on how the impact of modern technologies is influenced not only by further hard- and software developments, but also by the availability and suitability of protein-engineering tools. We identify how the largely independent research fields of chemical biology and fluorescence nanoscopy can influence each other to synergistically drive future technology that can visualize the localization, structure, and dynamics of molecular function without constraints. Copyright © 2013 WILEY Periodicals, Inc.

Time reversal and charge conjugation in an embedding quantum simulator.

PubMed

Zhang, Xiang; Shen, Yangchao; Zhang, Junhua; Casanova, Jorge; Lamata, Lucas; Solano, Enrique; Yung, Man-Hong; Zhang, Jing-Ning; Kim, Kihwan

2015-08-04

A quantum simulator is an important device that may soon outperform current classical computations. A basic arithmetic operation, the complex conjugate, however, is considered to be impossible to be implemented in such a quantum system due to the linear character of quantum mechanics. Here, we present the experimental quantum simulation of such an unphysical operation beyond the regime of unitary and dissipative evolutions through the embedding of a quantum dynamics in the electronic multilevels of a (171)Yb(+) ion. We perform time reversal and charge conjugation, which are paradigmatic examples of antiunitary symmetry operators, in the evolution of a Majorana equation without the tomographic knowledge of the evolving state. Thus, these operations can be applied regardless of the system size. Our approach offers the possibility to add unphysical operations to the toolbox of quantum simulation, and provides a route to efficiently compute otherwise intractable quantities, such as entanglement monotones.

Time reversal and charge conjugation in an embedding quantum simulator

PubMed Central

Zhang, Xiang; Shen, Yangchao; Zhang, Junhua; Casanova, Jorge; Lamata, Lucas; Solano, Enrique; Yung, Man-Hong; Zhang, Jing-Ning; Kim, Kihwan

2015-01-01

A quantum simulator is an important device that may soon outperform current classical computations. A basic arithmetic operation, the complex conjugate, however, is considered to be impossible to be implemented in such a quantum system due to the linear character of quantum mechanics. Here, we present the experimental quantum simulation of such an unphysical operation beyond the regime of unitary and dissipative evolutions through the embedding of a quantum dynamics in the electronic multilevels of a 171Yb+ ion. We perform time reversal and charge conjugation, which are paradigmatic examples of antiunitary symmetry operators, in the evolution of a Majorana equation without the tomographic knowledge of the evolving state. Thus, these operations can be applied regardless of the system size. Our approach offers the possibility to add unphysical operations to the toolbox of quantum simulation, and provides a route to efficiently compute otherwise intractable quantities, such as entanglement monotones. PMID:26239028

Quantifying multiple telecouplings using an integrated suite of spatially-explicit tools

NASA Astrophysics Data System (ADS)

Tonini, F.; Liu, J.

2016-12-01

Telecoupling is an interdisciplinary research umbrella concept that enables natural and social scientists to understand and generate information for managing how humans and nature can sustainably coexist worldwide. To systematically study telecoupling, it is essential to build a comprehensive set of spatially-explicit tools for describing and quantifying multiple reciprocal socioeconomic and environmental interactions between a focal area and other areas. Here we introduce the Telecoupling Toolbox, a new free and open-source set of tools developed to map and identify the five major interrelated components of the telecoupling framework: systems, flows, agents, causes, and effects. The modular design of the toolbox allows the integration of existing tools and software (e.g. InVEST) to assess synergies and tradeoffs associated with policies and other local to global interventions. We show applications of the toolbox using a number of representative studies that address a variety of scientific and management issues related to telecouplings throughout the world. The results suggest that the toolbox can thoroughly map and quantify multiple telecouplings under various contexts while providing users with an easy-to-use interface. It provides a powerful platform to address globally important issues, such as land use and land cover change, species invasion, migration, flows of ecosystem services, and international trade of goods and products.

A web-based tool for ranking landslide mitigation measures

NASA Astrophysics Data System (ADS)

Lacasse, S.; Vaciago, G.; Choi, Y. J.; Kalsnes, B.

2012-04-01

As part of the research done in the European project SafeLand "Living with landslide risk in Europe: Assessment, effects of global change, and risk management strategies", a compendium of structural and non-structural mitigation measures for different landslide types in Europe was prepared, and the measures were assembled into a web-based "toolbox". Emphasis was placed on providing a rational and flexible framework applicable to existing and future mitigation measures. The purpose of web-based toolbox is to assist decision-making and to guide the user in the choice of the most appropriate mitigation measures. The mitigation measures were classified into three categories, describing whether the mitigation measures addressed the landslide hazard, the vulnerability or the elements at risk themselves. The measures considered include structural measures reducing hazard and non-structural mitigation measures, reducing either the hazard or the consequences (or vulnerability and exposure of elements at risk). The structural measures include surface protection and control of surface erosion; measures modifying the slope geometry and/or mass distribution; measures modifying surface water regime - surface drainage; measures mo¬difying groundwater regime - deep drainage; measured modifying the mechanical charac¬teristics of unstable mass; transfer of loads to more competent strata; retaining structures (to modify slope geometry and/or to transfer stress to compe¬tent layer); deviating the path of landslide debris; dissipating the energy of debris flows; and arresting and containing landslide debris or rock fall. The non-structural mitigation measures, reducing either the hazard or the consequences: early warning systems; restricting or discouraging construction activities; increasing resistance or coping capacity of elements at risk; relocation of elements at risk; sharing of risk through insurance. The measures are described in the toolbox with fact sheets providing a brief description, guidance on design, schematic details, practical examples and references for each mitigation measure. Each of the measures was given a score on its ability and applicability for different types of landslides and boundary conditions, and a decision support matrix was established. The web-based toolbox organizes the information in the compendium and provides an algorithm to rank the measures on the basis of the decision support matrix, and on the basis of the risk level estimated at the site. The toolbox includes a description of the case under study and offers a simplified option for estimating the hazard and risk levels of the slide at hand. The user selects the mitigation measures to be included in the assessment. The toolbox then ranks, with built-in assessment factors and weights and/or with user-defined ranking values and criteria, the mitigation measures included in the analysis. The toolbox includes data management, e.g. saving data half-way in an analysis, returning to an earlier case, looking up prepared examples or looking up information on mitigation measures. The toolbox also generates a report and has user-forum and help features. The presentation will give an overview of the mitigation measures considered and examples of the use of the toolbox, and will take the attendees through the application of the toolbox.

WEC Design Response Toolbox v. 1.0

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

Coe, Ryan; Michelen, Carlos; Eckert-Gallup, Aubrey

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.

Screening and assessment of chronic pain among children with cerebral palsy: a process evaluation of a pain toolbox.

PubMed

Orava, Taryn; Provvidenza, Christine; Townley, Ashleigh; Kingsnorth, Shauna

2018-06-08

Though high numbers of children with cerebral palsy experience chronic pain, it remains under-recognized. This paper describes an evaluation of implementation supports and adoption of the Chronic Pain Assessment Toolbox for Children with Disabilities (the Toolbox) to enhance pain screening and assessment practices within a pediatric rehabilitation and complex continuing care hospital. A multicomponent knowledge translation strategy facilitated Toolbox adoption, inclusive of a clinical practice guideline, cerebral palsy practice points and assessment tools. Across the hospital, seven ambulatory care clinics with cerebral palsy caseloads participated in a staggered roll-out (Group 1: exclusive CP caseloads, March-December; Group 2: mixed diagnostic caseloads, August-December). Evaluation measures included client electronic medical record audit, document review and healthcare provider survey and interviews. A significant change in documentation of pain screening and assessment practice from pre-Toolbox (<2%) to post-Toolbox adoption (53%) was found. Uptake in Group 2 clinics lagged behind Group 1. Opportunities to use the Toolbox consistently (based on diagnostic caseload) and frequently (based on client appointments) were noted among contextual factors identified. Overall, the Toolbox was positively received and clinically useful. Findings affirm that the Toolbox, in conjunction with the application of integrated knowledge translation principles and an established knowledge translation framework, has potential to be a useful resource to enrich and standardize chronic pain screening and assessment practices among children with cerebral palsy. Implications for Rehabilitation It is important to engage healthcare providers in the conceptualization, development, implementation and evaluation of a knowledge-to-action best practice product. The Chronic Pain Toolbox for Children with Disabilities provides rehabilitation staff with guidance on pain screening and assessment best practice and offers a range of validated tools that can be incorporated in ambulatory clinic settings to meet varied client needs. Considering unique clinical contexts (i.e., opportunities for use, provider engagement, staffing absences/turnover) is required to optimize and sustain chronic pain screening and assessment practices in rehabilitation outpatient settings.

6 DOF Nonlinear AUV Simulation Toolbox

DTIC Science & Technology

1997-01-01

is to supply a flexible 3D -simulation platform for motion visualization, in-lab debugging and testing of mission-specific strategies as well as those...Explorer are modular designed [Smith] in order to cut time and cost for vehicle recontlguration. A flexible 3D -simulation platform is desired to... 3D models. Current implemented modules include a nonlinear dynamic model for the OEX, shared memory and semaphore manager tools, shared memory monitor

PFA toolbox: a MATLAB tool for Metabolic Flux Analysis.

PubMed

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.

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

Krishnamurthy, Dheepak

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

Simplifying the complexity of a coupled carbon turnover and pesticide degradation model

NASA Astrophysics Data System (ADS)

Marschmann, Gianna; Erhardt, André H.; Pagel, Holger; Kügler, Philipp; Streck, Thilo

2016-04-01

The mechanistic one-dimensional model PECCAD (PEsticide degradation Coupled to CArbon turnover in the Detritusphere; Pagel et al. 2014, Biogeochemistry 117, 185-204) has been developed as a tool to elucidate regulation mechanisms of pesticide degradation in soil. A feature of this model is that it integrates functional traits of microorganisms, identifiable by molecular tools, and physicochemical processes such as transport and sorption that control substrate availability. Predicting the behavior of microbially active interfaces demands a fundamental understanding of factors controlling their dynamics. Concepts from dynamical systems theory allow us to study general properties of the model such as its qualitative behavior, intrinsic timescales and dynamic stability: Using a Latin hypercube method we sampled the parameter space for physically realistic steady states of the PECCAD ODE system and set up a numerical continuation and bifurcation problem with the open-source toolbox MatCont in order to obtain a complete classification of the dynamical system's behaviour. Bifurcation analysis reveals an equilibrium state of the system entirely controlled by fungal kinetic parameters. The equilibrium is generally unstable in response to small perturbations except for a small band in parameter space where the pesticide pool is stable. Time scale separation is a phenomenon that occurs in almost every complex open physical system. Motivated by the notion of "initial-stage" and "late-stage" decomposers and the concept of r-, K- or L-selected microbial life strategies, we test the applicability of geometric singular perturbation theory to identify fast and slow time scales of PECCAD. Revealing a generic fast-slow structure would greatly simplify the analysis of complex models of organic matter turnover by reducing the number of unknowns and parameters and providing a systematic mathematical framework for studying their properties.

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

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

Smith, F.

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 amore » basis for further development of the CBP Toolbox.« less

A Toolbox of Metrology-Based Techniques for Optical System Alignment

NASA Technical Reports Server (NTRS)

Coulter, Phillip; Ohl, Raymond G.; Blake, Peter N.; Bos, Brent J.; Casto, Gordon V.; Eichhorn, William L.; Gum, Jeffrey S.; Hadjimichael, Theodore J.; Hagopian, John G.; Hayden, Joseph E.;

A Toolbox of Metrology-Based Techniques for Optical System Alignment

NASA Technical Reports Server (NTRS)

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.;

Improving Cognitive Skills of the Industrial Robot

NASA Astrophysics Data System (ADS)

Bezák, Pavol

2015-08-01

At present, there are plenty of industrial robots that are programmed to do the same repetitive task all the time. Industrial robots doing such kind of job are not able to understand whether the action is correct, effective or good. Object detection, manipulation and grasping is challenging due to the hand and object modeling uncertainties, unknown contact type and object stiffness properties. In this paper, the proposal of an intelligent humanoid hand object detection and grasping model is presented assuming that the object properties are known. The control is simulated in the Matlab Simulink/ SimMechanics, Neural Network Toolbox and Computer Vision System Toolbox.

ACCEPT: Introduction of the Adverse Condition and Critical Event Prediction Toolbox

NASA Technical Reports Server (NTRS)

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.

Kinematic simulation and analysis of robot based on MATLAB

NASA Astrophysics Data System (ADS)

Liao, Shuhua; Li, Jiong

2018-03-01

The history of industrial automation is characterized by quick update technology, however, without a doubt, the industrial robot is a kind of special equipment. With the help of MATLAB matrix and drawing capacity in the MATLAB environment each link coordinate system set up by using the d-h parameters method and equation of motion of the structure. Robotics, Toolbox programming Toolbox and GUIDE to the joint application is the analysis of inverse kinematics and path planning and simulation, preliminary solve the problem of college students the car mechanical arm positioning theory, so as to achieve the aim of reservation.

Modelling multi-pulse population dynamics from ultrafast spectroscopy.

PubMed

van Wilderen, Luuk J G W; Lincoln, Craig N; van Thor, Jasper J

2011-03-21

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments.

Modelling Multi-Pulse Population Dynamics from Ultrafast Spectroscopy

PubMed Central

van Wilderen, Luuk J. G. W.; Lincoln, Craig N.; van Thor, Jasper J.

2011-01-01

Current advanced laser, optics and electronics technology allows sensitive recording of molecular dynamics, from single resonance to multi-colour and multi-pulse experiments. Extracting the occurring (bio-) physical relevant pathways via global analysis of experimental data requires a systematic investigation of connectivity schemes. Here we present a Matlab-based toolbox for this purpose. The toolbox has a graphical user interface which facilitates the application of different reaction models to the data to generate the coupled differential equations. Any time-dependent dataset can be analysed to extract time-independent correlations of the observables by using gradient or direct search methods. Specific capabilities (i.e. chirp and instrument response function) for the analysis of ultrafast pump-probe spectroscopic data are included. The inclusion of an extra pulse that interacts with a transient phase can help to disentangle complex interdependent pathways. The modelling of pathways is therefore extended by new theory (which is included in the toolbox) that describes the finite bleach (orientation) effect of single and multiple intense polarised femtosecond pulses on an ensemble of randomly oriented particles in the presence of population decay. For instance, the generally assumed flat-top multimode beam profile is adapted to a more realistic Gaussian shape, exposing the need for several corrections for accurate anisotropy measurements. In addition, the (selective) excitation (photoselection) and anisotropy of populations that interact with single or multiple intense polarised laser pulses is demonstrated as function of power density and beam profile. Using example values of real world experiments it is calculated to what extent this effectively orients the ensemble of particles. Finally, the implementation includes the interaction with multiple pulses in addition to depth averaging in optically dense samples. In summary, we show that mathematical modelling is essential to model and resolve the details of physical behaviour of populations in ultrafast spectroscopy such as pump-probe, pump-dump-probe and pump-repump-probe experiments. PMID:21445294

BOLDSync: a MATLAB-based toolbox for synchronized stimulus presentation in functional MRI.

PubMed

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.

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

PubMed

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

2017-11-16

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

An overview on real-time control schemes for wheeled mobile robot

NASA Astrophysics Data System (ADS)

Radzak, M. S. A.; Ali, M. A. H.; Sha’amri, S.; Azwan, A. R.

2018-04-01

The purpose of this paper is to review real-time control motion algorithms for wheeled mobile robot (WMR) when navigating in environment such as road. Its need a good controller to avoid collision with any disturbance and maintain a track error at zero level. The controllers are used with other aiding sensors to measure the WMR’s velocities, posture, and interference to estimate the required torque to be applied on the wheels of mobile robot. Four main categories for wheeled mobile robot control systems have been found in literature which are namely: Kinematic based controller, Dynamic based controllers, artificial intelligence based control system, and Active Force control. A MATLAB/Simulink software is the main software to simulate and implement the control system. The real-time toolbox in MATLAB/SIMULINK are used to receive/send data from sensors/to actuator with presence of disturbances, however others software such C, C++ and visual basic are rare to be used.

The AI Bus architecture for distributed knowledge-based systems

NASA Technical Reports Server (NTRS)

Schultz, Roger D.; Stobie, Iain

1991-01-01

The AI Bus architecture is layered, distributed object oriented framework developed to support the requirements of advanced technology programs for an order of magnitude improvement in software costs. The consequent need for highly autonomous computer systems, adaptable to new technology advances over a long lifespan, led to the design of an open architecture and toolbox for building large scale, robust, production quality systems. The AI Bus accommodates a mix of knowledge based and conventional components, running on heterogeneous, distributed real world and testbed environment. The concepts and design is described of the AI Bus architecture and its current implementation status as a Unix C++ library or reusable objects. Each high level semiautonomous agent process consists of a number of knowledge sources together with interagent communication mechanisms based on shared blackboards and message passing acquaintances. Standard interfaces and protocols are followed for combining and validating subsystems. Dynamic probes or demons provide an event driven means for providing active objects with shared access to resources, and each other, while not violating their security.

A LAN Toolbox.

ERIC Educational Resources Information Center

Eddison, Elizabeth B.

1989-01-01

This bibliographic essay reviews sources that aid in the planning and management aspects of local area networks. Areas covered include system components; basic vocabularies; planning issues, including needs assessment, peripheral sharing alternatives and costs; and management issues, including purchasing, operating systems, installation, network…

PeTTSy: a computational tool for perturbation analysis of complex systems biology models.

PubMed

Domijan, Mirela; Brown, Paul E; Shulgin, Boris V; Rand, David A

2016-03-10

Over the last decade sensitivity analysis techniques have been shown to be very useful to analyse complex and high dimensional Systems Biology models. However, many of the currently available toolboxes have either used parameter sampling, been focused on a restricted set of model observables of interest, studied optimisation of a objective function, or have not dealt with multiple simultaneous model parameter changes where the changes can be permanent or temporary. Here we introduce our new, freely downloadable toolbox, PeTTSy (Perturbation Theory Toolbox for Systems). PeTTSy is a package for MATLAB which implements a wide array of techniques for the perturbation theory and sensitivity analysis of large and complex ordinary differential equation (ODE) based models. PeTTSy is a comprehensive modelling framework that introduces a number of new approaches and that fully addresses analysis of oscillatory systems. It examines sensitivity analysis of the models to perturbations of parameters, where the perturbation timing, strength, length and overall shape can be controlled by the user. This can be done in a system-global setting, namely, the user can determine how many parameters to perturb, by how much and for how long. PeTTSy also offers the user the ability to explore the effect of the parameter perturbations on many different types of outputs: period, phase (timing of peak) and model solutions. PeTTSy can be employed on a wide range of mathematical models including free-running and forced oscillators and signalling systems. To enable experimental optimisation using the Fisher Information Matrix it efficiently allows one to combine multiple variants of a model (i.e. a model with multiple experimental conditions) in order to determine the value of new experiments. It is especially useful in the analysis of large and complex models involving many variables and parameters. PeTTSy is a comprehensive tool for analysing large and complex models of regulatory and signalling systems. It allows for simulation and analysis of models under a variety of environmental conditions and for experimental optimisation of complex combined experiments. With its unique set of tools it makes a valuable addition to the current library of sensitivity analysis toolboxes. We believe that this software will be of great use to the wider biological, systems biology and modelling communities.

Assessing morphology and function of the semicircular duct system: introducing new in-situ visualization and software toolbox

PubMed Central

David, R.; Stoessel, A.; Berthoz, A.; Spoor, F.; Bennequin, D.

2016-01-01

The semicircular duct system is part of the sensory organ of balance and essential for navigation and spatial awareness in vertebrates. Its function in detecting head rotations has been modelled with increasing sophistication, but the biomechanics of actual semicircular duct systems has rarely been analyzed, foremost because the fragile membranous structures in the inner ear are hard to visualize undistorted and in full. Here we present a new, easy-to-apply and non-invasive method for three-dimensional in-situ visualization and quantification of the semicircular duct system, using X-ray micro tomography and tissue staining with phosphotungstic acid. Moreover, we introduce Ariadne, a software toolbox which provides comprehensive and improved morphological and functional analysis of any visualized duct system. We demonstrate the potential of these methods by presenting results for the duct system of humans, the squirrel monkey and the rhesus macaque, making comparisons with past results from neurophysiological, oculometric and biomechanical studies. Ariadne is freely available at http://www.earbank.org. PMID:27604473

RESPONSE PROTOCOL TOOLBOX: OVERVIEW, STATUS UPDATE, AND RELATIONSHIP TO OTHER WATER SECURITY PRODUCTS

EPA Science Inventory

The Response Protocol Toolbox was released by USEPA to address the complex, multi-faceted challenges of a water utility's planning and response to the threat or act of intentional contamination of drinking water (1). The Toolbox contains guidance that may be adopted voluntarily,...

RESPONSE PROTOCOL TOOLBOX: OVERVIEW, STATUS UPDATE, AND RELATIONSHIP TO OTHER WATER SECURITY PRODUCTS

EPA Science Inventory

The Response Protocol Toolbox was released by USEPA to address the complex, multi-faceted challenges of a water utility's planning and response to the threat or act of intentional contamination of drinking water(1). The Toolbox contains guidance that may be adopted voluntarily, a...

RESPONSE PROTOCOL TOOLBOX OVERVIEW, STATUS UPDATE, AND RELATIONSHIP TO OTHER WATER SECURITY PRODUCTS

EPA Science Inventory

The Response Protocol Toolbox was released by USEPA to address the complex, multi-faceted challenges of a water utility's planning and response to the threat or act of intentional contamination of drinking water (1). The Toolbox contains guidance that may be adopted voluntarily,...

The Brain's Versatile Toolbox.

ERIC Educational Resources Information Center

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…

Compressible Flow Toolbox

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

2006-01-01

The Compressible Flow Toolbox is primarily a MATLAB-language implementation of a set of algorithms that solve approximately 280 linear and nonlinear classical equations for compressible flow. The toolbox is useful for analysis of one-dimensional steady flow with either constant entropy, friction, heat transfer, or Mach number greater than 1. The toolbox also contains algorithms for comparing and validating the equation-solving algorithms against solutions previously published in open literature. The classical equations solved by the Compressible Flow Toolbox are as follows: The isentropic-flow equations, The Fanno flow equations (pertaining to flow of an ideal gas in a pipe with friction), The Rayleigh flow equations (pertaining to frictionless flow of an ideal gas, with heat transfer, in a pipe of constant cross section), The normal-shock equations, The oblique-shock equations, and The expansion equations.

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

PubMed

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

2017-11-01

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

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis

PubMed Central

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/. PMID:26882475

Synthesis of multi-loop automatic control systems by the nonlinear programming method

NASA Astrophysics Data System (ADS)

Voronin, A. V.; Emelyanova, T. A.

2017-01-01

The article deals with the problem of calculation of the multi-loop control systems optimal tuning parameters by numerical methods and nonlinear programming methods. For this purpose, in the paper the Optimization Toolbox of Matlab is used.

A toolbox for alleviating traffic congestion and enhancing mobility

DOT National Transportation Integrated Search

1997-01-01

Over 40 years ago, the United States embarked upon the largest public works project in its history--the construction of the Interstate highway system. The urban portions of this system along with the highways and public transportation services develo...

Interdisciplinary approach towards a systems medicine toolbox using the example of inflammatory diseases.

PubMed

Bauer, Christian R; Knecht, Carolin; Fretter, Christoph; Baum, Benjamin; Jendrossek, Sandra; Rühlemann, Malte; Heinsen, Femke-Anouska; Umbach, Nadine; Grimbacher, Bodo; Franke, Andre; Lieb, Wolfgang; Krawczak, Michael; Hütt, Marc-Thorsten; Sax, Ulrich

2017-05-01

Electronic access to multiple data types, from generic information on biological systems at different functional and cellular levels to high-throughput molecular data from human patients, is a prerequisite of successful systems medicine research. However, scientists often encounter technical and conceptual difficulties that forestall the efficient and effective use of these resources. We summarize and discuss some of these obstacles, and suggest ways to avoid or evade them.The methodological gap between data capturing and data analysis is huge in human medical research. Primary data producers often do not fully apprehend the scientific value of their data, whereas data analysts maybe ignorant of the circumstances under which the data were collected. Therefore, the provision of easy-to-use data access tools not only helps to improve data quality on the part of the data producers but also is likely to foster an informed dialogue with the data analysts.We propose a means to integrate phenotypic data, questionnaire data and microbiome data with a user-friendly Systems Medicine toolbox embedded into i2b2/tranSMART. Our approach is exemplified by the integration of a basic outlier detection tool and a more advanced microbiome analysis (alpha diversity) script. Continuous discussion with clinicians, data managers, biostatisticians and systems medicine experts should serve to enrich even further the functionality of toolboxes like ours, being geared to be used by 'informed non-experts' but at the same time attuned to existing, more sophisticated analysis tools. © The Author 2016. Published by Oxford University Press.

Using a Toolbox of Tailored Educational Lessons to Improve Fruit, Vegetable, and Physical Activity Behaviors among African American Women in California

ERIC Educational Resources Information Center

Backman, Desiree; Scruggs, Valarie; Atiedu, Akpene Ama; Bowie, Shene; Bye, Larry; Dennis, Angela; Hall, Melanie; Ossa, Alexandra; Wertlieb, Stacy; Foerster, Susan B.

2011-01-01

Objective: Evaluate the effectiveness of the "Fruit, Vegetable, and Physical Activity Toolbox for Community Educators" ("Toolbox"), an intervention originally designed for Spanish- and English-speaking audiences, in changing knowledge, attitudes, and behavior among low-income African American women. Design: Quasi-experimental…

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

DOT National Transportation Integrated Search

2012-02-01

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

Proposal for the design of a zero gravity tool storage device

NASA Technical Reports Server (NTRS)

Stuckwisch, Sue; Carrion, Carlos A.; Phillips, Lee; Laughlin, Julia; Francois, Jason

1994-01-01

Astronauts frequently use a variety of hand tools during space missions, especially on repair missions. A toolbox is needed to allow storage and retrieval of tools with minimal difficulties. The toolbox must contain tools during launch, landing, and on-orbit operations. The toolbox will be used in the Shuttle Bay and therefore must withstand the hazardous space environment. The three main functions of the toolbox in space are: to protect the tools from the space environment and from damaging one another, to allow for quick, one-handed access to the tools; and to minimize the heat transfer between the astronaut's hand and the tools. This proposal explores the primary design issues associated with the design of the toolbox. Included are the customer and design specifications, global and refined function structures, possible solution principles, concept variants, and finally design recommendations.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

JWST Wavefront Control Toolbox

NASA Technical Reports Server (NTRS)

Shin, Shahram Ron; Aronstein, David L.

2011-01-01

A Matlab-based toolbox has been developed for the wavefront control and optimization of segmented optical surfaces to correct for possible misalignments of James Webb Space Telescope (JWST) using influence functions. The toolbox employs both iterative and non-iterative methods to converge to an optimal solution by minimizing the cost function. The toolbox could be used in either of constrained and unconstrained optimizations. The control process involves 1 to 7 degrees-of-freedom perturbations per segment of primary mirror in addition to the 5 degrees of freedom of secondary mirror. The toolbox consists of a series of Matlab/Simulink functions and modules, developed based on a "wrapper" approach, that handles the interface and data flow between existing commercial optical modeling software packages such as Zemax and Code V. The limitations of the algorithm are dictated by the constraints of the moving parts in the mirrors.

MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB.

PubMed

Egert, U; Knott, Th; Schwarz, C; Nawrot, M; Brandt, A; Rotter, S; Diesmann, M

2002-05-30

Recent advances in electrophysiological techniques have created new tools for the acquisition and storage of neuronal activity recorded simultaneously with numerous electrodes. These techniques support the analysis of the function as well as the structure of individual electrogenic cells in the context of surrounding neuronal or cardiac network. Commercially available tools for the analysis of such data, however, cannot be easily adapted to newly emerging requirements for data analysis and visualization, and cross compatibility between them is limited. In this report we introduce a free open source toolbox called microelectrode array tools (MEA-Tools) for the analysis of multi-electrode data based on the common data analysis environment MATLAB (version 5.3-6.1, The Mathworks, Natick, MA). The toolbox itself is platform independent. The file interface currently supports files recorded with MCRack (Multi Channel Systems, Reutlingen, Germany) under Microsoft Windows 95, 98, NT, and 2000, but can be adapted to other data acquisition systems. Functions are controlled via command line input and graphical user interfaces, and support common requirements for the analysis of local field potentials, extracellular spike activity, and continuous recordings, in addition to supplementary data acquired by additional instruments, e.g. intracellular amplifiers. Data may be processed as continuous recordings or time windows triggered to some event.

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

NASA Astrophysics Data System (ADS)

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.

A manifold independent approach to understanding transport in stochastic dynamical systems

NASA Astrophysics Data System (ADS)

Bollt, Erik M.; Billings, Lora; Schwartz, Ira B.

2002-12-01

We develop a new collection of tools aimed at studying stochastically perturbed dynamical systems. Specifically, in the setting of bi-stability, that is a two-attractor system, it has previously been numerically observed that a small noise volume is sufficient to destroy would be zero-noise case barriers in the phase space (pseudo-barriers), thus creating a pre-heteroclinic tangency chaos-like behavior. The stochastic dynamical system has a corresponding Frobenius-Perron operator with a stochastic kernel, which describes how densities of initial conditions move under the noisy map. Thus in studying the action of the Frobenius-Perron operator, we learn about the transport of the map; we have employed a Galerkin-Ulam-like method to project the Frobenius-Perron operator onto a discrete basis set of characteristic functions to highlight this action localized in specified regions of the phase space. Graph theoretic methods allow us to re-order the resulting finite dimensional Markov operator approximation so as to highlight the regions of the original phase space which are particularly active pseudo-barriers of the stochastic dynamics. Our toolbox allows us to find: (1) regions of high activity of transport, (2) flux across pseudo-barriers, and also (3) expected time of escape from pseudo-basins. Some of these quantities are also possible via the manifold dependent stochastic Melnikov method, but Melnikov only applies to a very special class of models for which the unperturbed homoclinic orbit is available. Our methods are unique in that they can essentially be considered as a “black-box” of tools which can be applied to a wide range of stochastic dynamical systems in the absence of a priori knowledge of manifold structures. We use here a model of childhood diseases to showcase our methods. Our tools will allow us to make specific observations of: (1) loss of reducibility between basins with increasing noise, (2) identification in the phase space of active regions of stochastic transport, (3) stochastic flux which essentially completes the heteroclinic tangle.

Control Systems Lab Using a LEGO Mindstorms NXT Motor System

ERIC Educational Resources Information Center

Kim, Y.

2011-01-01

This paper introduces a low-cost LEGO Mindstorms NXT motor system for teaching classical and modern control theories in standard third-year undergraduate courses. The LEGO motor system can be used in conjunction with MATLAB, Simulink, and several necessary toolboxes to demonstrate: 1) a modeling technique; 2) proportional-integral-differential…

Sanitary Sewer Overflow Analysis and Planning (SSOAP) Toolbox

EPA Science Inventory

Rainfall-derived infiltration and inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby receiving waters and can also ...

A toolbox to visualise benefits resulting from flood hazard mitigation

NASA Astrophysics Data System (ADS)

Fuchs, Sven; Thaler, Thomas; Heiser, Micha

2017-04-01

In order to visualize the benefits resulting from technical mitigation, a toolbox was developed within an open-source environment that allows for an assessment of gains and losses for buildings exposed to flood hazards. Starting with different scenarios showing the changes in flood magnitude with respect to the considered management options, the computation was based on the amount and value of buildings exposed as well as their vulnerability, following the general concept of risk assessment. As a result, beneficiaries of risk reduction may be identified and - more general - also different mitigation options may be strategically evaluated with respect to the height of risk reduction for different elements exposed. As such, multiple management options can be ranked according to their costs and benefits, and in order of priority. A relational database composed from different modules was created in order to mirror the requirements of an open source application and to allow for future dynamics in the data availability as well as the spatiotemporal dynamics of this data (Fuchs et al. 2013). An economic module was used to compute the monetary value of buildings exposed using (a) the building footprint, (b) the information of the building cadaster such as building type, number of storeys and utilisation, and (c) regionally averaged construction costs. An exposition module was applied to connect the spatial GIS information (X and Y coordinates) of elements at risk to the hazard information in order to achieve information on exposure. An impact module linked this information to vulnerability functions (Totschnig and Fuchs 2013; Papathoma-Köhle et al. 2015) in order to achieve the monetary level of risk for every building exposed. These values were finally computed before and after the implementation of mitigation measure in order to show gains and losses, and visualised. The results can be exported in terms of spread sheets for further computation. References Fuchs S, 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

Rural ITS toolbox

DOT National Transportation Integrated Search

2001-11-01

This document identifies successful rural Intelligent Transportation Systems (ITS) projects and statewide applications. These applications are referred to as "tools" and include those in the process of being tested prior to full deployment. The tools...

Direct Duplex Detection: An Emerging Tool in the RNA Structure Analysis Toolbox.

PubMed

Weidmann, Chase A; Mustoe, Anthony M; Weeks, Kevin M

2016-09-01

While a variety of powerful tools exists for analyzing RNA structure, identifying long-range and intermolecular base-pairing interactions has remained challenging. Recently, three groups introduced a high-throughput strategy that uses psoralen-mediated crosslinking to directly identify RNA-RNA duplexes in cells. Initial application of these methods highlights the preponderance of long-range structures within and between RNA molecules and their widespread structural dynamics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Robust scalable stabilisability conditions for large-scale heterogeneous multi-agent systems with uncertain nonlinear interactions: towards a distributed computing architecture

NASA Astrophysics Data System (ADS)

Manfredi, Sabato

2016-06-01

Large-scale dynamic systems are becoming highly pervasive in their occurrence with applications ranging from system biology, environment monitoring, sensor networks, and power systems. They are characterised by high dimensionality, complexity, and uncertainty in the node dynamic/interactions that require more and more computational demanding methods for their analysis and control design, as well as the network size and node system/interaction complexity increase. Therefore, it is a challenging problem to find scalable computational method for distributed control design of large-scale networks. In this paper, we investigate the robust distributed stabilisation problem of large-scale nonlinear multi-agent systems (briefly MASs) composed of non-identical (heterogeneous) linear dynamical systems coupled by uncertain nonlinear time-varying interconnections. By employing Lyapunov stability theory and linear matrix inequality (LMI) technique, new conditions are given for the distributed control design of large-scale MASs that can be easily solved by the toolbox of MATLAB. The stabilisability of each node dynamic is a sufficient assumption to design a global stabilising distributed control. The proposed approach improves some of the existing LMI-based results on MAS by both overcoming their computational limits and extending the applicative scenario to large-scale nonlinear heterogeneous MASs. Additionally, the proposed LMI conditions are further reduced in terms of computational requirement in the case of weakly heterogeneous MASs, which is a common scenario in real application where the network nodes and links are affected by parameter uncertainties. One of the main advantages of the proposed approach is to allow to move from a centralised towards a distributed computing architecture so that the expensive computation workload spent to solve LMIs may be shared among processors located at the networked nodes, thus increasing the scalability of the approach than the network size. Finally, a numerical example shows the applicability of the proposed method and its advantage in terms of computational complexity when compared with the existing approaches.

Advanced functional network analysis in the geosciences: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Runge, Jakob; Schultz, Hanna C. H.; Wiedermann, Marc; Zech, Alraune; Feldhoff, Jan; Rheinwalt, Aljoscha; Kutza, Hannes; Radebach, Alexander; Marwan, Norbert; Kurths, Jürgen

2013-04-01

Functional networks are a powerful tool for analyzing large geoscientific datasets such as global fields of climate time series originating from observations or model simulations. pyunicorn (pythonic unified complex network and recurrence analysis toolbox) is an open-source, fully object-oriented and easily parallelizable package written in the language Python. It allows for constructing functional networks (aka climate networks) representing the structure of statistical interrelationships in large datasets and, subsequently, investigating this structure using advanced methods of complex network theory such as measures for networks of interacting networks, node-weighted statistics or network surrogates. Additionally, pyunicorn allows to study the complex dynamics of geoscientific systems as recorded by time series by means of recurrence networks and visibility graphs. The range of possible applications of the package is outlined drawing on several examples from climatology.

40 CFR 141.718 - Treatment performance toolbox components.

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (a) Combined filter performance. Systems using conventional filtration treatment or direct filtration... the criteria in this paragraph. Combined filter effluent (CFE) turbidity must be less than or equal to... § 141.74(a) and (c). (b) Individual filter performance. Systems using conventional filtration treatment...

40 CFR 141.718 - Treatment performance toolbox components.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (a) Combined filter performance. Systems using conventional filtration treatment or direct filtration... the criteria in this paragraph. Combined filter effluent (CFE) turbidity must be less than or equal to... § 141.74(a) and (c). (b) Individual filter performance. Systems using conventional filtration treatment...

Building Interdisciplinary Research Models Through Interactive Education.

PubMed

Hessels, Amanda J; Robinson, Brian; O'Rourke, Michael; Begg, Melissa D; Larson, Elaine L

2015-12-01

Critical interdisciplinary research skills include effective communication with diverse disciplines and cultivating collaborative relationships. Acquiring these skills during graduate education may foster future interdisciplinary research quality and productivity. The project aim was to develop and evaluate an interactive Toolbox workshop approach within an interprofessional graduate level course to enhance student learning and skill in interdisciplinary research. We sought to examine the student experience of integrating the Toolbox workshop in modular format over the duration of a 14-week course. The Toolbox Health Sciences Instrument includes six modules that were introduced in a 110-minute dialogue session during the first class and then integrated into the course in a series of six individual workshops in three phases over the course of the semester. Seventeen students participated; the majority were nursing students. Three measures were used to assess project outcomes: pre-post intervention Toolbox survey, competency self-assessment, and a postcourse survey. All measures indicated the objectives were met by a change in survey responses, improved competencies, and favorable experience of the Toolbox modular intervention. Our experience indicates that incorporating this Toolbox modular approach into research curricula can enhance individual level scientific capacity, future interdisciplinary research project success, and ultimately impact on practice and policy. © 2015 Wiley Periodicals, Inc.

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

PubMed Central

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

2015-01-01

The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

The RAVEN Toolbox and Its Use for Generating a Genome-scale Metabolic Model for Penicillium chrysogenum

PubMed Central

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. PMID:23555215

Monitoring the soil degradation by Metastatistical Analysis

NASA Astrophysics Data System (ADS)

Oleschko, K.; Gaona, C.; Tarquis, A.

2009-04-01

The effectiveness of fractal toolbox to capture the critical behavior of soil structural patterns during the chemical and physical degradation was documented by our numerous experiments (Oleschko et al., 2008 a; 2008 b). The spatio-temporal dynamics of these patterns was measured and mapped with high precision in terms of fractal descriptors. All tested fractal techniques were able to detect the statistically significant differences in structure between the perfect spongy and massive patterns of uncultivated and sodium-saline agricultural soils, respectively. For instance, the Hurst exponent, extracted from the Chernozeḿ micromorphological images and from the time series of its physical and mechanical properties measured in situ, detected the roughness decrease (and therefore the increase in H - from 0.17 to 0.30 for images) derived from the loss of original structure complexity. The combined use of different fractal descriptors brings statistical precision into the quantification of natural system degradation and provides a means for objective soil structure comparison (Oleschko et al., 2000). The ability of fractal parameters to capture critical behavior and phase transition was documented for different contrasting situations, including from Andosols deforestation and erosion, to Vertisols high fructuring and consolidation. The Hurst exponent is used to measure the type of persistence and degree of complexity of structure dynamics. We conclude that there is an urgent need to select and adopt a standardized toolbox for fractal analysis and complexity measures in Earth Sciences. We propose to use the second-order (meta-) statistics as subtle measures of complexity (Atmanspacher et al., 1997). The high degree of correlation was documented between the fractal and high-order statistical descriptors (four central moments of stochastic variable distribution) used to the system heterogeneity and variability analysis. We proposed to call this combined fractal/statistical toolbox Metastatistical Analysis and recommend it to the projects directed to soil degradation monitoring. References: 1. Oleschko, K., B.S. Figueroa, M.E. Miranda, M.A. Vuelvas and E.R. Solleiro, Soil & Till. Res. 55, 43 (2000). 2. Oleschko, K., Korvin, G., Figueroa S. B., Vuelvas, M.A., Balankin, A., Flores L., Carreño, D. Fractal radar scattering from soil. Physical Review E.67, 041403, 2003. 3. Zamora-Castro S., Oleschko, K. Flores, L., Ventura, E. Jr., Parrot, J.-F., 2008. Fractal mapping of pore and solids attributes. Vadose Zone Journal, v. 7, Issue2: 473-492. 4. Oleschko, K., Korvin, G., Muñoz, A., Velásquez, J., Miranda, M.E., Carreon, D., Flores, L., Martínez, M., Velásquez-Valle, M., Brambilla, F., Parrot, J.-F. Ronquillo, G., 2008. Fractal mapping of soil moisture content from remote sensed multi-scale data. Nonlinear Proceses in Geophysics Journal, 15: 711-725. 5. Atmanspacher, H., Räth, Ch., Wiedenmann, G., 1997. Statistics and meta-statistics in the concept of complexity. Physica A, 234: 819-829.

Detecting causality in policy diffusion processes.

PubMed

Grabow, Carsten; Macinko, James; Silver, Diana; Porfiri, Maurizio

2016-08-01

A universal question in network science entails learning about the topology of interaction from collective dynamics. Here, we address this question by examining diffusion of laws across US states. We propose two complementary techniques to unravel determinants of this diffusion process: information-theoretic union transfer entropy and event synchronization. In order to systematically investigate their performance on law activity data, we establish a new stochastic model to generate synthetic law activity data based on plausible networks of interactions. Through extensive parametric studies, we demonstrate the ability of these methods to reconstruct networks, varying in size, link density, and degree heterogeneity. Our results suggest that union transfer entropy should be preferred for slowly varying processes, which may be associated with policies attending to specific local problems that occur only rarely or with policies facing high levels of opposition. In contrast, event synchronization is effective for faster enactment rates, which may be related to policies involving Federal mandates or incentives. This study puts forward a data-driven toolbox to explain the determinants of legal activity applicable to political science, across dynamical systems, information theory, and complex networks.

Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations

NASA Astrophysics Data System (ADS)

Zuo, Zhicheng; Liu, Jin

2016-11-01

The CRISPR-associated endonuclease Cas9 from Streptococcus pyogenes (spCas9) along with a single guide RNA (sgRNA) has emerged as a versatile toolbox for genome editing. Despite recent advances in the mechanism studies on spCas9-sgRNA-mediated double-stranded DNA (dsDNA) recognition and cleavage, it is still unclear how the catalytic Mg2+ ions induce the conformation changes toward the catalytic active state. It also remains controversial whether Cas9 generates blunt-ended or staggered-ended breaks with overhangs in the DNA. To investigate these issues, here we performed the first all-atom molecular dynamics simulations of the spCas9-sgRNA-dsDNA system with and without Mg2+ bound. The simulation results showed that binding of two Mg2+ ions at the RuvC domain active site could lead to structurally and energetically favorable coordination ready for the non-target DNA strand cleavage. Importantly, we demonstrated with our simulations that Cas9-catalyzed DNA cleavage produces 1-bp staggered ends rather than generally assumed blunt ends.

Detecting causality in policy diffusion processes

NASA Astrophysics Data System (ADS)

Grabow, Carsten; Macinko, James; Silver, Diana; Porfiri, Maurizio

2016-08-01

A universal question in network science entails learning about the topology of interaction from collective dynamics. Here, we address this question by examining diffusion of laws across US states. We propose two complementary techniques to unravel determinants of this diffusion process: information-theoretic union transfer entropy and event synchronization. In order to systematically investigate their performance on law activity data, we establish a new stochastic model to generate synthetic law activity data based on plausible networks of interactions. Through extensive parametric studies, we demonstrate the ability of these methods to reconstruct networks, varying in size, link density, and degree heterogeneity. Our results suggest that union transfer entropy should be preferred for slowly varying processes, which may be associated with policies attending to specific local problems that occur only rarely or with policies facing high levels of opposition. In contrast, event synchronization is effective for faster enactment rates, which may be related to policies involving Federal mandates or incentives. This study puts forward a data-driven toolbox to explain the determinants of legal activity applicable to political science, across dynamical systems, information theory, and complex networks.

Promoting Complex Systems Learning through the Use of Conceptual Representations in Hypermedia

ERIC Educational Resources Information Center

Liu, Lei; Hmelo-Silver, Cindy E.

2009-01-01

Studying complex systems is increasingly important in many science domains. Many features of complex systems make it difficult for students to develop deep understanding. Our previous research indicated that a function-centered conceptual representation is part of the disciplinary toolbox of biologists, suggesting that it is an appropriate…

SSOAP - A USEPA TOOLBOX FOR SSO ANALYSIS AND CONTROL PLANNING

EPA Science Inventory

Rainfall Derived Infiltration and Inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby streams and can also cause seriou...

DEVELOPMENT OF SANITARY SEWER OVERFLOW ANALYSIS AND PLANNING (SSOAP) TOOLBOX

EPA Science Inventory

Rainfall Derived Infiltration and Inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby streams. RDII can also cause se...

SSOAP - A TOOLBOX FOR SANITARY SEWER OVERFLOW ANALYSIS AND PLANNING

EPA Science Inventory

Rainfall Derived Infiltration and Inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby streams and can also cause serio...

SSOAP - A TOOLBOX FOR SANITARY SEWER OVERFLOW ANALYSIS AND PLANNING

EPA Science Inventory

Rainfall Derived Infiltration and Inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby streams and can also cause seriou...

Computer-assisted design for scaling up systems based on DNA reaction networks.

PubMed

Aubert, Nathanaël; Mosca, Clément; Fujii, Teruo; Hagiya, Masami; Rondelez, Yannick

2014-04-06

In the past few years, there have been many exciting advances in the field of molecular programming, reaching a point where implementation of non-trivial systems, such as neural networks or switchable bistable networks, is a reality. Such systems require nonlinearity, be it through signal amplification, digitalization or the generation of autonomous dynamics such as oscillations. The biochemistry of DNA systems provides such mechanisms, but assembling them in a constructive manner is still a difficult and sometimes counterintuitive process. Moreover, realistic prediction of the actual evolution of concentrations over time requires a number of side reactions, such as leaks, cross-talks or competitive interactions, to be taken into account. In this case, the design of a system targeting a given function takes much trial and error before the correct architecture can be found. To speed up this process, we have created DNA Artificial Circuits Computer-Assisted Design (DACCAD), a computer-assisted design software that supports the construction of systems for the DNA toolbox. DACCAD is ultimately aimed to design actual in vitro implementations, which is made possible by building on the experimental knowledge available on the DNA toolbox. We illustrate its effectiveness by designing various systems, from Montagne et al.'s Oligator or Padirac et al.'s bistable system to new and complex networks, including a two-bit counter or a frequency divider as well as an example of very large system encoding the game Mastermind. In the process, we highlight a variety of behaviours, such as enzymatic saturation and load effect, which would be hard to handle or even predict with a simpler model. We also show that those mechanisms, while generally seen as detrimental, can be used in a positive way, as functional part of a design. Additionally, the number of parameters included in these simulations can be large, especially in the case of complex systems. For this reason, we included the possibility to use CMA-ES, a state-of-the-art optimization algorithm that will automatically evolve parameters chosen by the user to try to match a specified behaviour. Finally, because all possible functionality cannot be captured by a single software, DACCAD includes the possibility to export a system in the synthetic biology markup language, a widely used language for describing biological reaction systems. DACCAD can be downloaded online at http://www.yannick-rondelez.com/downloads/.

SOCIB Glider toolbox: from sensor to data repository

NASA Astrophysics Data System (ADS)

Pau Beltran, Joan; Heslop, Emma; Ruiz, Simón; Troupin, Charles; Tintoré, Joaquín

2015-04-01

Nowadays in oceanography, gliders constitutes a mature, cost-effective technology for the acquisition of measurements independently of the sea state (unlike ships), providing subsurface data during sustained periods, including extreme weather events. The SOCIB glider toolbox is a set of MATLAB/Octave scripts and functions developed in order to manage the data collected by a glider fleet. They cover the main stages of the data management process, both in real-time and delayed-time modes: metadata aggregation, downloading, processing, and automatic generation of data products and figures. The toolbox is distributed under the GNU licence (http://www.gnu.org/copyleft/gpl.html) and is available at http://www.socib.es/users/glider/glider_toolbox.

At the Frontiers of Modeling Intensive Longitudinal Data: Dynamic Structural Equation Models for the Affective Measurements from the COGITO Study.

PubMed

Hamaker, E L; Asparouhov, T; Brose, A; Schmiedek, F; Muthén, B

2018-04-06

With the growing popularity of intensive longitudinal research, the modeling techniques and software options for such data are also expanding rapidly. Here we use dynamic multilevel modeling, as it is incorporated in the new dynamic structural equation modeling (DSEM) toolbox in Mplus, to analyze the affective data from the COGITO study. These data consist of two samples of over 100 individuals each who were measured for about 100 days. We use composite scores of positive and negative affect and apply a multilevel vector autoregressive model to allow for individual differences in means, autoregressions, and cross-lagged effects. Then we extend the model to include random residual variances and covariance, and finally we investigate whether prior depression affects later depression scores through the random effects of the daily diary measures. We end with discussing several urgent-but mostly unresolved-issues in the area of dynamic multilevel modeling.

Quantitative imaging of heterogeneous dynamics in drying and aging paints

PubMed Central

van der Kooij, Hanne M.; Fokkink, Remco; van der Gucht, Jasper; Sprakel, Joris

2016-01-01

Drying and aging paint dispersions display a wealth of complex phenomena that make their study fascinating yet challenging. To meet the growing demand for sustainable, high-quality paints, it is essential to unravel the microscopic mechanisms underlying these phenomena. Visualising the governing dynamics is, however, intrinsically difficult because the dynamics are typically heterogeneous and span a wide range of time scales. Moreover, the high turbidity of paints precludes conventional imaging techniques from reaching deep inside the paint. To address these challenges, we apply a scattering technique, Laser Speckle Imaging, as a versatile and quantitative tool to elucidate the internal dynamics, with microscopic resolution and spanning seven decades of time. We present a toolbox of data analysis and image processing methods that allows a tailored investigation of virtually any turbid dispersion, regardless of the geometry and substrate. Using these tools we watch a variety of paints dry and age with unprecedented detail. PMID:27682840

High-Throughput Sequencing: A Roadmap Toward Community Ecology

PubMed Central

Poisot, Timothée; Péquin, Bérangère; Gravel, Dominique

2013-01-01

High-throughput sequencing is becoming increasingly important in microbial ecology, yet it is surprisingly under-used to generate or test biogeographic hypotheses. In this contribution, we highlight how adding these methods to the ecologist toolbox will allow the detection of new patterns, and will help our understanding of the structure and dynamics of diversity. Starting with a review of ecological questions that can be addressed, we move on to the technical and analytical issues that will benefit from an increased collaboration between different disciplines. PMID:23610649

TopoToolbox: using sensor topography to calculate psychologically meaningful measures from event-related EEG/MEG.

PubMed

Tian, Xing; Poeppel, David; Huber, David E

2011-01-01

The open-source toolbox "TopoToolbox" is a suite of functions that use sensor topography to calculate psychologically meaningful measures (similarity, magnitude, and timing) from multisensor event-related EEG and MEG data. Using a GUI and data visualization, TopoToolbox can be used to calculate and test the topographic similarity between different conditions (Tian and Huber, 2008). This topographic similarity indicates whether different conditions involve a different distribution of underlying neural sources. Furthermore, this similarity calculation can be applied at different time points to discover when a response pattern emerges (Tian and Poeppel, 2010). Because the topographic patterns are obtained separately for each individual, these patterns are used to produce reliable measures of response magnitude that can be compared across individuals using conventional statistics (Davelaar et al. Submitted and Huber et al., 2008). TopoToolbox can be freely downloaded. It runs under MATLAB (The MathWorks, Inc.) and supports user-defined data structure as well as standard EEG/MEG data import using EEGLAB (Delorme and Makeig, 2004).

User Guide for Compressible Flow Toolbox Version 2.1 for Use With MATLAB(Registered Trademark); Version 7

NASA Technical Reports Server (NTRS)

Melcher, Kevin J.

2006-01-01

This report provides a user guide for the Compressible Flow Toolbox, a collection of algorithms that solve almost 300 linear and nonlinear classical compressible flow relations. The algorithms, implemented in the popular MATLAB programming language, are useful for analysis of one-dimensional steady flow with constant entropy, friction, heat transfer, or shock discontinuities. The solutions do not include any gas dissociative effects. The toolbox also contains functions for comparing and validating the equation-solving algorithms against solutions previously published in the open literature. The classical equations solved by the Compressible Flow Toolbox are: isentropic-flow equations, Fanno flow equations (pertaining to flow of an ideal gas in a pipe with friction), Rayleigh flow equations (pertaining to frictionless flow of an ideal gas, with heat transfer, in a pipe of constant cross section.), normal-shock equations, oblique-shock equations, and Prandtl-Meyer expansion equations. At the time this report was published, the Compressible Flow Toolbox was available without cost from the NASA Software Repository.

EPA SSOAP Toolbox Application for Condition and Capacity Assessment of Wastewater Collection Systems - Paper

EPA Science Inventory

The nation’s sanitary sewer infrastructure is aging, with some sewers dating back more than 100 years. Nationwide, there are more than 19,500 municipal sanitary-sewer collection systems serving an estimated 150 million people and about 40,000 sanitary sewer overflow (SSO) events ...

EPA SSOAP Toolbox Application for Condition and Capacity Assessment of Wastewater Collection Systems

EPA Science Inventory

The Nation’s sanitary sewer infrastructure is aging, with some sewers dating back over 100 years. Nationwide, there are more than 19,500 municipal sanitary-sewer collection systems serving an estimated 150 million people and about 40,000 sanitary sewer overflow (SSO) events per ...

A TOOLBOX FOR SANITARY SEWER OVERFLOW ANALYSIS AND PLANNING (SSOAP) AND APPLICATIONS

EPA Science Inventory

Rainfall Derived Infiltration and Inflow (RDII) into sanitary sewer systems has long been recognized as a source of operating problems in sewerage systems. RDII is the main cause of sanitary sewer overflows (SSOs) to basements, streets, or nearby streams and can also cause seriou...

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

PubMed Central

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

2017-01-01

Reference electrode standardization technique (REST) has been increasingly acknowledged and applied as a re-reference technique to transform an actual multi-channels recordings to approximately zero reference ones in electroencephalography/event-related potentials (EEG/ERPs) community around the world in recent years. However, a more easy-to-use toolbox for re-referencing scalp EEG data to zero reference is still lacking. Here, we have therefore developed two open-source MATLAB toolboxes for REST of scalp EEG. One version of REST is closely integrated into EEGLAB, which is a popular MATLAB toolbox for processing the EEG data; and another is a batch version to make it more convenient and efficient for experienced users. Both of them are designed to provide an easy-to-use for novice researchers and flexibility for experienced researchers. All versions of the REST toolboxes can be freely downloaded at http://www.neuro.uestc.edu.cn/rest/Down.html, and the detailed information including publications, comments and documents on REST can also be found from this website. An example of usage is given with comparative results of REST and average reference. We hope these user-friendly REST toolboxes could make the relatively novel technique of REST easier to study, especially for applications in various EEG studies. PMID:29163006

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

PubMed

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

2017-01-01

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

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

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.

A versatile software package for inter-subject correlation based analyses of fMRI.

PubMed

Kauppi, Jukka-Pekka; Pajula, Juha; Tohka, Jussi

2014-01-01

In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli. Despite of the suitability of ISC based approach to analyze complex fMRI data, no generic software tools have been made available for this purpose, limiting a widespread use of ISC based analysis techniques among neuroimaging community. In this paper, we present a graphical user interface (GUI) based software package, ISC Toolbox, implemented in Matlab for computing various ISC based analyses. Many advanced computations such as comparison of ISCs between different stimuli, time window ISC, and inter-subject phase synchronization are supported by the toolbox. The analyses are coupled with re-sampling based statistical inference. The ISC based analyses are data and computation intensive and the ISC toolbox is equipped with mechanisms to execute the parallel computations in a cluster environment automatically and with an automatic detection of the cluster environment in use. Currently, SGE-based (Oracle Grid Engine, Son of a Grid Engine, or Open Grid Scheduler) and Slurm environments are supported. In this paper, we present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. We also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time. The ISC Toolbox is available in https://code.google.com/p/isc-toolbox/

A versatile software package for inter-subject correlation based analyses of fMRI

PubMed Central

Kauppi, Jukka-Pekka; Pajula, Juha; Tohka, Jussi

2014-01-01

In the inter-subject correlation (ISC) based analysis of the functional magnetic resonance imaging (fMRI) data, the extent of shared processing across subjects during the experiment is determined by calculating correlation coefficients between the fMRI time series of the subjects in the corresponding brain locations. This implies that ISC can be used to analyze fMRI data without explicitly modeling the stimulus and thus ISC is a potential method to analyze fMRI data acquired under complex naturalistic stimuli. Despite of the suitability of ISC based approach to analyze complex fMRI data, no generic software tools have been made available for this purpose, limiting a widespread use of ISC based analysis techniques among neuroimaging community. In this paper, we present a graphical user interface (GUI) based software package, ISC Toolbox, implemented in Matlab for computing various ISC based analyses. Many advanced computations such as comparison of ISCs between different stimuli, time window ISC, and inter-subject phase synchronization are supported by the toolbox. The analyses are coupled with re-sampling based statistical inference. The ISC based analyses are data and computation intensive and the ISC toolbox is equipped with mechanisms to execute the parallel computations in a cluster environment automatically and with an automatic detection of the cluster environment in use. Currently, SGE-based (Oracle Grid Engine, Son of a Grid Engine, or Open Grid Scheduler) and Slurm environments are supported. In this paper, we present a detailed account on the methods behind the ISC Toolbox, the implementation of the toolbox and demonstrate the possible use of the toolbox by summarizing selected example applications. We also report the computation time experiments both using a single desktop computer and two grid environments demonstrating that parallelization effectively reduces the computing time. The ISC Toolbox is available in https://code.google.com/p/isc-toolbox/ PMID:24550818

Finite element based N-Port model for preliminary design of multibody systems

NASA Astrophysics Data System (ADS)

Sanfedino, Francesco; Alazard, Daniel; Pommier-Budinger, Valérie; Falcoz, Alexandre; Boquet, Fabrice

2018-02-01

This article presents and validates a general framework to build a linear dynamic Finite Element-based model of large flexible structures for integrated Control/Structure design. An extension of the Two-Input Two-Output Port (TITOP) approach is here developed. The authors had already proposed such framework for simple beam-like structures: each beam was considered as a TITOP sub-system that could be interconnected to another beam thanks to the ports. The present work studies bodies with multiple attaching points by allowing complex interconnections among several sub-structures in tree-like assembly. The TITOP approach is extended to generate NINOP (N-Input N-Output Port) models. A Matlab toolbox is developed integrating beam and bending plate elements. In particular a NINOP formulation of bending plates is proposed to solve analytic two-dimensional problems. The computation of NINOP models using the outputs of a MSC/Nastran modal analysis is also investigated in order to directly use the results provided by a commercial finite element software. The main advantage of this tool is to provide a model of a multibody system under the form of a block diagram with a minimal number of states. This model is easy to operate for preliminary design and control. An illustrative example highlights the potential of the proposed approach: the synthesis of the dynamical model of a spacecraft with two deployable and flexible solar arrays.

Complexity reduction of biochemical rate expressions.

PubMed

Schmidt, Henning; Madsen, Mads F; Danø, Sune; Cedersund, Gunnar

2008-03-15

The current trend in dynamical modelling of biochemical systems is to construct more and more mechanistically detailed and thus complex models. The complexity is reflected in the number of dynamic state variables and parameters, as well as in the complexity of the kinetic rate expressions. However, a greater level of complexity, or level of detail, does not necessarily imply better models, or a better understanding of the underlying processes. Data often does not contain enough information to discriminate between different model hypotheses, and such overparameterization makes it hard to establish the validity of the various parts of the model. Consequently, there is an increasing demand for model reduction methods. We present a new reduction method that reduces complex rational rate expressions, such as those often used to describe enzymatic reactions. The method is a novel term-based identifiability analysis, which is easy to use and allows for user-specified reductions of individual rate expressions in complete models. The method is one of the first methods to meet the classical engineering objective of improved parameter identifiability without losing the systems biology demand of preserved biochemical interpretation. The method has been implemented in the Systems Biology Toolbox 2 for MATLAB, which is freely available from http://www.sbtoolbox2.org. The Supplementary Material contains scripts that show how to use it by applying the method to the example models, discussed in this article.

Expanded experimental parameter space of semiflexible polymer assemblies through programmable nanomaterials

NASA Astrophysics Data System (ADS)

Smith, David; Schuldt, Carsten; Lorenz, Jessica; Tschirner, Teresa; Moebius-Winkler, Maximilian; Kaes, Josef; Glaser, Martin; Haendler, Tina; Schnauss, Joerg

2015-03-01

Biologically evolved materials are often used as inspiration in the development of new materials as well as examinations into the underlying physical principles governing their behavior. For instance, the biopolymer constituents of the highly dynamic cellular cytoskeleton such as actin have inspired a deep understanding of soft polymer-based materials. However, the molecular toolbox provided by biological systems has been evolutionarily optimized to carry out the necessary functions of cells, and the inability modify basic properties such as biopolymer stiffness hinders a meticulous examination of parameter space. Using actin as inspiration, we circumvent these limitations using model systems assembled from programmable materials such as DNA. Nanorods with comparable, but controllable dimensions and mechanical properties as actin can be constructed from small sets of specially designed DNA strands. In entangled gels, these allow us to systematically determine the dependence of network mechanical properties on parameters such as persistence length and crosslink strength. At higher concentrations in the presence of local attractive forces, we see a transition to highly-ordered bundled and ``aster'' phases similar to those previously characterized in systems of actin or microtubules.

Development of NTCIP-based portable traffic signal evaluation system.

DOT National Transportation Integrated Search

2014-10-01

The objective of this project was to develop a custom toolbox for monitoring and troubleshooting operational : issues and faults at signalized intersections and diamond interchanges, and for providing a mechanism to : facilitate signal timing optimiz...

Expanding the KATE toolbox

NASA Technical Reports Server (NTRS)

Thomas, Stan J.

1993-01-01

KATE (Knowledge-based Autonomous Test Engineer) is a model-based software system developed in the Artificial Intelligence Laboratory at the Kennedy Space Center for monitoring, fault detection, and control of launch vehicles and ground support systems. In order to bring KATE to the level of performance, functionality, and integratability needed for firing room applications, efforts are underway to implement KATE in the C++ programming language using an X-windows interface. Two programs which were designed and added to the collection of tools which comprise the KATE toolbox are described. The first tool, called the schematic viewer, gives the KATE user the capability to view digitized schematic drawings in the KATE environment. The second tool, called the model editor, gives the KATE model builder a tool for creating and editing knowledge base files. Design and implementation issues having to do with these two tools are discussed. It will be useful to anyone maintaining or extending either the schematic viewer or the model editor.

Air Sensor Toolbox

EPA Pesticide Factsheets

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.

Demonstration of a Fractured Rock Geophysical Toolbox (FRGT) for Characterization and Monitoring of DNAPL Biodegradation in Fractured Rock Aquifers

DTIC Science & Technology

2016-01-01

USER’S GUIDE Demonstration of a Fractured Rock Geophysical Toolbox (FRGT) for Characterization and Monitoring of DNAPL Biodegradation in...Toolbox (FRGT) for Characterization and Monitoring of DNAPL Biodegradation in Fractured Rock Aquifers F.D. Day-Lewis, C.D. Johnson, J.H. Williams, C.L...are doomed to failure. DNAPL biodegradation charactrization and monitoring, remediation, fractured rock aquifers. Unclassified Unclassified UU UL 6

Explaining Society: An Expanded Toolbox for Social Scientists

PubMed Central

Bell, David C.; Atkinson-Schnell, Jodie L.; DiBacco, Aron E.

2012-01-01

We propose for social scientists a theoretical toolbox containing a set of motivations that neurobiologists have recently validated. We show how these motivations can be used to create a theory of society recognizably similar to existing stable societies (sustainable, self-reproducing, and largely peaceful). Using this toolbox, we describe society in terms of three institutions: economy (a source of sustainability), government (peace), and the family (reproducibility). Conducting a thought experiment in three parts, we begin with a simple theory with only two motivations. We then create successive theories that systematically add motivations, showing that each element in the toolbox makes its own contribution to explain the workings of a stable society and that the family has a critical role in this process. PMID:23082093

Statistical inference approach to structural reconstruction of complex networks from binary time series

NASA Astrophysics Data System (ADS)

Ma, Chuang; Chen, Han-Shuang; Lai, Ying-Cheng; Zhang, Hai-Feng

2018-02-01

Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains challenging. We articulate a statistical inference based approach to this problem. In particular, exploiting the expectation-maximization (EM) algorithm, we develop a method to ascertain the neighbors of any node in the network based solely on binary data, thereby recovering the full topology of the network. A key ingredient of our method is the maximum-likelihood estimation of the probabilities associated with actual or nonexistent links, and we show that the EM algorithm can distinguish the two kinds of probability values without any ambiguity, insofar as the length of the available binary time series is reasonably long. Our method does not require any a priori knowledge of the detailed dynamical processes, is parameter-free, and is capable of accurate reconstruction even in the presence of noise. We demonstrate the method using combinations of distinct types of binary dynamical processes and network topologies, and provide a physical understanding of the underlying reconstruction mechanism. Our statistical inference based reconstruction method contributes an additional piece to the rapidly expanding "toolbox" of data based reverse engineering of complex networked systems.

Statistical inference approach to structural reconstruction of complex networks from binary time series.

PubMed

Ma, Chuang; Chen, Han-Shuang; Lai, Ying-Cheng; Zhang, Hai-Feng

2018-02-01

Complex networks hosting binary-state dynamics arise in a variety of contexts. In spite of previous works, to fully reconstruct the network structure from observed binary data remains challenging. We articulate a statistical inference based approach to this problem. In particular, exploiting the expectation-maximization (EM) algorithm, we develop a method to ascertain the neighbors of any node in the network based solely on binary data, thereby recovering the full topology of the network. A key ingredient of our method is the maximum-likelihood estimation of the probabilities associated with actual or nonexistent links, and we show that the EM algorithm can distinguish the two kinds of probability values without any ambiguity, insofar as the length of the available binary time series is reasonably long. Our method does not require any a priori knowledge of the detailed dynamical processes, is parameter-free, and is capable of accurate reconstruction even in the presence of noise. We demonstrate the method using combinations of distinct types of binary dynamical processes and network topologies, and provide a physical understanding of the underlying reconstruction mechanism. Our statistical inference based reconstruction method contributes an additional piece to the rapidly expanding "toolbox" of data based reverse engineering of complex networked systems.

Toolbox for Renewable Energy Project Development

EPA Pesticide Factsheets

The Toolbox for Renewable Energy Project Development summarizes key project development issues, addresses how to overcome major hurdles, and provides a curated directory of project development resources.

Numerical Study of Impingement Location of Liquid Jet Poured from a Tilting Ladle with Lip Spout

NASA Astrophysics Data System (ADS)

Castilla, R.; Gamez-Montero, P. J.; Raush, G.; Khamashta, M.; Codina, E.

2017-04-01

A new approach for simulating liquid poured from a tilting lip spout is presented, using neither a dynamic mesh nor the moving solid solution method. In this case only the tilting ladle is moving, so we propose to rotate the gravitational acceleration at an angular velocity prescribed by a geometrical and dynamical calculation to keep the poured flow rate constant. This angular velocity is applied to modify the orientation of the gravity vector in computational fluid dynamics (CFD) simulations using the OpenFOAM® toolbox. Also, fictitious forces are considered. The modified solver is used to calculate the impingement location for six spout geometries and compare the jet dispersion there. This method could offer an inexpensive tool to calculate optimal spout geometries to reduce sprue size in the metal casting industry.

Comparative analysis of existing models for power-grid synchronization

NASA Astrophysics Data System (ADS)

Nishikawa, Takashi; Motter, Adilson E.

2015-01-01

The dynamics of power-grid networks is becoming an increasingly active area of research within the physics and network science communities. The results from such studies are typically insightful and illustrative, but are often based on simplifying assumptions that can be either difficult to assess or not fully justified for realistic applications. Here we perform a comprehensive comparative analysis of three leading models recently used to study synchronization dynamics in power-grid networks—a fundamental problem of practical significance given that frequency synchronization of all power generators in the same interconnection is a necessary condition for a power grid to operate. We show that each of these models can be derived from first principles within a common framework based on the classical model of a generator, thereby clarifying all assumptions involved. This framework allows us to view power grids as complex networks of coupled second-order phase oscillators with both forcing and damping terms. Using simple illustrative examples, test systems, and real power-grid datasets, we study the inherent frequencies of the oscillators as well as their coupling structure, comparing across the different models. We demonstrate, in particular, that if the network structure is not homogeneous, generators with identical parameters need to be modeled as non-identical oscillators in general. We also discuss an approach to estimate the required (dynamical) system parameters that are unavailable in typical power-grid datasets, their use for computing the constants of each of the three models, and an open-source MATLAB toolbox that we provide for these computations.

Stochastic theory of non-Markovian open quantum system

NASA Astrophysics Data System (ADS)

Zhao, Xinyu

In this thesis, a stochastic approach to solving non-Markovian open quantum system called "non-Markovian quantum state diffusion" (NMQSD) approach is discussed in details. The NMQSD approach can serve as an analytical and numerical tool to study the dynamics of the open quantum systems. We explore three main topics of the NMQSD approach. First, we extend the NMQSD approach to many-body open systems such as two-qubit system and coupled N-cavity system. Based on the exact NMQSD equations and the corresponding master equations, we investigate several interesting non-Markovian features due to the memory effect of the environment such as the entanglement generation in two-qubit system and the coherence and entanglement transfer between cavities. Second, we extend the original NMQSD approach to the case that system is coupled to a fermionic bath or a spin bath. By introducing the anti-commutative Grassmann noise and the fermionic coherent state, we derive a fermionic NMQSD equation and the corresponding master equation. The fermionic NMQSD is illustrated by several examples. In a single qubit dissipative example, we have explicitly demonstrated that the NMQSD approach and the ordinary quantum mechanics give rise to the exactly same results. We also show the difference between fermionic bath and bosonic bath. Third, we combine the bosonic and fermionic NMQSD approach to develop a unified NMQSD approach to study the case that an open system is coupled to a bosonic bath and a fermionic bath simultaneously. For all practical purposes, we develop a set of useful computer programs (NMQSD Toolbox) to implement the NMQSD equation in realistic computations. In particular, we develop an algorithm to calculate the exact O operator involved in the NMQSD equation. The NMQSD toolbox is designed to be user friendly, so it will be especially valuable for a non-expert who has interest to employ the NMQSD equation to solve a practical problem. Apart from the central topics on the NMQSD approach, we also study the environment-assisted error correction (EAEC) scheme. We have proposed two new schemes beyond the original EAEC scheme. Our schemes can be used to recover an unknown entangled initial state for a dephasing channel and recover an arbitrary unknown initial state for a dissipative channel using a generalized quantum measurement.

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

NASA Astrophysics Data System (ADS)

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.

Characterization of Disease-Related Covariance Topographies with SSMPCA Toolbox: Effects of Spatial Normalization and PET Scanners

PubMed Central

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

2013-01-01

In order 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 [18F]fluorodeoxyglucose PET scans from PD patients 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 PD patients 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. PMID:23671030

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

PubMed

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. Copyright © 2013 Wiley Periodicals, Inc.

MNPBEM - A Matlab toolbox for the simulation of plasmonic nanoparticles

NASA Astrophysics Data System (ADS)

Hohenester, Ulrich; Trügler, Andreas

2012-02-01

MNPBEM is a Matlab toolbox for the simulation of metallic nanoparticles (MNP), using a boundary element method (BEM) approach. The main purpose of the toolbox is to solve Maxwell's equations for a dielectric environment where bodies with homogeneous and isotropic dielectric functions are separated by abrupt interfaces. Although the approach is in principle suited for arbitrary body sizes and photon energies, it is tested (and probably works best) for metallic nanoparticles with sizes ranging from a few to a few hundreds of nanometers, and for frequencies in the optical and near-infrared regime. The toolbox has been implemented with Matlab classes. These classes can be easily combined, which has the advantage that one can adapt the simulation programs flexibly for various applications. Program summaryProgram title: MNPBEM Catalogue identifier: AEKJ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKJ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v2 No. of lines in distributed program, including test data, etc.: 15 700 No. of bytes in distributed program, including test data, etc.: 891 417 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 GByte Classification: 18 Nature of problem: Solve Maxwell's equations for dielectric particles with homogeneous dielectric functions separated by abrupt interfaces. Solution method: Boundary element method using electromagnetic potentials. Running time: Depending on surface discretization between seconds and hours.

Engineering entrainment and adaptation in limit cycle systems : From biological inspiration to applications in robotics.

PubMed

Buchli, Jonas; Righetti, Ludovic; Ijspeert, Auke Jan

2006-12-01

Periodic behavior is key to life and is observed in multiple instances and at multiple time scales in our metabolism, our natural environment, and our engineered environment. A natural way of modeling or generating periodic behavior is done by using oscillators, i.e., dynamical systems that exhibit limit cycle behavior. While there is extensive literature on methods to analyze such dynamical systems, much less work has been done on methods to synthesize an oscillator to exhibit some specific desired characteristics. The goal of this article is twofold: (1) to provide a framework for characterizing and designing oscillators and (2) to review how classes of well-known oscillators can be understood and related to this framework. The basis of the framework is to characterize oscillators in terms of their fundamental temporal and spatial behavior and in terms of properties that these two behaviors can be designed to exhibit. This focus on fundamental properties is important because it allows us to systematically compare a large variety of oscillators that might at first sight appear very different from each other. We identify several specifications that are useful for design, such as frequency-locking behavior, phase-locking behavior, and specific output signal shape. We also identify two classes of design methods by which these specifications can be met, namely offline methods and online methods. By relating these specifications to our framework and by presenting several examples of how oscillators have been designed in the literature, this article provides a useful methodology and toolbox for designing oscillators for a wide range of purposes. In particular, the focus on synthesis of limit cycle dynamical systems should be useful both for engineering and for computational modeling of physical or biological phenomena.

Acrylamide mitigation strategies: critical appraisal of the FoodDrinkEurope toolbox.

PubMed

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.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, Per; Benveniste, Jerome

2017-04-01

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.

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, Per; Benveniste, Jerome; Team Gut

2016-04-01

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.

The Computational Ecologist’s Toolbox

EPA Science Inventory

Computational ecology, nestled in the broader field of data science, is an interdisciplinary field that attempts to improve our understanding of complex ecological systems through the use of modern computational methods. Computational ecology is based on a union of competence in...

Agricultural Conservation Planning Toolbox User's Manual

USDA-ARS?s Scientific Manuscript database

Agricultural Conservation Planning Framework (ACPF) comprises an approach for applying concepts of precision conservation to watershed planning in agricultural landscapes. To enable application of this approach, USDA/ARS has developed a set of Geographic Information System (GIS) based software tools...

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

DOT National Transportation Integrated Search

2010-12-01

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

Final Ecosystem Goods and Services Classification System (FEGS-CS)

EPA Pesticide Factsheets

Eco-Box is a toolbox for exposure assessors. Its purpose is to provide a compendium of exposure assessment and risk characterization tools that will present comprehensive step-by-step guidance and links to relevant exposure assessment data bases

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

PubMed

Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K

2011-04-15

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. 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 software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.

Rad Toolbox User's Guide

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

Eckerman, Keith F.; Sjoreen, Andrea L.

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 acceptedmore » 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.« less

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

PubMed

Clayson, Peter E; Miller, Gregory A

2017-01-01

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

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

PubMed

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

2013-01-01

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

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

PubMed Central

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

2013-01-01

Recent advances in sensor and recording technology have allowed scientists to acquire very large time-series datasets. Researchers often analyze these datasets in the context of events, which are intervals of time where the properties of the signal change relative to a baseline signal. We have developed DETECT, a MATLAB toolbox for detecting event time intervals in long, multi-channel time series. Our primary goal is to produce a toolbox that is simple for researchers to use, allowing them to quickly train a model on multiple classes of events, assess the accuracy of the model, and determine how closely the results agree with their own manual identification of events without requiring extensive programming knowledge or machine learning experience. As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and show the functionality of the tools found in the toolbox. We also discuss the application of DETECT for identifying irregular heartbeat waveforms found in electrocardiogram (ECG) data as an additional illustration. PMID:23638169

A preclinical cognitive test battery to parallel the National Institute of Health Toolbox in humans: bridging the translational gap.

PubMed

Snigdha, Shikha; Milgram, Norton W; Willis, Sherry L; Albert, Marylin; Weintraub, S; Fortin, Norbert J; Cotman, Carl W

2013-07-01

A major goal of animal research is to identify interventions that can promote successful aging and delay or reverse age-related cognitive decline in humans. Recent advances in standardizing cognitive assessment tools for humans have the potential to bring preclinical work closer to human research in aging and Alzheimer's disease. The National Institute of Health (NIH) has led an initiative to develop a comprehensive Toolbox for Neurologic Behavioral Function (NIH Toolbox) to evaluate cognitive, motor, sensory and emotional function for use in epidemiologic and clinical studies spanning 3 to 85 years of age. This paper aims to analyze the strengths and limitations of animal behavioral tests that can be used to parallel those in the NIH Toolbox. We conclude that there are several paradigms available to define a preclinical battery that parallels the NIH Toolbox. We also suggest areas in which new tests may benefit the development of a comprehensive preclinical test battery for assessment of cognitive function in animal models of aging and Alzheimer's disease. Copyright © 2013 Elsevier Inc. All rights reserved.

A preclinical cognitive test battery to parallel the National Institute of Health Toolbox in humans: bridging the translational gap

PubMed Central

Snigdha, Shikha; Milgram, Norton W.; Willis, Sherry L.; Albert, Marylin; Weintraub, S.; Fortin, Norbert J.; Cotman, Carl W.

2013-01-01

A major goal of animal research is to identify interventions that can promote successful aging and delay or reverse age-related cognitive decline in humans. Recent advances in standardizing cognitive assessment tools for humans have the potential to bring preclinical work closer to human research in aging and Alzheimer’s disease. The National Institute of Health (NIH) has led an initiative to develop a comprehensive Toolbox for Neurologic Behavioral Function (NIH Toolbox) to evaluate cognitive, motor, sensory and emotional function for use in epidemiologic and clinical studies spanning 3 to 85 years of age. This paper aims to analyze the strengths and limitations of animal behavioral tests that can be used to parallel those in the NIH Toolbox. We conclude that there are several paradigms available to define a preclinical battery that parallels the NIH Toolbox. We also suggest areas in which new tests may benefit the development of a comprehensive preclinical test battery for assessment of cognitive function in animal models of aging and Alzheimer’s disease. PMID:23434040

A GIS tool for two-dimensional glacier-terminus change tracking

NASA Astrophysics Data System (ADS)

Urbanski, Jacek Andrzej

2018-02-01

This paper presents a Glacier Termini Tracking (GTT) toolbox for the two-dimensional analysis of glacier-terminus position changes. The input consists of a vector layer with several termini lines relating to the same glacier at different times. The output layers allow analyses to be conducted of glacier-terminus retreats, changes in retreats over time and along the ice face, and glacier-terminus fluctuations over time. The application of three tools from the toolbox is demonstrated via the analysis of eight glacier-terminus retreats and fluctuations at the Hornsund fjord in south Svalbard. It is proposed that this toolbox may also be useful in the study of other line features that change over time, like coastlines and rivers. The toolbox has been coded in Python and runs via ArcGIS.

The GMT/MATLAB Toolbox

NASA Astrophysics Data System (ADS)

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.

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

DTIC Science & Technology

2013-04-24

DETECT: A MATLAB Toolbox for Event Detection and Identification in Time Series, with Applications to Artifact Detection in EEG Signals Vernon...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...As an illustration, we discuss application of the DETECT toolbox for detecting signal artifacts found in continuous multi-channel EEG recordings and

Real time wind farm emulation using SimWindFarm toolbox

NASA Astrophysics Data System (ADS)

Topor, Marcel

2016-06-01

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

40 CFR 141.718 - Treatment performance toolbox components.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for.... (a) Combined filter performance. Systems using conventional filtration treatment or direct filtration... the criteria in this paragraph. Combined filter effluent (CFE) turbidity must be less than or equal to...

40 CFR 141.718 - Treatment performance toolbox components.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for.... (a) Combined filter performance. Systems using conventional filtration treatment or direct filtration... the criteria in this paragraph. Combined filter effluent (CFE) turbidity must be less than or equal to...

40 CFR 141.718 - Treatment performance toolbox components.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) WATER PROGRAMS (CONTINUED) NATIONAL PRIMARY DRINKING WATER REGULATIONS Enhanced Treatment for.... (a) Combined filter performance. Systems using conventional filtration treatment or direct filtration... the criteria in this paragraph. Combined filter effluent (CFE) turbidity must be less than or equal to...

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

PubMed Central

Magri, Cesare; Whittingstall, Kevin; Singh, Vanessa; Logothetis, Nikos K; Panzeri, Stefano

2009-01-01

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 and data-robust computations of the most relevant quantities used in information theoretic analysis of neural data. The toolbox can be easily used within Matlab, the environment used by most neuroscience laboratories for the acquisition, preprocessing and plotting of neural data. It can therefore significantly enlarge the domain of application of information theory to neuroscience, and lead to new discoveries about the neural code. PMID:19607698

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

PubMed

Magri, Cesare; Whittingstall, Kevin; Singh, Vanessa; Logothetis, Nikos K; Panzeri, Stefano

2009-07-16

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. 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. The new toolbox presented here implements fast and data-robust computations of the most relevant quantities used in information theoretic analysis of neural data. The toolbox can be easily used within Matlab, the environment used by most neuroscience laboratories for the acquisition, preprocessing and plotting of neural data. It can therefore significantly enlarge the domain of application of information theory to neuroscience, and lead to new discoveries about the neural code.

Improving student comprehension of the interconnectivity of the hydrologic cycle with a novel 'hydrology toolbox', integrated watershed model, and companion textbook

NASA Astrophysics Data System (ADS)

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

2013-12-01

Concepts in introductory hydrology courses are often taught in the context of process-based modeling that ultimately is integrated into a watershed model. In an effort to reduce the learning curve associated with applying hydrologic concepts to real-world applications, we developed and incorporated a 'hydrology toolbox' that complements a new, companion textbook into introductory undergraduate hydrology courses. The hydrology toolbox contains the basic building blocks (functions coded in MATLAB) for an integrated spatially-distributed watershed model that makes hydrologic topics (e.g. precipitation, snow, radiation, evaporation, unsaturated flow, infiltration, groundwater, and runoff) more user-friendly and accessible for students. The toolbox functions can be used in a modular format so that students can study individual hydrologic processes and become familiar with the hydrology toolbox. This approach allows such courses to emphasize understanding and application of hydrologic concepts rather than computer coding or programming. While topics in introductory hydrology courses are often introduced and taught independently or semi-independently, they are inherently interconnected. These toolbox functions are therefore linked together at the end of the course to reinforce a holistic understanding of how these hydrologic processes are measured, interconnected, and modeled. They are integrated into a spatially-distributed watershed model or numerical laboratory where students can explore a range of topics such as rainfall-runoff modeling, urbanization, deforestation, watershed response to changes in parameters or forcings, etc. Model output can readily be visualized and analyzed by students to understand watershed response in a real river basin or a simple 'toy' basin. These tools complement the textbook, each of which has been well received by students in multiple hydrology courses with various disciplinary backgrounds. The same governing equations that students have studied in the textbook and used in the toolbox have been encapsulated in the watershed model. Therefore, the combination of the hydrology toolbox, integrated watershed model, and textbook tends to eliminate the potential disconnect between process-based modeling and an 'off-the-shelf' watershed model.

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

NASA Astrophysics Data System (ADS)

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

2017-04-01

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

BiKEGG: a COBRA toolbox extension for bridging the BiGG and KEGG databases.

PubMed

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.

Broadview Radar Altimetry Toolbox

NASA Astrophysics Data System (ADS)

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

2017-04-01

The universal altimetry toolbox, BRAT (Broadview Radar Altimetry Toolbox) which can read all previous and current altimetry missions' data, incorporates now the capability to read the upcoming Sentinel3 L1 and L2 products. ESA endeavoured to develop and supply this capability to support the users of the future Sentinel3 SAR Altimetry Mission. BRAT is a collection of tools and tutorial documents designed to facilitate the processing of radar altimetry data. This project started in 2005 from the joint efforts of ESA (European Space Agency) and CNES (Centre National d'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats. The BratGUI is the frontend for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with MATLAB/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the dataformatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as NetCDF, ASCII text files, KML (Google Earth) and raster images (JPEG, PNG, etc.). Several kinds of computations can be done within BRAT involving combinations of data fields that the user can save for posterior reuse or using the already embedded formulas that include the standard oceanographic altimetry formulas. The Radar Altimeter Tutorial, that contains a strong introduction to altimetry, shows its applications in different fields such as Oceanography, Cryosphere, Geodesy, Hydrology among others. Included are also "use cases", with step-by-step examples, on how to use the toolbox in the different contexts. The Sentinel3 SAR Altimetry Toolbox shall benefit from the current BRAT version. While developing the toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific "use cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The Broadview Radar Altimetry Toolbox is a continuation of the Basic Radar Altimetry Toolbox. While developing the new toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific "use cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The first release of the new Radar Altimetry Toolbox was published in September 2015. It incorporates the capability to read S3 products as well as the new CryoSat2 Baseline C. The second release of the Toolbox, published in October 2016, has a new graphical user interface and other visualisation improvements. The third release (January 2017) includes more features and solves issues from the previous versions.

Smoke Ready Toolbox for Wildfires

EPA Pesticide Factsheets

This site provides an online Smoke Ready Toolbox for Wildfires, which lists resources and tools that provide information on health impacts from smoke exposure, current fire conditions and forecasts and strategies to reduce exposure to smoke.

Developing a congestion mitigation toolbox.

DOT National Transportation Integrated Search

2011-09-30

Researchers created A Michigan Toolbox for Mitigating Traffic Congestion to be a useful desk reference for practitioners and an educational tool for elected officials acting through public policy boards to better understand the development, planning,...

CBP TOOLBOX VERSION 2.0: CODE INTEGRATION ENHANCEMENTS

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

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.more » 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.« less

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

PubMed

Tam, Wing-Kin; Yang, Zhi

2018-05-01

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

Designing School Systems for All Students: A Toolbox to Fix America's Schools

ERIC Educational Resources Information Center

Manley, Robert J.; Hawkins, Richard J.

2009-01-01

"Designing School Systems for All Students" provides a clear methodology for school leaders, teachers, and school board members to follow as they redesign their schools for the benefit of students. The authors demonstrate how school leaders set the expectations for all students to learn and grow as important contributors to the culture. In the…

Dheepak Krishnamurthy | NREL

Science.gov Websites

. doi: 10.1109/TPWRS.2015.2399171 D. Krishnamurthy; C. Uckun; Z. Zhou; P. Thimmapuram; A. Botterud Systems, vol.PP, no.99, pp.1-1 doi: 10.1109/TPWRS.2017.2685347 A. Pratt, D. Krishnamurthy, M. Ruth, H. Wu : 10.1109/MELE.2016.2614188 D. Krishnamurthy, psst: An open-source power system simulation toolbox in Python

SANITARY SEWER OVERFLOW ANALYSIS AND PLANNING (SSOAP) TOOLBOX

EPA Science Inventory

Description: The Nation's sanitary-sewer infrastructure is aging, with some sewers dating back over 100 years. Nationwide, there are more than 19,500 municipal sanitary-sewer collection systems serving an estimated 150 million people and about 40,000 SSO events per year. Becau...

EPA SSOAP Toolbox – Evolution and Applications

EPA Science Inventory

The nation’s sanitary sewer infrastructure is aging, with some sewers dating back more than 100 years. Nationwide, there are more than 19,500 municipal sanitary-sewer collection systems serving an estimated 150 million people and about 40,000 sanitary sewer overflow (SSO) ...

SSOAP - A USEPA Toolbox for Sanitary Sewer Overflow Analysis and Control Planning - Presentation

EPA Science Inventory

The United States Environmental Protection Agency (USEPA) has identified a need to use proven methodologies to develop computer tools that help communities properly characterize rainfall-derived infiltration and inflow (RDII) into sanitary sewer systems and develop sanitary sewer...

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

DOE PAGES

Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.; ...

2017-04-12

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

New understanding of rhizosphere processes enabled by advances in molecular and spatially resolved techniques

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

Hess, Nancy J.; Paša-Tolić, Ljiljana; Bailey, Vanessa L.

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

Long series of geomagnetic measurements - unique at satellite era

NASA Astrophysics Data System (ADS)

Mandea, Mioara; Balasis, Georgios

2017-04-01

We have long appreciated that magnetic measurements obtained at Earth's surface are of great value in characterizing geomagnetic field behavior and then probing the deep interior of our Planet. The existence of new magnetic satellite missions data offer a new detailed global understanding of the geomagnetic field. However, when our interest moves over long-time scales, the very long series of measurements play an important role. Here, we firstly provide an updated series of geomagnetic declination in Paris, shortly after a very special occasion: its value has reached zero after some 350 years of westerly values. We take this occasion to emphasize the importance of long series of continuous measurements, mainly when various techniques are used to detect the abrupt changes in geomagnetic field, the geomagnetic jerks. Many novel concepts originated in dynamical systems or information theory have been developed, partly motivated by specific research questions from the geosciences. This continuously extending toolbox of nonlinear time series analysis is a key to understand the complexity of geomagnetic field. Here, motivated by these efforts, a series of entropy analysis are applied to geomagnetic field time series aiming to detect dynamical complex changes associated with geomagnetic jerks.

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

Hess, Nancy J.; Pasa-Tolic, Ljiljana; Bailey, Vanessa L.

Understanding the role played by microorganisms within soil systems is challenged by the unique intersection of physics, chemistry, mineralogy and biology in fostering habitat for soil microbial communities. To address these challenges will require observations across multiple spatial and temporal scales to capture the dynamics and emergent behavior from complex and interdependent processes. The heterogeneity and complexity of the rhizosphere require advanced techniques that press the simultaneous frontiers of spatial resolution, analyte sensitivity and specificity, reproducibility, large dynamic range, and high throughput. Fortunately many exciting technical advancements are now available to inform and guide the development of new hypotheses. Themore » aim of this Special issue is to provide a holistic view of the rhizosphere in the perspective of modern molecular biology methodologies that enabled a highly-focused, detailed view on the processes in the rhizosphere, including numerous, strong and complex interactions between plant roots, soil constituents and microorganisms. We discuss the current rhizosphere research challenges and knowledge gaps, as well as perspectives and approaches using newly available state-of-the-art toolboxes. These new approaches and methodologies allow the study of rhizosphere processes and properties, and rhizosphere as a central component of ecosystems and biogeochemical cycles.« less

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

PubMed Central

2018-01-01

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

A new method for the prediction of chatter stability lobes based on dynamic cutting force simulation model and support vector machine

NASA Astrophysics Data System (ADS)

Peng, Chong; Wang, Lun; Liao, T. Warren

2015-10-01

Currently, chatter has become the critical factor in hindering machining quality and productivity in machining processes. To avoid cutting chatter, a new method based on dynamic cutting force simulation model and support vector machine (SVM) is presented for the prediction of chatter stability lobes. The cutting force is selected as the monitoring signal, and the wavelet energy entropy theory is used to extract the feature vectors. A support vector machine is constructed using the MATLAB LIBSVM toolbox for pattern classification based on the feature vectors derived from the experimental cutting data. Then combining with the dynamic cutting force simulation model, the stability lobes diagram (SLD) can be estimated. Finally, the predicted results are compared with existing methods such as zero-order analytical (ZOA) and semi-discretization (SD) method as well as actual cutting experimental results to confirm the validity of this new method.

A Molecular Toolbox for Rapid Generation of Viral Vectors to Up- or Down-Regulate Neuronal Gene Expression in vivo

PubMed Central

White, Melanie D.; Milne, Ruth V. J.; Nolan, Matthew F.

2011-01-01

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 miRNA). We show that AAV assembled to express HCN1 miRNA produces efficacious and specific in vivo knockdown of HCN1 channels. Comparison of in vivo viral transduction using HCN1 miRNA 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. PMID:21772812

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

PubMed Central

Hull, Michael J.; Willshaw, David J.

2014-01-01

The broad structure of a modeling study can often be explained over a cup of coffee, but converting this high-level conceptual idea into graphs of the final simulation results may require many weeks of sitting at a computer. Although models themselves can be complex, often many mental resources are wasted working around complexities of the software ecosystem such as fighting to manage files, interfacing between tools and data formats, finding mistakes in code or working out the units of variables. morphforge is a high-level, Python toolbox for building and managing simulations of small populations of multicompartmental biophysical model neurons. An entire in silico experiment, including the definition of neuronal morphologies, channel descriptions, stimuli, visualization and analysis of results can be written within a single short Python script using high-level objects. Multiple independent simulations can be created and run from a single script, allowing parameter spaces to be investigated. Consideration has been given to the reuse of both algorithmic and parameterizable components to allow both specific and stochastic parameter variations. Some other features of the toolbox include: the automatic generation of human-readable documentation (e.g., PDF files) about a simulation; the transparent handling of different biophysical units; a novel mechanism for plotting simulation results based on a system of tags; and an architecture that supports both the use of established formats for defining channels and synapses (e.g., MODL files), and the possibility to support other libraries and standards easily. We hope that this toolbox will allow scientists to quickly build simulations of multicompartmental model neurons for research and serve as a platform for further tool development. PMID:24478690

Local soil quality assessment of north-central Namibia: integrating farmers' and technical knowledge

NASA Astrophysics Data System (ADS)

Prudat, Brice; Bloemertz, Lena; Kuhn, Nikolaus J.

2018-02-01

Soil degradation is a major threat for farmers of semi-arid north-central Namibia. Soil conservation practices can be promoted by the development of soil quality (SQ) evaluation toolboxes that provide ways to evaluate soil degradation. However, such toolboxes must be adapted to local conditions to reach farmers. Based on qualitative (interviews and soil descriptions) and quantitative (laboratory analyses) data, we developed a set of SQ indicators relevant for our study area that integrates farmers' field experiences (FFEs) and technical knowledge. We suggest using participatory mapping to delineate soil units (Oshikwanyama soil units, KwSUs) based on FFEs, which highlight mostly soil properties that integrate long-term productivity and soil hydrological characteristics (i.e. internal SQ). The actual SQ evaluation of a location depends on the KwSU described and is thereafter assessed by field soil texture (i.e. chemical fertility potential) and by soil colour shade (i.e. SOC status). This three-level information aims to reveal SQ improvement potential by comparing, for any location, (a) estimated clay content against median clay content (specific to KwSU) and (b) soil organic status against calculated optimal values (depends on clay content). The combination of farmers' and technical assessment cumulates advantages of both systems of knowledge, namely the integrated long-term knowledge of the farmers and a short- and medium-term SQ status assessment. The toolbox is a suggestion for evaluating SQ and aims to help farmers, rural development planners and researchers from all fields of studies understanding SQ issues in north-central Namibia. This suggested SQ toolbox is adapted to a restricted area of north-central Namibia, but similar tools could be developed in most areas where small-scale agriculture prevails.

A Michigan toolbox for mitigating traffic congestion.

DOT National Transportation Integrated Search

2011-09-30

"Researchers created A Michigan Toolbox for Mitigating Traffic Congestion to be a useful desk reference : for practitioners and an educational tool for elected officials acting through public policy boards to better : understand the development, plan...

EPA ExpoBox Toolbox Search

EPA Pesticide Factsheets

EPA ExpoBox is a toolbox for exposure assessors. Its purpose is to provide a compendium of exposure assessment and risk characterization tools that will present comprehensive step-by-step guidance and links to relevant assessment data bases,

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

Code of Federal Regulations, 2013 CFR

2013-07-01

... criteria are in § 141.716(b). Pre Filtration Toolbox Options (3) Presedimentation basin with coagulation 0... separate granular media filtration stage if treatment train includes coagulation prior to first filter...

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

Code of Federal Regulations, 2014 CFR

2014-07-01

... criteria are in § 141.716(b). Pre Filtration Toolbox Options (3) Presedimentation basin with coagulation 0... separate granular media filtration stage if treatment train includes coagulation prior to first filter...

Air Sensor Toolbox for Citizen Scientists

EPA Pesticide Factsheets

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.

A portable toolbox to monitor and evaluate signal operations.

DOT National Transportation Integrated Search

2011-10-01

Researchers from the Texas Transportation Institute developed a portable tool consisting of a fieldhardened : computer interfacing with the traffic signal cabinet through special enhanced Bus Interface Units. : The toolbox consisted of a monitoring t...

Air Sensor Toolbox: Resources and Funding

EPA Pesticide Factsheets

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.

A multiplexed microfluidic toolbox for the rapid optimization of affinity-driven partition in aqueous two phase systems.

PubMed

Bras, Eduardo J S; Soares, Ruben R G; Azevedo, Ana M; Fernandes, Pedro; Arévalo-Rodríguez, Miguel; Chu, Virginia; Conde, João P; Aires-Barros, M Raquel

2017-09-15

Antibodies and other protein products such as interferons and cytokines are biopharmaceuticals of critical importance which, in order to be safely administered, have to be thoroughly purified in a cost effective and efficient manner. The use of aqueous two-phase extraction (ATPE) is a viable option for this purification, but these systems are difficult to model and optimization procedures require lengthy and expensive screening processes. Here, a methodology for the rapid screening of antibody extraction conditions using a microfluidic channel-based toolbox is presented. A first microfluidic structure allows a simple negative-pressure driven rapid screening of up to 8 extraction conditions simultaneously, using less than 20μL of each phase-forming solution per experiment, while a second microfluidic structure allows the integration of multi-step extraction protocols based on the results obtained with the first device. In this paper, this microfluidic toolbox was used to demonstrate the potential of LYTAG fusion proteins used as affinity tags to optimize the partitioning of antibodies in ATPE processes, where a maximum partition coefficient (K) of 9.2 in a PEG 3350/phosphate system was obtained for the antibody extraction in the presence of the LYTAG-Z dual ligand. This represents an increase of approx. 3.7 fold when compared with the same conditions without the affinity molecule (K=2.5). Overall, this miniaturized and versatile approach allowed the rapid optimization of molecule partition followed by a proof-of-concept demonstration of an integrated back extraction procedure, both of which are critical procedures towards obtaining high purity biopharmaceuticals using ATPE. Copyright © 2017 Elsevier B.V. All rights reserved.

Optical performance assessment under environmental and mechanical perturbations in large, deployable telescopes

NASA Astrophysics Data System (ADS)

Folley, Christopher; Bronowicki, Allen

2005-09-01

Prediction of optical performance for large, deployable telescopes under environmental conditions and mechanical disturbances is a crucial part of the design verification process of such instruments for all phases of design and operation: ground testing, commissioning, and on-orbit operation. A Structural-Thermal-Optical-Performance (STOP) analysis methodology is often created that integrates the output of one analysis with the input of another. The integration of thermal environment predictions with structural models is relatively well understood, while the integration of structural deformation results into optical analysis/design software is less straightforward. A Matlab toolbox has been created that effectively integrates the predictions of mechanical deformations on optical elements generated by, for example, finite element analysis, and computes optical path differences for the distorted prescription. The engine of the toolbox is the real ray-tracing algorithm that allows the optical surfaces to be defined in a single, global coordinate system thereby allowing automatic alignment of the mechanical coordinate system with the optical coordinate system. Therefore, the physical location of the optical surfaces is identical in the optical prescription and the finite element model. The application of rigid body displacements to optical surfaces, however, is more general than for use solely in STOP analysis, such as the analysis of misalignments during the commissioning process. Furthermore, all the functionality of Matlab is available for optimization and control. Since this is a new tool for use on flight programs, it has been verified against CODE V. The toolbox' functionality, to date, is described, verification results are presented, and, as an example of its utility, results of a thermal distortion analysis are presented using the James Webb Space Telescope (JWST) prescription.

Delay differential analysis of time series.

PubMed

Lainscsek, Claudia; Sejnowski, Terrence J

2015-03-01

Nonlinear dynamical system analysis based on embedding theory has been used for modeling and prediction, but it also has applications to signal detection and classification of time series. An embedding creates a multidimensional geometrical object from a single time series. Traditionally either delay or derivative embeddings have been used. The delay embedding is composed of delayed versions of the signal, and the derivative embedding is composed of successive derivatives of the signal. The delay embedding has been extended to nonuniform embeddings to take multiple timescales into account. Both embeddings provide information on the underlying dynamical system without having direct access to all the system variables. Delay differential analysis is based on functional embeddings, a combination of the derivative embedding with nonuniform delay embeddings. Small delay differential equation (DDE) models that best represent relevant dynamic features of time series data are selected from a pool of candidate models for detection or classification. We show that the properties of DDEs support spectral analysis in the time domain where nonlinear correlation functions are used to detect frequencies, frequency and phase couplings, and bispectra. These can be efficiently computed with short time windows and are robust to noise. For frequency analysis, this framework is a multivariate extension of discrete Fourier transform (DFT), and for higher-order spectra, it is a linear and multivariate alternative to multidimensional fast Fourier transform of multidimensional correlations. This method can be applied to short or sparse time series and can be extended to cross-trial and cross-channel spectra if multiple short data segments of the same experiment are available. Together, this time-domain toolbox provides higher temporal resolution, increased frequency and phase coupling information, and it allows an easy and straightforward implementation of higher-order spectra across time compared with frequency-based methods such as the DFT and cross-spectral analysis.

EPA EMERGENCY PLANNING TOOLBOX

EPA Science Inventory

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...

Ironbound Community Citizen Science Toolbox Fact Sheet

EPA Pesticide Factsheets

EPA is partnering with Newark’s Ironbound Community Corporation (ICC) to design, develop, and pilot a Citizen Science Toolbox that will enable communities to collect their own environmental data and increase their ability to understand local conditions.

Evaluating a 2D image-based computerized approach for measuring riverine pebble roundness

NASA Astrophysics Data System (ADS)

Cassel, Mathieu; Piégay, Hervé; Lavé, Jérôme; Vaudor, Lise; Hadmoko Sri, Danang; Wibiwo Budi, Sandy; Lavigne, Franck

2018-06-01

The geometrical characteristics of pebbles are important features to study transport pathways, sedimentary history, depositional environments, abrasion processes or to target sediment sources. Both the shape and roundness of pebbles can be described by a still growing number of metrics in 2D and 3D or by visual charts. Despite new developments, existing tools remain proprietary and no pebble roundness toolbox has been available widely within the scientific community. The toolbox developed by Roussillon et al. (2009) automatically computes the size, shape and roundness indexes of pebbles from their 2D maximal projection plans. Using a digital camera, this toolbox operates using 2D pictures taken of pebbles placed on a one square meter red board, allowing data collection to be quickly and efficiently acquired at a large scale. Now that the toolbox is freely available for download,

Highway Safety Information System guidebook for the Maine state data files. Volume 1 : SAS file formats

DOT National Transportation Integrated Search

2012-05-05

As part of the Federal Highway Administration (FHWA) Traffic Analysis Toolbox (Volume XIII), this guide was designed to help corridor stakeholders implement the ICM AMS methodology successfully and effectively. It provides a step-by-step approach to ...

EPA's Sustainable Port Communities: a Knowledge System Approach to Increasing Resiliency

EPA Science Inventory

Create a Sustainability Assessment Toolbox for US ports that: • Addresses multiple issues faced by ports • Builds on work from other EPA Research Programs • Complements other resiliency work from federal and NGO partners, e.g.: EPA’s Office of Transportat...

The Model Optimization, Uncertainty, and SEnsitivity analysis (MOUSE) toolbox: overview and application

USDA-ARS?s Scientific Manuscript database

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

Building a Genome Engineering Toolbox in Non-Model Prokaryotic Microbes

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

Eckert, Carrie A; Freed, Emily; Smolinski, Sharon

The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g. sunlight, CO2, non-food biomass) to biofuels and bioproducts at sufficient titers and costs. For model microbes such as E. coli, advances in DNA reading and writing technologies are driving adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks such as photosynthesis, autotrophic growth, and cellulose degradation have very few, if any, genetic tools for metabolicmore » engineering. Therefore, it is important to begin to develop 'design rules' for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and available genetic tools to expand our ability to genetically engineer non-model systems.« less

Building a genome engineering toolbox in nonmodel prokaryotic microbes.

PubMed

Freed, Emily; Fenster, Jacob; Smolinski, Sharon L; Walker, Julie; Henard, Calvin A; Gill, Ryan; Eckert, Carrie A

2018-05-11

The realization of a sustainable bioeconomy requires our ability to understand and engineer complex design principles for the development of platform organisms capable of efficient conversion of cheap and sustainable feedstocks (e.g., sunlight, CO 2 , and nonfood biomass) into biofuels and bioproducts at sufficient titers and costs. For model microbes, such as Escherichia coli, advances in DNA reading and writing technologies are driving the adoption of new paradigms for engineering biological systems. Unfortunately, microbes with properties of interest for the utilization of cheap and renewable feedstocks, such as photosynthesis, autotrophic growth, and cellulose degradation, have very few, if any, genetic tools for metabolic engineering. Therefore, it is important to develop "design rules" for building a genetic toolbox for novel microbes. Here, we present an overview of our current understanding of these rules for the genetic manipulation of prokaryotic microbes and the available genetic tools to expand our ability to genetically engineer nonmodel systems. © 2018 Wiley Periodicals, Inc.

Near-optimal experimental design for model selection in systems biology.

PubMed

Busetto, Alberto Giovanni; Hauser, Alain; Krummenacher, Gabriel; Sunnåker, Mikael; Dimopoulos, Sotiris; Ong, Cheng Soon; Stelling, Jörg; Buhmann, Joachim M

2013-10-15

Biological systems are understood through iterations of modeling and experimentation. Not all experiments, however, are equally valuable for predictive modeling. This study introduces an efficient method for experimental design aimed at selecting dynamical models from data. Motivated by biological applications, the method enables the design of crucial experiments: it determines a highly informative selection of measurement readouts and time points. We demonstrate formal guarantees of design efficiency on the basis of previous results. By reducing our task to the setting of graphical models, we prove that the method finds a near-optimal design selection with a polynomial number of evaluations. Moreover, the method exhibits the best polynomial-complexity constant approximation factor, unless P = NP. We measure the performance of the method in comparison with established alternatives, such as ensemble non-centrality, on example models of different complexity. Efficient design accelerates the loop between modeling and experimentation: it enables the inference of complex mechanisms, such as those controlling central metabolic operation. Toolbox 'NearOED' available with source code under GPL on the Machine Learning Open Source Software Web site (mloss.org).

Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing.

PubMed

Li, Chao; Shi, Liu; Tao, Yaqin; Mao, Xiaoxia; Xiang, Yang; Li, Genxi

2017-08-30

Toehold-mediated DNA strand displacement reaction (SDR) plays pivotal roles for the construction of diverse dynamic DNA nanodevices. To date, many elements have been introduced into SDR system to achieve controllable activation and fine regulation. However, as the most relevant stimuli for nucleic acid involved reaction, nucleic acid-recognizing enzymes (NAEs) have received nearly no attention so far despite SDR often takes place in NAEs-enriched environment (i.e., biological fluids). Herein, we report a set of NAEs-controlled SDR strategies, which take full advantage of NAEs' properties. In this study, three different kinds of enzymes belonging to several classes (i.e., exonuclease, endonuclease and polymerase) have been used to activate or inhibit SDR, and more importantly, some mechanisms behind these strategies on how NAEs affect SDR have also been revealed. The exploration to use NAEs as possible cues to operate SDR will expand the available toolbox to build novel stimuli-fueled DNA nanodevices and could open the door to many applications including enzyme-triggered biocomputing and biosensing.

Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package

NASA Astrophysics Data System (ADS)

Donges, Jonathan F.; Heitzig, Jobst; Beronov, Boyan; Wiedermann, Marc; Runge, Jakob; Feng, Qing Yi; Tupikina, Liubov; Stolbova, Veronika; Donner, Reik V.; Marwan, Norbert; Dijkstra, Henk A.; Kurths, Jürgen

2015-11-01

We introduce the pyunicorn (Pythonic unified complex network and recurrence analysis toolbox) open source software package for applying and combining modern methods of data analysis and modeling from complex network theory and nonlinear time series analysis. pyunicorn is a fully object-oriented and easily parallelizable package written in the language Python. It allows for the construction of functional networks such as climate networks in climatology or functional brain networks in neuroscience representing the structure of statistical interrelationships in large data sets of time series and, subsequently, investigating this structure using advanced methods of complex network theory such as measures and models for spatial networks, networks of interacting networks, node-weighted statistics, or network surrogates. Additionally, pyunicorn provides insights into the nonlinear dynamics of complex systems as recorded in uni- and multivariate time series from a non-traditional perspective by means of recurrence quantification analysis, recurrence networks, visibility graphs, and construction of surrogate time series. The range of possible applications of the library is outlined, drawing on several examples mainly from the field of climatology.

Broadview Radar Altimetry Toolbox

NASA Astrophysics Data System (ADS)

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

2016-04-01

The universal altimetry toolbox, BRAT (Broadview Radar Altimetry Toolbox) which can read all previous and current altimetry missions' data, incorporates now the capability to read the upcoming 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'Etudes Spatiales), and it is freely available at http://earth.esa.int/brat. The tools enable users to interact with the most common altimetry data formats. The BratGUI is the front-end for the powerful command line tools that are part of the BRAT suite. BRAT can also be used in conjunction with MATLAB/IDL (via reading routines) or in C/C++/Fortran via a programming API, allowing the user to obtain desired data, bypassing the data-formatting hassle. BRAT can be used simply to visualise data quickly, or to translate the data into other formats such as NetCDF, ASCII text files, KML (Google Earth) 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 specific "use-cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The Broadview Radar Altimetry Toolbox is a continuation of the Basic Radar Altimetry Toolbox. While developing the new toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific "use-cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The first Release of the new Radar Altimetry Toolbox was published in September 2015. It incorporates the capability to read S3 products as well as the new CryoSat-2 Baseline C. The second Release of the Toolbox, planned for March 2016, will have a new graphical user interface and some visualisation improvements. The third release, planned for September 2016, will incorporate new datasets such as the lake and rivers or the envissat reprocessed, new features regarding data interpolation and formulas updates.

Broadview Radar Altimetry Toolbox

NASA Astrophysics Data System (ADS)

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 specific "use-cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The Broadview Radar Altimetry Toolbox is a continuation of the Basic Radar Altimetry Toolbox. While developing the new toolbox we will revamp of the Graphical User Interface and provide, among other enhancements, support for reading the upcoming S3 datasets and specific "use-cases" for SAR altimetry in order to train the users and make them aware of the great potential of SAR altimetry for coastal and inland applications. As for any open source framework, contributions from users having developed their own functions are welcome. The first Release of the new Radar Altimetry Toolbox was published in September 2015. It incorporates the capability to read S3 products as well as the new CryoSat-2 Baseline C. The second Release of the Toolbox, planned for March 2016, will have a new graphical user interface and some visualisation improvements. The third release, planned for September 2016, will incorporate new datasets such as the lake and rivers or the EnviSat reprocessed, new features regarding data interpolation and formulas updates.

Development of a Permafrost Modeling Cyberinfrastructure

NASA Astrophysics Data System (ADS)

Overeem, I.; Jafarov, E. E.; Piper, M.; Schaefer, K. M.

2016-12-01

Permafrost is seen as an essential Arctic climate indicator, and feedback of thawing permafrost to the global climate system through the impacts on the global carbon cycle remain an important research topic. Observations can assess the current state of permafrost, but models are eventually essential to make predictions of future permafrost extent. The purpose of our project, which we call PermaModel, is to develop an easy-to-access and comprehensive cyberinfrastructure aimed at promoting and improving permafrost modeling. The PermaModel Integrated Modeling Toolbox (IMT) includes three permafrost models of increasing complexity. The IMT will be housed within the existing cyberinfrastructure of the Community Surface Dynamics Modeling System (CSDMS), and made publically accessible through the CSDMS Web Modeling Tool (WMT). The WMT will provide easy online access to students, scientists, and stakeholders who want to use permafrost models, but lack the expertise. We plan to include multiple sets of sample inputs, representing a variety of conditions and locations, to enable immediate use of the IMT. We present here the first permafrost model, which is envisioned to be the most suitable for teaching purposes. The model promotes understanding of a 1D heat equation and permafrost active layer dynamics under monthly temperature/climate drivers in an online environment. Modeling labs are presented through the CSDMS Educational Repository and we solicit feedback from faculty for further design of these resources.

Traffic analysis toolbox volume XIII : integrated corridor management analysis, modeling, and simulation guide

DOT National Transportation Integrated Search

2017-02-01

As part of the Federal Highway Administration (FHWA) Traffic Analysis Toolbox (Volume XIII), this guide was designed to help corridor stakeholders implement the Integrated Corridor Management (ICM) Analysis, Modeling, and Simulation (AMS) methodology...

Traffic analysis toolbox volume XIII : integrated corridor management analysis, modeling, and simulation guide.

DOT National Transportation Integrated Search

2017-02-01

As part of the Federal Highway Administration (FHWA) Traffic Analysis Toolbox (Volume XIII), this guide was designed to help corridor stakeholders implement the Integrated Corridor Management (ICM) Analysis, Modeling, and Simulation (AMS) methodology...

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

NASA Astrophysics Data System (ADS)

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 version is compared with the previous version. Although, the toolbox is mainly tested for the Baltic Sea yet, it can easily be adapted to different datasets and parameters, regardless of the geographic region. In this presentation the usability of the toolbox is demonstrated along with several results of the validation process.

Finite-time robust passive control for a class of switched reaction-diffusion stochastic complex dynamical networks with coupling delays and impulsive control

NASA Astrophysics Data System (ADS)

Syed Ali, M.; Yogambigai, J.; Kwon, O. M.

2018-03-01

Finite-time boundedness and finite-time passivity for a class of switched stochastic complex dynamical networks (CDNs) with coupling delays, parameter uncertainties, reaction-diffusion term and impulsive control are studied. Novel finite-time synchronisation criteria are derived based on passivity theory. This paper proposes a CDN consisting of N linearly and diffusively coupled identical reaction- diffusion neural networks. By constructing of a suitable Lyapunov-Krasovskii's functional and utilisation of Jensen's inequality and Wirtinger's inequality, new finite-time passivity criteria for the networks are established in terms of linear matrix inequalities (LMIs), which can be checked numerically using the effective LMI toolbox in MATLAB. Finally, two interesting numerical examples are given to show the effectiveness of the theoretical results.

Investigation of a Graphical CONOPS Development Environment for Agile Systems Engineering - Phase 2

DTIC Science & Technology

2010-05-31

Westerman, Crawshaw , Hockey, and Sauer, 1998) for practitioners. Thus, CTA extends research by providing a toolbox of methods for understanding teams...drive process and performance. Washington, DC: American Psychological Association. pp. 3-8. Shrayne, N. M., Westerman, S. J., Crawshaw , C. M

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

USDA-ARS?s Scientific Manuscript database

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

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

NASA Astrophysics Data System (ADS)

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.

SSOAP Toolbox Enhancements and Case Study

EPA Science Inventory

Recognizing the need for tools to support the development of sanitary sewer overflow (SSO) control plans, in October 2009 the U.S. Environmental Protection Agency (EPA) released the first version of the Sanitary Sewer Overflow Analysis and Planning (SSOAP) Toolbox. This first ve...

Programmable Control in Extracellular Matrix-mimicking Polymer Hydrogels.

PubMed

Hof, Kevin S; Bastings, Maartje M C

2017-06-28

The extracellular matrix (ECM) and cells have a reciprocal relationship, one shapes the other and vice versa. One of the main challenges of synthetic material systems for developmental cell culturing, organoid and stem cell work includes the implementation of this reciprocal nature. The largest hurdle to achieve true cell-instructive materials in biomaterials engineering is a lack of spatial and temporal control over material properties and the display of bioactive signals compared to the natural cell environment. ECM-mimicking hydrogels have been developed using a wide range of polymers, assembly and cross-linking strategies. While our synthetic toolbox is larger than nature, often our systems underperform when compared to ECM systems with natural components like Matrigel. Material properties and three-dimensional structure ill-represent the three-dimensional ECM reciprocal nature and ligand presentation is an oversimplified version of the complexity found in nature. We hypothesize that the lack of programmable control in properties and ligand presentation forms the basis of this mismatch in performance and analyze the presence of control in current state of the art ECM-mimicking systems based on covalent, supramolecular and recombinant polymers. We conclude that through combining the dynamics of supramolecular materials, robustness from covalent systems and the programmable spatial control of bio-activation in recombinant ECM materials, the optimal synthetic artificial ECM could be assembled.

An Educational Model for Hands-On Hydrology Education

NASA Astrophysics Data System (ADS)

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.

Emotion assessment using the NIH Toolbox

PubMed Central

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

2013-01-01

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. PMID:23479549

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

PubMed

Dalmaijer, Edwin S; Mathôt, Sebastiaan; Van der Stigchel, Stefan

2014-12-01

The PyGaze toolbox is an open-source software package for Python, a high-level programming language. It is designed for creating eyetracking experiments in Python syntax with the least possible effort, and it offers programming ease and script readability without constraining functionality and flexibility. PyGaze can be used for visual and auditory stimulus presentation; for response collection via keyboard, mouse, joystick, and other external hardware; and for the online detection of eye movements using a custom algorithm. A wide range of eyetrackers of different brands (EyeLink, SMI, and Tobii systems) are supported. The novelty of PyGaze lies in providing an easy-to-use layer on top of the many different software libraries that are required for implementing eyetracking experiments. Essentially, PyGaze is a software bridge for eyetracking research.

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

Galperin, Michael

The progress of experimental techniques at the nanoscale in the last decade made optical measurements in current-carrying nanojunctions a reality, thus indicating the emergence of a new field of research coined optoelectronics. Optical spectroscopy of open nonequilibrium systems is a natural meeting point for (at least) two research areas: nonlinear optical spectroscopy and quantum transport, each with its own theoretical toolbox. We review recent progress in the field comparing theoretical treatments of optical response in nanojunctions as is accepted in nonlinear spectroscopy and quantum transport communities. A unified theoretical description of spectroscopy in nanojunctions is presented. Here, we argue thatmore » theoretical approaches of the quantum transport community (and in particular, the Green function based considerations) yield a convenient tool for optoelectronics when the radiation field is treated classically, and that differences between the toolboxes may become critical when studying the quantum radiation field in junctions.« less

Advances in Sewer Condition and Capacity Assessment – Development and Applications of EPA SSOAP Toolbox

EPA Science Inventory

In the United States, sanitary sewer infrastructure is aging, with some sewers dating back over 100 years. Nationwide, there are more than 19,500 municipal sanitary-sewer collection systems serving an estimated 150 million people and about 40,000 sanitary sewer overflow (SSO) ev...

Update on the Status of Sanitary Sewer Overflow Analysis and Planning (SSOAP) Toolbox

EPA Science Inventory

A properly designed, operated and maintained sanitary sewer system is meant to collect and convey all of the sewage that flows into it to a wastewater treatment plant. However, occasional unintentional discharges of raw sewage from municipal sanitary sewers – called sanitary sewe...

Predicting thermal regimes of stream networks across the northeast United States: Natural and anthropogenic influences

EPA Science Inventory

We used STARS (Spatial Tools for the Analysis of River Systems), an ArcGIS geoprocessing toolbox, to create spatial stream networks. We then developed and assessed spatial statistical models for each of these metrics, incorporating spatial autocorrelation based on both distance...

Focused Field Investigations for Sewer Condition Assessment with EPA SSOAP Toolbox

EPA Science Inventory

The Nation’s sanitary sewer infrastructure is aging, and is currently one of the top national water program priorities. The U.S. Environmental Protection Agency (EPA) developed the Sanitary Sewer Overflow Analysis and Planning (SSOAP) Toolbox to assist communities in developing ...

A Toolbox for Corrective Action: Resource Conservation and Recovery Act Facilities Investigation Remedy Selection Track

EPA Pesticide Factsheets

The purpose of this toolbox is to help EPA Regional staff and their partners to take advantage of the efficiency and quality gains from the Resource Conservation and Recovery Act (RCRA) Facilities Investigation Remedy Selection Track (FIRST) approach.

Traffic analysis toolbox volume IX : work zone modeling and simulation, a guide for analysts

DOT National Transportation Integrated Search

2009-03-01

This document is the second volume in the FHWA Traffic Analysis Toolbox: Work Zone Analysis series. Whereas the first volume provides guidance to decision-makers at agencies and jurisdictions considering the role of analytical tools in work zone plan...

A Transcription Activator-Like Effector (TALE) Toolbox for Genome Engineering

PubMed Central

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

2013-01-01

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 one 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, respectively, qRT-PCR and Surveyor nuclease. The TALE toolbox described here will enable a broad range of biological applications. PMID:22222791

Velocity Mapping Toolbox (VMT): a processing and visualization suite for moving-vessel ADCP measurements

USGS Publications Warehouse

Parsons, D.R.; Jackson, P.R.; Czuba, J.A.; Engel, F.L.; Rhoads, B.L.; Oberg, K.A.; Best, J.L.; Mueller, D.S.; Johnson, K.K.; Riley, J.D.

2013-01-01

The use of acoustic Doppler current profilers (ADCP) for discharge measurements and three-dimensional flow mapping has increased rapidly in recent years and has been primarily driven by advances in acoustic technology and signal processing. Recent research has developed a variety of methods for processing data obtained from a range of ADCP deployments and this paper builds on this progress by describing new software for processing and visualizing ADCP data collected along transects in rivers or other bodies of water. The new utility, the Velocity Mapping Toolbox (VMT), allows rapid processing (vector rotation, projection, averaging and smoothing), visualization (planform and cross-section vector and contouring), and analysis of a range of ADCP-derived datasets. The paper documents the data processing routines in the toolbox and presents a set of diverse examples that demonstrate its capabilities. The toolbox is applicable to the analysis of ADCP data collected in a wide range of aquatic environments and is made available as open-source code along with this publication.

NBodyLab Simulation Experiments with GRAPE-6a AND MD-GRAPE2 Acceleration

NASA Astrophysics Data System (ADS)

Johnson, V.; Ates, A.

2005-12-01

NbodyLab is an astrophysical N-body simulation testbed for student research. It is accessible via a web interface and runs as a backend framework under Linux. NbodyLab can generate data models or perform star catalog lookups, transform input data sets, perform direct summation gravitational force calculations using a variety of integration schemes, and produce analysis and visualization output products. NEMO (Teuben 1994), a popular stellar dynamics toolbox, is used for some functions. NbodyLab integrators can optionally utilize two types of low-cost desktop supercomputer accelerators, the newly available GRAPE-6a (125 Gflops peak) and the MD-GRAPE2 (64-128 Gflops peak). The initial version of NBodyLab was presented at ADASS 2002. This paper summarizes software enhancements developed subsequently, focusing on GRAPE-6a related enhancements, and gives examples of computational experiments and astrophysical research, including star cluster and solar system studies, that can be conducted with the new testbed functionality.

Detrended Fluctuation Analysis: A Scale-Free View on Neuronal Oscillations

PubMed Central

Hardstone, Richard; Poil, Simon-Shlomo; Schiavone, Giuseppina; Jansen, Rick; Nikulin, Vadim V.; Mansvelder, Huibert D.; Linkenkaer-Hansen, Klaus

2012-01-01

Recent years of research have shown that the complex temporal structure of ongoing oscillations is scale-free and characterized by long-range temporal correlations. Detrended fluctuation analysis (DFA) has proven particularly useful, revealing that genetic variation, normal development, or disease can lead to differences in the scale-free amplitude modulation of oscillations. Furthermore, amplitude dynamics is remarkably independent of the time-averaged oscillation power, indicating that the DFA provides unique insights into the functional organization of neuronal systems. To facilitate understanding and encourage wider use of scaling analysis of neuronal oscillations, we provide a pedagogical explanation of the DFA algorithm and its underlying theory. Practical advice on applying DFA to oscillations is supported by MATLAB scripts from the Neurophysiological Biomarker Toolbox (NBT) and links to the NBT tutorial website http://www.nbtwiki.net/. Finally, we provide a brief overview of insights derived from the application of DFA to ongoing oscillations in health and disease, and discuss the putative relevance of criticality for understanding the mechanism underlying scale-free modulation of oscillations. PMID:23226132

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

Youssef, Tarek A.; Elsayed, Ahmed T.; Mohammed, Osama A.

This study presents the design and implementation of a communication and control infrastructure for smart grid operation. The proposed infrastructure enhances the reliability of the measurements and control network. The advantages of utilizing the data-centric over message-centric communication approach are discussed in the context of smart grid applications. The data distribution service (DDS) is used to implement a data-centric common data bus for the smart grid. This common data bus improves the communication reliability, enabling distributed control and smart load management. These enhancements are achieved by avoiding a single point of failure while enabling peer-to-peer communication and an automatic discoverymore » feature for dynamic participating nodes. The infrastructure and ideas presented in this paper were implemented and tested on the smart grid testbed. A toolbox and application programing interface for the testbed infrastructure are developed in order to facilitate interoperability and remote access to the testbed. This interface allows control, monitoring, and performing of experiments remotely. Furthermore, it could be used to integrate multidisciplinary testbeds to study complex cyber-physical systems (CPS).« less

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

PubMed Central

Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

2011-01-01

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. PMID:21577273

ElectroMagnetoEncephalography software: overview and integration with other EEG/MEG toolboxes.

PubMed

Peyk, Peter; De Cesarei, Andrea; Junghöfer, Markus

2011-01-01

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.

UAS-NAS Live Virtual Constructive Distributed Environment (LVC): LVC Gateway, Gateway Toolbox, Gateway Data Logger (GDL), SaaProc Software Design Description

NASA Technical Reports Server (NTRS)

Jovic, Srboljub

2015-01-01

This document provides the software design description for the two core software components, the LVC Gateway, the LVC Gateway Toolbox, and two participants, the LVC Gateway Data Logger and the SAA Processor (SaaProc).

Expanding the seat belt program strategies toolbox: a starter kit for trying new program ideas : traffic tech.

DOT National Transportation Integrated Search

2016-10-01

The National Highway Traffic Safety Administration has just : released a new resource for developing seat belt programs in : the traffic safety communityExpanding the Seat Belt Program : Toolbox: A Starter Kit for Trying New Program Ideas. : Resea...

Focused Field Investigations for Sewer Condition Assessment with EPA SSOAP Toolbox - slides

EPA Science Inventory

The Nation’s sanitary sewer infrastructure is aging, and is currently one of the top national water program priorities. The U.S. Environmental Protection Agency (EPA) developed the Sanitary Sewer Overflow Analysis and Planning (SSOAP) Toolbox to assist communities in developing S...

Blue light-mediated transcriptional activation and repression of gene expression in bacteria

PubMed Central

Jayaraman, Premkumar; Devarajan, Kavya; Chua, Tze Kwang; Zhang, Hanzhong; Gunawan, Erry; Poh, Chueh Loo

2016-01-01

Light-regulated modules offer unprecedented new ways to control cellular behavior in precise spatial and temporal resolution. The availability of such tools may dramatically accelerate the progression of synthetic biology applications. Nonetheless, current optogenetic toolbox of prokaryotes has potential issues such as lack of rapid and switchable control, less portable, low dynamic expression and limited parts. To address these shortcomings, we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222. We demonstrated that by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely. We show that both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light. In addition, the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model. We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal. Overall, our modular approach layers a transformative platform for next-generation light-controllable synthetic biology systems in prokaryotes. PMID:27353329

Research on fuzzy PID control to electronic speed regulator

NASA Astrophysics Data System (ADS)

Xu, Xiao-gang; Chen, Xue-hui; Zheng, Sheng-guo

2007-12-01

As an important part of diesel engine, the speed regulator plays an important role in stabilizing speed and improving engine's performance. Because there are so many model parameters of diesel-engine considered in traditional PID control and these parameters present non-linear characteristic.The method to adjust engine speed using traditional PID is not considered as a best way. Especially for the diesel-engine generator set. In this paper, the Fuzzy PID control strategy is proposed. Some problems about its utilization in electronic speed regulator are discussed. A mathematical model of electric control system for diesel-engine generator set is established and the way of the PID parameters in the model to affect the function of system is analyzed. And then it is proposed the differential coefficient must be applied in control design for reducing dynamic deviation of system and adjusting time. Based on the control theory, a study combined control with PID calculation together for turning fuzzy PID parameter is implemented. And also a simulation experiment about electronic speed regulator system was conducted using Matlab/Simulink and the Fuzzy-Toolbox. Compared with the traditional PID Algorithm, the simulated results presented obvious improvements in the instantaneous speed governing rate and steady state speed governing rate of diesel-engine generator set when the fuzzy logic control strategy used.

Computer-Assisted Drug Formulation Design: Novel Approach in Drug Delivery.

PubMed

Metwally, Abdelkader A; Hathout, Rania M

2015-08-03

We hypothesize that, by using several chemo/bio informatics tools and statistical computational methods, we can study and then predict the behavior of several drugs in model nanoparticulate lipid and polymeric systems. Accordingly, two different matrices comprising tripalmitin, a core component of solid lipid nanoparticles (SLN), and PLGA were first modeled using molecular dynamics simulation, and then the interaction of drugs with these systems was studied by means of computing the free energy of binding using the molecular docking technique. These binding energies were hence correlated with the loadings of these drugs in the nanoparticles obtained experimentally from the available literature. The obtained relations were verified experimentally in our laboratory using curcumin as a model drug. Artificial neural networks were then used to establish the effect of the drugs' molecular descriptors on the binding energies and hence on the drug loading. The results showed that the used soft computing methods can provide an accurate method for in silico prediction of drug loading in tripalmitin-based and PLGA nanoparticulate systems. These results have the prospective of being applied to other nano drug-carrier systems, and this integrated statistical and chemo/bio informatics approach offers a new toolbox to the formulation science by proposing what we present as computer-assisted drug formulation design (CADFD).

Nonequilibrium steady states and resonant tunneling in time-periodically driven systems with interactions

NASA Astrophysics Data System (ADS)

Qin, Tao; Hofstetter, Walter

2018-03-01

Time-periodically driven systems are a versatile toolbox for realizing interesting effective Hamiltonians. Heating, caused by excitations to high-energy states, is a challenge for experiments. While most setups so far address the relatively weakly interacting regime, it is of general interest to study heating in strongly correlated systems. Using Floquet dynamical mean-field theory, we study nonequilibrium steady states (NESS) in the Falicov-Kimball model, with time-periodically driven kinetic energy or interaction. We systematically investigate the nonequilibrium properties of the NESS. For a driven kinetic energy, we show that resonant tunneling, where the interaction is an integer multiple of the driving frequency, plays an important role in the heating. In the strongly correlated regime, we show that this can be well understood using Fermi's golden rule and the Schrieffer-Wolff transformation for a time-periodically driven system. We furthermore demonstrate that resonant tunneling can be used to control the population of Floquet states to achieve "photodoping." For driven interactions introduced by an oscillating magnetic field near a widely adopted Feshbach resonance, we find that the double occupancy is strongly modulated. Our calculations apply to shaken ultracold-atom systems and to solid-state systems in a spatially uniform but time-dependent electric field. They are also closely related to lattice modulation spectroscopy. Our calculations are helpful to understand the latest experiments on strongly correlated Floquet systems.

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

PubMed

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/.

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

PubMed Central

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/. PMID:26807911

An ethics toolbox for neurotechnology.

PubMed

Farah, Martha J

2015-04-08

Advances in neurotechnology will raise new ethical dilemmas, to which scientists and the rest of society must respond. Here I present a "toolbox" of concepts to help us analyze these issues and communicate with each other about them across differences of ethical intuition. Copyright © 2015 Elsevier Inc. All rights reserved.

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

USDA-ARS?s Scientific Manuscript database

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...

LAB ANALYSIS OF EMERGENCY WATER SAMPLES CONTAINING UNKNOWN CONTAMINANTS: CONSIDERATIONS FROM THE USEPA RESPONSE PROTOCOL TOOLBOX

EPA Science Inventory

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...

Integrating model behavior, optimization, and sensitivity/uncertainty analysis: overview and application of the MOUSE software toolbox

USDA-ARS?s Scientific Manuscript database

This paper provides an overview of the Model Optimization, Uncertainty, and SEnsitivity Analysis (MOUSE) software application, an open-source, Java-based toolbox of visual and numerical analysis components for the evaluation of environmental models. MOUSE is based on the OPTAS model calibration syst...

Testing Adaptive Toolbox Models: A Bayesian Hierarchical Approach

ERIC Educational Resources Information Center

Scheibehenne, Benjamin; Rieskamp, Jorg; Wagenmakers, Eric-Jan

2013-01-01

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

An overview of recent advances in system identification

NASA Technical Reports Server (NTRS)

Juang, Jer-Nan

1994-01-01

This paper presents an overview of the recent advances in system identification for modal testing and control of large flexible structures. Several techniques are discussed including the Observer/Kalman Filter Identification, the Observer/Controller Identification, and the State-Space System Identification in the Frequency Domain. The System/Observer/Controller Toolbox developed at NASA Langley Research Center is used to show the applications of these techniques to real aerospace structures such as the Hubble spacecraft telescope and the active flexible aircraft wing.

Dynamic evolution of double Λ five-level atom interacting with one-mode electromagnetic cavity field

NASA Astrophysics Data System (ADS)

Abdel-Wahab, N. H.; Salah, Ahmed

2017-12-01

In this paper, the model describing a double Λ five-level atom interacting with a single mode electromagnetic cavity field in the (off) non-resonate case is studied. We obtained the constants of motion for the considered model. Also, the state vector of the wave function is given by using the Schrödinger equation when the atom is initially prepared in its excited state. The dynamical evolutions for the collapse revivals, the antibunching of photons and the field squeezing phenomena are investigated when the field is considered in a coherent state. The influence of detuning parameters on these phenomena is investigated. We noticed that the atom-field properties are influenced by changing the detuning parameters. The investigation of these aspects by numerical simulations is carried out using the Quantum Toolbox in Python (QuTip).

Characterization of Carboxylic Acid Reductases as Enzymes in the Toolbox for Synthetic Chemistry.

PubMed

Finnigan, William; Thomas, Adam; Cromar, Holly; Gough, Ben; Snajdrova, Radka; Adams, Joseph P; Littlechild, Jennifer A; Harmer, Nicholas J

2017-03-20

Carboxylic acid reductase enzymes (CARs) meet the demand in synthetic chemistry for a green and regiospecific route to aldehydes from their respective carboxylic acids. However, relatively few of these enzymes have been characterized. A sequence alignment with members of the ANL (Acyl-CoA synthetase/ NRPS adenylation domain/Luciferase) superfamily of enzymes shed light on CAR functional dynamics. Four unstudied enzymes were selected by using a phylogenetic analysis of known and hypothetical CARs, and for the first time, a thorough biochemical characterization was performed. Kinetic analysis of these enzymes with various substrates shows that they have a broad but similar substrate specificity. Electron-rich acids are favored, which suggests that the first step in the proposed reaction mechanism, attack by the carboxylate on the α-phosphate of adenosine triphosphate (ATP), is the step that determines the substrate specificity and reaction kinetics. The effects of pH and temperature provide a clear operational window for the use of these CARs, whereas an investigation of product inhibition by NADP + , adenosine monophosphate, and pyrophosphate indicates that the binding of substrates at the adenylation domain is ordered with ATP binding first. This study consolidates CARs as important and exciting enzymes in the toolbox for sustainable chemistry and provides specifications for their use as a biocatalyst.

What's New in the Toolbox for Constipation and Fecal Incontinence?

PubMed

Lee, Yeong Yeh

2014-01-01

Constipation and fecal incontinence (FI) are common complaints predominantly affecting the elderly and women. They are associated with significant morbidity and high healthcare costs. The causes are often multi-factorial 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.

Dynamic simulation of the effect of soft toric contact lenses movement on retinal image quality.

PubMed

Niu, Yafei; Sarver, Edwin J; Stevenson, Scott B; Marsack, Jason D; Parker, Katrina E; Applegate, Raymond A

2008-04-01

To report the development of a tool designed to dynamically simulate the effect of soft toric contact lens movement on retinal image quality, initial findings on three eyes, and the next steps to be taken to improve the utility of the tool. Three eyes of two subjects wearing soft toric contact lenses were cyclopleged with 1% cyclopentolate and 2.5% phenylephrine. Four hundred wavefront aberration measurements over a 5-mm pupil were recorded during soft contact lens wear at 30 Hz using a complete ophthalmic analysis system aberrometer. Each wavefront error measurement was input into Visual Optics Laboratory (version 7.15, Sarver and Associates, Inc.) to generate a retinal simulation of a high contrast log MAR visual acuity chart. The individual simulations were combined into a single dynamic movie using a custom MatLab PsychToolbox program. Visual acuity was measured for each eye reading the movie with best cycloplegic spectacle correction through a 3-mm artificial pupil to minimize the influence of the eyes' uncorrected aberrations. Comparison of the simulated acuity was made to values recorded while the subject read unaberrated charts with contact lenses through a 5-mm artificial pupil. For one study eye, average acuity was the same as the natural contact lens viewing condition. For the other two study eyes visual acuity of the best simulation was more than one line worse than natural viewing conditions. Dynamic simulation of retinal image quality, although not yet perfect, is a promising technique for visually illustrating the optical effects on image quality because of the movements of alignment-sensitive corrections.

BoolFilter: an R package for estimation and identification of partially-observed Boolean dynamical systems.

PubMed

Mcclenny, Levi D; Imani, Mahdi; Braga-Neto, Ulisses M

2017-11-25

Gene regulatory networks govern the function of key cellular processes, such as control of the cell cycle, response to stress, DNA repair mechanisms, and more. Boolean networks have been used successfully in modeling gene regulatory networks. In the Boolean network model, the transcriptional state of each gene is represented by 0 (inactive) or 1 (active), and the relationship among genes is represented by logical gates updated at discrete time points. However, the Boolean gene states are never observed directly, but only indirectly and incompletely through noisy measurements based on expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays. The Partially-Observed Boolean Dynamical System (POBDS) signal model is distinct from other deterministic and stochastic Boolean network models in removing the requirement of a directly observable Boolean state vector and allowing uncertainty in the measurement process, addressing the scenario encountered in practice in transcriptomic analysis. BoolFilter is an R package that implements the POBDS model and associated algorithms for state and parameter estimation. It allows the user to estimate the Boolean states, network topology, and measurement parameters from time series of transcriptomic data using exact and approximated (particle) filters, as well as simulate the transcriptomic data for a given Boolean network model. Some of its infrastructure, such as the network interface, is the same as in the previously published R package for Boolean Networks BoolNet, which enhances compatibility and user accessibility to the new package. We introduce the R package BoolFilter for Partially-Observed Boolean Dynamical Systems (POBDS). The BoolFilter package provides a useful toolbox for the bioinformatics community, with state-of-the-art algorithms for simulation of time series transcriptomic data as well as the inverse process of system identification from data obtained with various expression technologies such as cDNA microarrays, RNA-Seq, and cell imaging-based assays.

Estimating the Resources for Quantum Computation with the QuRE Toolbox

DTIC Science & Technology

2013-05-31

quantum computing. Quantum Info. Comput., 9(7):666–682, July 2009. [13] M. Saffman, T. G. Walker, and K. Mølmer. Quantum information with rydberg atoms...109(5):735–750, 2011. [24] Aram Harrow , Avinatan Hassidim, and Seth Lloyd. Quantum algorithm for solving linear systems of equations. Phys. Rev

40 CFR 141.720 - Inactivation toolbox components.

Code of Federal Regulations, 2013 CFR

2013-07-01

... between the indicated values: Log credit = (0.0397 × (1.09757)Temp) × CT. (c) Site-specific study. The... this section on a site-specific basis. The State must base this approval on a site-specific study a... in this table are applicable only to post-filter applications of UV in filtered systems and to...

40 CFR 141.720 - Inactivation toolbox components.

Code of Federal Regulations, 2010 CFR

2010-07-01

... between the indicated values: Log credit = (0.0397 × (1.09757)Temp) × CT. (c) Site-specific study. The... this section on a site-specific basis. The State must base this approval on a site-specific study a... in this table are applicable only to post-filter applications of UV in filtered systems and to...

40 CFR 141.720 - Inactivation toolbox components.

Code of Federal Regulations, 2011 CFR

2011-07-01

... between the indicated values: Log credit = (0.0397 × (1.09757)Temp) × CT. (c) Site-specific study. The... this section on a site-specific basis. The State must base this approval on a site-specific study a... in this table are applicable only to post-filter applications of UV in filtered systems and to...

40 CFR 141.720 - Inactivation toolbox components.

Code of Federal Regulations, 2012 CFR

2012-07-01

... between the indicated values: Log credit = (0.0397 × (1.09757)Temp) × CT. (c) Site-specific study. The... this section on a site-specific basis. The State must base this approval on a site-specific study a... in this table are applicable only to post-filter applications of UV in filtered systems and to...

40 CFR 141.720 - Inactivation toolbox components.

Code of Federal Regulations, 2014 CFR

2014-07-01

... treatment unit process with a measurable disinfectant residual level and a liquid volume. Under this... through reactor validation testing, as described in paragraph (d)(2) of this section. The UV dose values....0 12 11 143 (vii) 3.5 15 15 163 (viii) 4.0 22 22 186 (2) Reactor validation testing. Systems must...

Photonics and spectroscopy in nanojunctions: a theoretical insight

DOE PAGES

Galperin, Michael

2017-04-11

The progress of experimental techniques at the nanoscale in the last decade made optical measurements in current-carrying nanojunctions a reality, thus indicating the emergence of a new field of research coined optoelectronics. Optical spectroscopy of open nonequilibrium systems is a natural meeting point for (at least) two research areas: nonlinear optical spectroscopy and quantum transport, each with its own theoretical toolbox. We review recent progress in the field comparing theoretical treatments of optical response in nanojunctions as is accepted in nonlinear spectroscopy and quantum transport communities. A unified theoretical description of spectroscopy in nanojunctions is presented. Here, we argue thatmore » theoretical approaches of the quantum transport community (and in particular, the Green function based considerations) yield a convenient tool for optoelectronics when the radiation field is treated classically, and that differences between the toolboxes may become critical when studying the quantum radiation field in junctions.« less

Qualitative methods in health services and management research: pockets of excellence and progress, but still a long way to go.

PubMed

Devers, Kelly J

2011-02-01

The 10-year systematic review of published health services and management research by Weiner et al. (2011) chronicles the contributions of qualitative methods, highlights areas of substantial progress, and identifies areas in need of more progress. This article (Devers, 2011) discusses possible reasons for lack of progress in some areas--related to the under-supply of well-trained qualitative researchers and more tangible demand for their research--and mechanisms for future improvement. To ensure a robust health services research toolbox, the field must take additional steps to provide stronger education and training in qualitative methods and more funding and publication opportunities. Given the rapidly changing health care system post the passage of national health reform and the chalresearch issues associated with it, the health services research and management field will not meet its future challenges with quantitative methods alone or with a half-empty toolbox.

Expanding the metabolic engineering toolbox with directed evolution.

PubMed

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. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering a robust DNA split proximity circuit with minimized circuit leakage

PubMed Central

Ang, Yan Shan; Tong, Rachel; Yung, Lin-Yue Lanry

2016-01-01

DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically analyzed the sources and characteristics of various types of leakage in a split proximity circuit which was engineered to spatially probe for target sites held within close proximity. Direct evidence that 3′-truncated oligonucleotides were the major impurity contributing to circuit leakage was presented. More importantly, a unique strategy of translocating a single nucleotide between domains, termed ‘inter-domain bridging’, was introduced to eliminate toehold-independent leakages while enhancing the strand displacement kinetics across a three-way junction. We also analyzed the dynamics of intermediate complexes involved in the circuit computation in order to define the working range of domain lengths for the reporter toehold and association region respectively. The final circuit design was successfully implemented on a model streptavidin-biotin system and demonstrated to be robust against both circuit leakage and biological interferences. We anticipate that this simple signal transduction strategy can be used to probe for diverse biomolecular interactions when used in conjunction with specific target recognition moieties. PMID:27207880

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

NASA Astrophysics Data System (ADS)

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.

Motion synthesis and force distribution analysis for a biped robot.

PubMed

Trojnacki, Maciej T; Zielińska, Teresa

2011-01-01

In this paper, the method of generating biped robot motion using recorded human gait is presented. The recorded data were modified taking into account the velocity available for robot drives. Data includes only selected joint angles, therefore the missing values were obtained considering the dynamic postural stability of the robot, which means obtaining an adequate motion trajectory of the so-called Zero Moment Point (ZMT). Also, the method of determining the ground reaction forces' distribution during the biped robot's dynamic stable walk is described. The method was developed by the authors. Following the description of equations characterizing the dynamics of robot's motion, the values of the components of ground reaction forces were symbolically determined as well as the coordinates of the points of robot's feet contact with the ground. The theoretical considerations have been supported by computer simulation and animation of the robot's motion. This was done using Matlab/Simulink package and Simulink 3D Animation Toolbox, and it has proved the proposed method.

A self-teaching image processing and voice-recognition-based, intelligent and interactive system to educate visually impaired children

NASA Astrophysics Data System (ADS)

Iqbal, Asim; Farooq, Umar; Mahmood, Hassan; Asad, Muhammad Usman; Khan, Akrama; Atiq, Hafiz Muhammad

2010-02-01

A self teaching image processing and voice recognition based system is developed to educate visually impaired children, chiefly in their primary education. System comprises of a computer, a vision camera, an ear speaker and a microphone. Camera, attached with the computer system is mounted on the ceiling opposite (on the required angle) to the desk on which the book is placed. Sample images and voices in the form of instructions and commands of English, Urdu alphabets, Numeric Digits, Operators and Shapes are already stored in the database. A blind child first reads the embossed character (object) with the help of fingers than he speaks the answer, name of the character, shape etc into the microphone. With the voice command of a blind child received by the microphone, image is taken by the camera which is processed by MATLAB® program developed with the help of Image Acquisition and Image processing toolbox and generates a response or required set of instructions to child via ear speaker, resulting in self education of a visually impaired child. Speech recognition program is also developed in MATLAB® with the help of Data Acquisition and Signal Processing toolbox which records and process the command of the blind child.

Towards a Comprehensive Catalog of Volcanic Seismicity

NASA Astrophysics Data System (ADS)

Thompson, G.

2014-12-01

Catalogs of earthquakes located using differential travel-time techniques are a core product of volcano observatories, and while vital, they represent an incomplete perspective of volcanic seismicity. Many (often most) earthquakes are too small to locate accurately, and are omitted from available catalogs. Low frequency events, tremor and signals related to rockfalls, pyroclastic flows and lahars are not systematically catalogued, and yet from a hazard management perspective are exceedingly important. Because STA/LTA detection schemes break down in the presence of high amplitude tremor, swarms or dome collapses, catalogs may suggest low seismicity when seismicity peaks. We propose to develop a workflow and underlying software toolbox that can be applied to near-real-time and offline waveform data to produce comprehensive catalogs of volcanic seismicity. Existing tools to detect and locate phaseless signals will be adapted to fit within this framework. For this proof of concept the toolbox will be developed in MATLAB, extending the existing GISMO toolbox (an object-oriented MATLAB toolbox for seismic data analysis). Existing database schemas such as the CSS 3.0 will need to be extended to describe this wider range of volcano-seismic signals. WOVOdat may already incorporate many of the additional tables needed. Thus our framework may act as an interface between volcano observatories (or campaign-style research projects) and WOVOdat. We aim to take the further step of reducing volcano-seismic catalogs to sets of continuous metrics that are useful for recognizing data trends, and for feeding alarm systems and forecasting techniques. Previous experience has shown that frequency index, peak frequency, mean frequency, mean event rate, median event rate, and cumulative magnitude (or energy) are potentially useful metrics to generate for all catalogs at a 1-minute sample rate (directly comparable with RSAM and similar metrics derived from continuous data). Our framework includes tools to plot these metrics in a consistent manner. We work with data from unrest at Redoubt volcano and Soufriere Hills volcano to develop our framework.

Impact-oriented steering--the concept of NGO-IDEAs 'impact toolbox'.

PubMed

2008-03-01

The NGO-IDEAs 'Impact Toolbox' has been developed with a group of NGOs all of which are active in the area of saving and credit in South India. This compilation of methods to apply in impact-oriented steering was devised by the executive staff of the Indian partner NGOs, also known as the Resource Persons, in 2006 and tested from late 2006 to early 2007. At first glance, the approach may appear to be highly specialised and difficult to transfer. However, in fact it follows principles that can be adapted for several NGOs in other countries and in other sectors. The following article presents the concept of the NGO-IDEAs 'Impact Toolbox'.

PSYCHOACOUSTICS: a comprehensive MATLAB toolbox for auditory testing.

PubMed

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.

PSYCHOACOUSTICS: a comprehensive MATLAB toolbox for auditory testing

PubMed Central

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. PMID:25101013

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

PubMed Central

Karpievitch, Yuliya V; Almeida, Jonas S

2006-01-01

Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet. PMID:16539707

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

PubMed

Karpievitch, Yuliya V; Almeida, Jonas S

2006-03-15

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.

Policy Analysis for Sustainable Development: The Toolbox for the Environmental Social Scientist

ERIC Educational Resources Information Center

Runhaar, Hens; Dieperink, Carel; Driessen, Peter

2006-01-01

Purpose: The paper seeks to propose the basic competencies of environmental social scientists regarding policy analysis for sustainable development. The ultimate goal is to contribute to an improvement of educational programmes in higher education by suggesting a toolbox that should be integrated in the curriculum. Design/methodology/approach:…

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

EPA Science Inventory

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...

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

ERIC Educational Resources Information Center

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…

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

ERIC Educational Resources Information Center

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…

TopoToolbox: Using Sensor Topography to Calculate Psychologically Meaningful Measures from Event-Related EEG/MEG

PubMed Central

Tian, Xing; Poeppel, David; Huber, David E.

2011-01-01

The open-source toolbox “TopoToolbox” is a suite of functions that use sensor topography to calculate psychologically meaningful measures (similarity, magnitude, and timing) from multisensor event-related EEG and MEG data. Using a GUI and data visualization, TopoToolbox can be used to calculate and test the topographic similarity between different conditions (Tian and Huber, 2008). This topographic similarity indicates whether different conditions involve a different distribution of underlying neural sources. Furthermore, this similarity calculation can be applied at different time points to discover when a response pattern emerges (Tian and Poeppel, 2010). Because the topographic patterns are obtained separately for each individual, these patterns are used to produce reliable measures of response magnitude that can be compared across individuals using conventional statistics (Davelaar et al. Submitted and Huber et al., 2008). TopoToolbox can be freely downloaded. It runs under MATLAB (The MathWorks, Inc.) and supports user-defined data structure as well as standard EEG/MEG data import using EEGLAB (Delorme and Makeig, 2004). PMID:21577268

Image processing and pattern recognition with CVIPtools MATLAB toolbox: automatic creation of masks for veterinary thermographic images

NASA Astrophysics Data System (ADS)

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.

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

Vinuesa, Ricardo; Fick, Lambert; Negi, Prabal

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 L x = 2h, L y = 2h and L z = 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 meshmore » 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).« less

Validation of an Actuator Line Model Coupled to a Dynamic Stall Model for Pitching Motions Characteristic to Vertical Axis Turbines

NASA Astrophysics Data System (ADS)

Mendoza, Victor; Bachant, Peter; Wosnik, Martin; Goude, Anders

2016-09-01

Vertical axis wind turbines (VAWT) can be used to extract renewable energy from wind flows. A simpler design, low cost of maintenance, and the ability to accept flow from all directions perpendicular to the rotor axis are some of the most important advantages over conventional horizontal axis wind turbines (HAWT). However, VAWT encounter complex and unsteady fluid dynamics, which present significant modeling challenges. One of the most relevant phenomena is dynamic stall, which is caused by the unsteady variation of angle of attack throughout the blade rotation, and is the focus of the present study. Dynamic stall is usually used as a passive control for VAWT operating conditions, hence the importance of predicting its effects. In this study, a coupled model is implemented with the open-source CFD toolbox OpenFOAM for solving the Navier-Stokes equations, where an actuator line model and dynamic stall model are used to compute the blade loading and body force. Force coefficients obtained from the model are validated with experimental data of pitching airfoil in similar operating conditions as an H-rotor type VAWT. Numerical results show reasonable agreement with experimental data for pitching motion.

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Dynamic optimization case studies in DYNOPT tool

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

Dynamic programming is typically applied to optimization problems. As the analytical solutions are generally very difficult, chosen software tools are used widely. These software packages are often third-party products bound for standard simulation software tools on the market. As typical examples of such tools, TOMLAB and DYNOPT could be effectively applied for solution of problems of dynamic programming. DYNOPT will be presented in this paper due to its licensing policy (free product under GPL) and simplicity of use. DYNOPT is a set of MATLAB functions for determination of optimal control trajectory by given description of the process, the cost to be minimized, subject to equality and inequality constraints, using orthogonal collocation on finite elements method. The actual optimal control problem is solved by complete parameterization both the control and the state profile vector. It is assumed, that the optimized dynamic model may be described by a set of ordinary differential equations (ODEs) or differential-algebraic equations (DAEs). This collection of functions extends the capability of the MATLAB Optimization Tool-box. The paper will introduce use of DYNOPT in the field of dynamic optimization problems by means of case studies regarding chosen laboratory physical educational models.

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

PubMed

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

2016-06-15

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

Optimizing detection and analysis of slow waves in sleep EEG.

PubMed

Mensen, Armand; Riedner, Brady; Tononi, Giulio

2016-12-01

Analysis of individual slow waves in EEG recording during sleep provides both greater sensitivity and specificity compared to spectral power measures. However, parameters for detection and analysis have not been widely explored and validated. We present a new, open-source, Matlab based, toolbox for the automatic detection and analysis of slow waves; with adjustable parameter settings, as well as manual correction and exploration of the results using a multi-faceted visualization tool. We explore a large search space of parameter settings for slow wave detection and measure their effects on a selection of outcome parameters. Every choice of parameter setting had some effect on at least one outcome parameter. In general, the largest effect sizes were found when choosing the EEG reference, type of canonical waveform, and amplitude thresholding. Previously published methods accurately detect large, global waves but are conservative and miss the detection of smaller amplitude, local slow waves. The toolbox has additional benefits in terms of speed, user-interface, and visualization options to compare and contrast slow waves. The exploration of parameter settings in the toolbox highlights the importance of careful selection of detection METHODS: The sensitivity and specificity of the automated detection can be improved by manually adding or deleting entire waves and or specific channels using the toolbox visualization functions. The toolbox standardizes the detection procedure, sets the stage for reliable results and comparisons and is easy to use without previous programming experience. Copyright © 2016 Elsevier B.V. All rights reserved.

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

PubMed

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

2016-02-27

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.

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

NASA Astrophysics Data System (ADS)

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.

Online model evaluation of large-eddy simulations covering Germany with a horizontal resolution of 156 m

NASA Astrophysics Data System (ADS)

Hansen, Akio; Ament, Felix; Lammert, Andrea

2017-04-01

Large-eddy simulations have been performed since several decades, but due to computational limits most studies were restricted to small domains or idealised initial-/boundary conditions. Within the High definition clouds and precipitation for advancing climate prediction (HD(CP)2) project realistic weather forecasting like LES simulations were performed with the newly developed ICON LES model for several days. The domain covers central Europe with a horizontal resolution down to 156 m. The setup consists of more than 3 billion grid cells, by what one 3D dump requires roughly 500 GB. A newly developed online evaluation toolbox was created to check instantaneously for realistic model simulations. The toolbox automatically combines model results with observations and generates several quicklooks for various variables. So far temperature-/humidity profiles, cloud cover, integrated water vapour, precipitation and many more are included. All kind of observations like aircraft observations, soundings or precipitation radar networks are used. For each dataset, a specific module is created, which allows for an easy handling and enhancement of the toolbox. Most of the observations are automatically downloaded from the Standardized Atmospheric Measurement Database (SAMD). The evaluation tool should support scientists at monitoring computational costly model simulations as well as to give a first overview about model's performance. The structure of the toolbox as well as the SAMD database are presented. Furthermore, the toolbox was applied on an ICON LES sensitivity study, where example results are shown.

Optics Toolbox: An Intelligent Relational Database System For Optical Designers

NASA Astrophysics Data System (ADS)

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 < 2.0 and FOV of 28 degrees ± 5% Again for the purpose of this discussion, we will define an expert system as a program which contains expert knowledge, can ask intelligent questions, and can form conclusions based on the answers given and the knowledge which it contains. Most expert systems store this knowledge in the form of rules-of-thumb, which are written in an 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-database support, as well as a first-order optical design expert system with a rule interpreter which has full access to the relational database. The system schematic is shown in Figure 1.

Evidence for a Common Toolbox Based on Necrotrophy in a Fungal Lineage Spanning Necrotrophs, Biotrophs, Endophytes, Host Generalists and Specialists

PubMed Central

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 of necrotrophic generalists in the Sclerotiniaceae, while specialists and biotrophs deploy oah, or other as-yet-unknown toolbox genes, differently. PMID:22253834

plasmaFoam: An OpenFOAM framework for computational plasma physics and chemistry

NASA Astrophysics Data System (ADS)

Venkattraman, Ayyaswamy; Verma, Abhishek Kumar

2016-09-01

As emphasized in the 2012 Roadmap for low temperature plasmas (LTP), scientific computing has emerged as an essential tool for the investigation and prediction of the fundamental physical and chemical processes associated with these systems. While several in-house and commercial codes exist, with each having its own advantages and disadvantages, a common framework that can be developed by researchers from all over the world will likely accelerate the impact of computational studies on advances in low-temperature plasma physics and chemistry. In this regard, we present a finite volume computational toolbox to perform high-fidelity simulations of LTP systems. This framework, primarily based on the OpenFOAM solver suite, allows us to enhance our understanding of multiscale plasma phenomenon by performing massively parallel, three-dimensional simulations on unstructured meshes using well-established high performance computing tools that are widely used in the computational fluid dynamics community. In this talk, we will present preliminary results obtained using the OpenFOAM-based solver suite with benchmark three-dimensional simulations of microplasma devices including both dielectric and plasma regions. We will also discuss the future outlook for the solver suite.

NASA Tech Briefs, June 2010

NASA Technical Reports Server (NTRS)

2010-01-01

Topics covered include: Situational Awareness from a Low-Cost Camera System; Data Acquisition System for Multi-Frequency Radar Flight Operations Preparation; Mercury Toolset for Spatiotemporal Metadata; Social Tagging of Mission Data; Integrating Radar Image Data with Google Maps; Demonstration of a Submillimeter-Wave HEMT Oscillator Module at 330 GHz; Flexible Peripheral Component Interconnect Input/Output Card; Interface Supports Lightweight Subsystem Routing for Flight Applications; MMIC Amplifiers and Wafer Probes for 350 to 500 GHz; Public Risk Assessment Program; Particle Swarm Optimization Toolbox; Telescience Support Center Data System Software; Update on PISCES; Ground and Space Radar Volume Matching and Comparison Software; Web-Based Interface for Command and Control of Network Sensors; Orbit Determination Toolbox; Distributed Observer Network; Computer-Automated Evolution of Spacecraft X-Band Antennas; Practical Loop-Shaping Design of Feedback Control Systems; Fully Printed High-Frequency Phased-Array Antenna on Flexible Substrate; Formula for the Removal and Remediation of Polychlorinated Biphenyls in Painted Structures; Integrated Solar Concentrator and Shielded Radiator; Water Membrane Evaporator; Modeling of Failure for Analysis of Triaxial Braided Carbon Fiber Composites; Catalyst for Carbon Monoxide Oxidation; Titanium Hydroxide - a Volatile Species at High Temperature; Selective Functionalization of Carbon Nanotubes: Part II; Steerable Hopping Six-Legged Robot; Launchable and Retrievable Tetherobot; Hybrid Heat Exchangers; Orbital Winch for High-Strength, Space-Survivable Tethers; Parameterized Linear Longitudinal Airship Model; and Physics of Life: A Model for Non-Newtonian Properties of Living Systems.

Biosynthetic Polymers as Functional Materials

PubMed Central

2016-01-01

The synthesis of functional polymers encoded with biomolecules has been an extensive area of research for decades. As such, a diverse toolbox of polymerization techniques and bioconjugation methods has been developed. The greatest impact of this work has been in biomedicine and biotechnology, where fully synthetic and naturally derived biomolecules are used cooperatively. Despite significant improvements in biocompatible and functionally diverse polymers, our success in the field is constrained by recognized limitations in polymer architecture control, structural dynamics, and biostabilization. This Perspective discusses the current status of functional biosynthetic polymers and highlights innovative strategies reported within the past five years that have made great strides in overcoming the aforementioned barriers. PMID:27375299

Enhancing Adaptability of U.S. Military Forces. Part A: Main Report

DTIC Science & Technology

2011-01-01

virtual ...Research   and  Engineering,  Rapid  Capability  Fielding  Toolbox  Study,  stated  that   virtual  environment  tools  can...the   “approved”  basis   for   requirements   is   divorced   from   reality ,   and   setting   system  

Methods for Detecting Early Warnings of Critical Transitions in Time Series Illustrated Using Simulated Ecological Data

PubMed Central

Dakos, Vasilis; Carpenter, Stephen R.; Brock, William A.; Ellison, Aaron M.; Guttal, Vishwesha; Ives, Anthony R.; Kéfi, Sonia; Livina, Valerie; Seekell, David A.; van Nes, Egbert H.; Scheffer, Marten

2012-01-01

Many dynamical systems, including lakes, organisms, ocean circulation patterns, or financial markets, are now thought to have tipping points where critical transitions to a contrasting state can happen. Because critical transitions can occur unexpectedly and are difficult to manage, there is a need for methods that can be used to identify when a critical transition is approaching. Recent theory shows that we can identify the proximity of a system to a critical transition using a variety of so-called ‘early warning signals’, and successful empirical examples suggest a potential for practical applicability. However, while the range of proposed methods for predicting critical transitions is rapidly expanding, opinions on their practical use differ widely, and there is no comparative study that tests the limitations of the different methods to identify approaching critical transitions using time-series data. Here, we summarize a range of currently available early warning methods and apply them to two simulated time series that are typical of systems undergoing a critical transition. In addition to a methodological guide, our work offers a practical toolbox that may be used in a wide range of fields to help detect early warning signals of critical transitions in time series data. PMID:22815897

In vivo imaging of skeletal muscle in mice highlights muscle defects in a model of myotubular myopathy

PubMed Central

Mercier, Luc; Böhm, Johann; Fekonja, Nina; Allio, Guillaume; Lutz, Yves; Koch, Marc; Goetz, Jacky G.; Laporte, Jocelyn

2016-01-01

ABSTRACT Skeletal muscle structure and function are altered in different myopathies. However, the understanding of the molecular and cellular mechanisms mainly rely on in vitro and ex vivo investigations in mammalian models. In order to monitor in vivo the intracellular structure of the neuromuscular system in its environment under normal and pathological conditions, we set-up and validated non-invasive imaging of ear and leg muscles in mice. This original approach allows simultaneous imaging of different cellular and intracellular structures such as neuromuscular junctions and sarcomeres, reconstruction of the 3D architecture of the neuromuscular system, and video recording of dynamic events such as spontaneous muscle fiber contraction. Second harmonic generation was combined with vital dyes and fluorescent-coupled molecules. Skin pigmentation, although limiting, did not prevent intravital imaging. Using this versatile toolbox on the Mtm1 knockout mouse, a model for myotubular myopathy which is a severe congenital myopathy in human, we identified several hallmarks of the disease such as defects in fiber size and neuromuscular junction shape. Intravital imaging of the neuromuscular system paves the way for the follow-up of disease progression or/and disease amelioration upon therapeutic tests. It has also the potential to reduce the number of animals needed to reach scientific conclusions. PMID:28243519

An experimental toolbox for the generation of cold and ultracold polar molecules

NASA Astrophysics Data System (ADS)

Zeppenfeld, Martin; Gantner, Thomas; Glöckner, Rosa; Ibrügger, Martin; Koller, Manuel; Prehn, Alexander; Wu, Xing; Chervenkov, Sotir; Rempe, Gerhard

2017-01-01

Cold and ultracold molecules enable fascinating applications in quantum science. We present our toolbox of techniques to generate the required molecule ensembles, including buffergas cooling, centrifuge deceleration and optoelectrical Sisyphus cooling. We obtain excellent control over both the motional and internal molecular degrees of freedom, allowing us to aim at various applications.

Water Power Data and Tools | Water Power | NREL

Science.gov Websites

computer modeling tools and data with state-of-the-art design and analysis. Photo of a buoy designed around National Wind Technology Center's Information Portal as well as a WEC-Sim fact sheet. WEC Design Response Toolbox The WEC Design Response Toolbox provides extreme response and fatigue analysis tools specifically

Tensor Toolbox for MATLAB v. 3.0

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

Kola, Tamara; Bader, Brett W.; Acar Ataman, Evrim NMN

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

MOFA Software for the COBRA Toolbox

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

Griesemer, Marc; Navid, Ali

MOFA-COBRA is a software code for Matlab that performs Multi-Objective Flux Analysis (MOFA), a solving of linear programming problems. Teh leading software package for conducting different types of analyses using constrain-based models is the COBRA Toolbox for Matlab. MOFA-COBRA is an added tool for COBRA that solves multi-objective problems using a novel algorithm.

The panacea toolbox of a PhD biomedical student.

PubMed

Skaik, Younis

2014-01-01

Doing a PhD (doctor of philosophy) for the sake of contribution to knowledge should give the student an immense enthusiasm through the PhD period. It is the time in one's life that one spends to "hit the nail on the head" in a specific area and topic of interest. A PhD consists mostly of hard work and tenacity; however, luck and genius might also play a little role. You can pass all PhD phases without having both luck and genius. The PhD student should have pre-PhD and PhD toolboxes, which are "sine quibus non" for getting successfully a PhD degree. In this manuscript, the toolboxes of the PhD student are discussed.

Spectral analysis and filtering techniques in digital spatial data processing

USGS Publications Warehouse

Pan, Jeng-Jong

1989-01-01

A filter toolbox has been developed at the EROS Data Center, US Geological Survey, for retrieving or removing specified frequency information from two-dimensional digital spatial data. This filter toolbox provides capabilities to compute the power spectrum of a given data and to design various filters in the frequency domain. Three types of filters are available in the toolbox: point filter, line filter, and area filter. Both the point and line filters employ Gaussian-type notch filters, and the area filter includes the capabilities to perform high-pass, band-pass, low-pass, and wedge filtering techniques. These filters are applied for analyzing satellite multispectral scanner data, airborne visible and infrared imaging spectrometer (AVIRIS) data, gravity data, and the digital elevation models (DEM) data. -from Author

Plasmon Geometric Phase and Plasmon Hall Shift

NASA Astrophysics Data System (ADS)

Shi, Li-kun; Song, Justin C. W.

2018-04-01

The collective plasmonic modes of a metal comprise a simple pattern of oscillating charge density that yields enhanced light-matter interaction. Here we unveil that beneath this familiar facade plasmons possess a hidden internal structure that fundamentally alters its dynamics. In particular, we find that metals with nonzero Hall conductivity host plasmons with an intricate current density configuration that sharply departs from that of ordinary zero Hall conductivity metals. This nontrivial internal structure dramatically enriches the dynamics of plasmon propagation, enabling plasmon wave packets to acquire geometric phases as they scatter. At boundaries, these phases accumulate allowing plasmon waves that reflect off to experience a nonreciprocal parallel shift. This plasmon Hall shift, tunable by Hall conductivity as well as plasmon wavelength, displaces the incident and reflected plasmon trajectories and can be readily probed by near-field photonics techniques. Anomalous plasmon geometric phases dramatically enrich the nanophotonics toolbox, and yield radical new means for directing plasmonic beams.

Improve Data Mining and Knowledge Discovery Through the Use of MatLab

NASA Technical Reports Server (NTRS)

Shaykhian, Gholam Ali; Martin, Dawn (Elliott); Beil, Robert

2011-01-01

Data mining is widely used to mine business, engineering, and scientific data. Data mining uses pattern based queries, searches, or other analyses of one or more electronic databases/datasets in order to discover or locate a predictive pattern or anomaly indicative of system failure, criminal or terrorist activity, etc. There are various algorithms, techniques and methods used to mine data; including neural networks, genetic algorithms, decision trees, nearest neighbor method, rule induction association analysis, slice and dice, segmentation, and clustering. These algorithms, techniques and methods used to detect patterns in a dataset, have been used in the development of numerous open source and commercially available products and technology for data mining. Data mining is best realized when latent information in a large quantity of data stored is discovered. No one technique solves all data mining problems; challenges are to select algorithms or methods appropriate to strengthen data/text mining and trending within given datasets. In recent years, throughout industry, academia and government agencies, thousands of data systems have been designed and tailored to serve specific engineering and business needs. Many of these systems use databases with relational algebra and structured query language to categorize and retrieve data. In these systems, data analyses are limited and require prior explicit knowledge of metadata and database relations; lacking exploratory data mining and discoveries of latent information. This presentation introduces MatLab(R) (MATrix LABoratory), an engineering and scientific data analyses tool to perform data mining. MatLab was originally intended to perform purely numerical calculations (a glorified calculator). Now, in addition to having hundreds of mathematical functions, it is a programming language with hundreds built in standard functions and numerous available toolboxes. MatLab's ease of data processing, visualization and its enormous availability of built in functionalities and toolboxes make it suitable to perform numerical computations and simulations as well as a data mining tool. Engineers and scientists can take advantage of the readily available functions/toolboxes to gain wider insight in their perspective data mining experiments.

Improve Data Mining and Knowledge Discovery through the use of MatLab

NASA Technical Reports Server (NTRS)

Shaykahian, Gholan Ali; Martin, Dawn Elliott; Beil, Robert

2011-01-01

Data mining is widely used to mine business, engineering, and scientific data. Data mining uses pattern based queries, searches, or other analyses of one or more electronic databases/datasets in order to discover or locate a predictive pattern or anomaly indicative of system failure, criminal or terrorist activity, etc. There are various algorithms, techniques and methods used to mine data; including neural networks, genetic algorithms, decision trees, nearest neighbor method, rule induction association analysis, slice and dice, segmentation, and clustering. These algorithms, techniques and methods used to detect patterns in a dataset, have been used in the development of numerous open source and commercially available products and technology for data mining. Data mining is best realized when latent information in a large quantity of data stored is discovered. No one technique solves all data mining problems; challenges are to select algorithms or methods appropriate to strengthen data/text mining and trending within given datasets. In recent years, throughout industry, academia and government agencies, thousands of data systems have been designed and tailored to serve specific engineering and business needs. Many of these systems use databases with relational algebra and structured query language to categorize and retrieve data. In these systems, data analyses are limited and require prior explicit knowledge of metadata and database relations; lacking exploratory data mining and discoveries of latent information. This presentation introduces MatLab(TradeMark)(MATrix LABoratory), an engineering and scientific data analyses tool to perform data mining. MatLab was originally intended to perform purely numerical calculations (a glorified calculator). Now, in addition to having hundreds of mathematical functions, it is a programming language with hundreds built in standard functions and numerous available toolboxes. MatLab's ease of data processing, visualization and its enormous availability of built in functionalities and toolboxes make it suitable to perform numerical computations and simulations as well as a data mining tool. Engineers and scientists can take advantage of the readily available functions/toolboxes to gain wider insight in their perspective data mining experiments.

Rangeland Brush Estimation Toolbox (RaBET): An Approach for Evaluating Brush Management Conservation Efforts in Western Grazing Lands

NASA Astrophysics Data System (ADS)

Holifield Collins, C.; Kautz, M. A.; Skirvin, S. M.; Metz, L. J.

2016-12-01

There are over 180 million hectares of rangelands and grazed forests in the central and western United States. Due to the loss of perennial grasses and subsequent increased runoff and erosion that can degrade the system, woody cover species cannot be allowed to proliferate unchecked. The USDA-Natural Resources Conservation Service (NRCS) has allocated extensive resources to employ brush management (removal) as a conservation practice to control woody species encroachment. The Rangeland-Conservation Effects Assessment Project (CEAP) has been tasked with determining how effective the practice has been, however their land managers lack a cost-effective means to conduct these assessments at the necessary scale. An ArcGIS toolbox for generating large-scale, Landsat-based, spatial maps of woody cover on grazing lands in the western United States was developed through a collaboration with NRCS Rangeland-CEAP. The toolbox contains two main components of operation, image generation and temporal analysis, and utilizes simple interfaces requiring minimum user inputs. The image generation tool utilizes geographically specific algorithms developed from combining moderate-resolution (30-m) Landsat imagery and high-resolution (1-m) National Agricultural Imagery Program (NAIP) aerial photography to produce the woody cover scenes at the Major Land Resource (MLRA) scale. The temporal analysis tool can be used on these scenes to assess treatment effectiveness and monitor woody cover reemergence. RaBET provides rangeland managers an operational, inexpensive decision support tool to aid in the application of brush removal treatments and assessing their effectiveness.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data.

PubMed

Muir, Dylan R; Kampa, Björn M

2014-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories.

FocusStack and StimServer: a new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data

PubMed Central

Muir, Dylan R.; Kampa, Björn M.

2015-01-01

Two-photon calcium imaging of neuronal responses is an increasingly accessible technology for probing population responses in cortex at single cell resolution, and with reasonable and improving temporal resolution. However, analysis of two-photon data is usually performed using ad-hoc solutions. To date, no publicly available software exists for straightforward analysis of stimulus-triggered two-photon imaging experiments. In addition, the increasing data rates of two-photon acquisition systems imply increasing cost of computing hardware required for in-memory analysis. Here we present a Matlab toolbox, FocusStack, for simple and efficient analysis of two-photon calcium imaging stacks on consumer-level hardware, with minimal memory footprint. We also present a Matlab toolbox, StimServer, for generation and sequencing of visual stimuli, designed to be triggered over a network link from a two-photon acquisition system. FocusStack is compatible out of the box with several existing two-photon acquisition systems, and is simple to adapt to arbitrary binary file formats. Analysis tools such as stack alignment for movement correction, automated cell detection and peri-stimulus time histograms are already provided, and further tools can be easily incorporated. Both packages are available as publicly-accessible source-code repositories1. PMID:25653614

Extending Inferential Group Analysis in Type 2 Diabetic Patients with Multivariate GLM Implemented in SPM8.

PubMed

Ferreira, Fábio S; Pereira, João M S; Duarte, João V; Castelo-Branco, Miguel

2017-01-01

Although voxel based morphometry studies are still the standard for analyzing brain structure, their dependence on massive univariate inferential methods is a limiting factor. A better understanding of brain pathologies can be achieved by applying inferential multivariate methods, which allow the study of multiple dependent variables, e.g. different imaging modalities of the same subject. Given the widespread use of SPM software in the brain imaging community, the main aim of this work is the implementation of massive multivariate inferential analysis as a toolbox in this software package. applied to the use of T1 and T2 structural data from diabetic patients and controls. This implementation was compared with the traditional ANCOVA in SPM and a similar multivariate GLM toolbox (MRM). We implemented the new toolbox and tested it by investigating brain alterations on a cohort of twenty-eight type 2 diabetes patients and twenty-six matched healthy controls, using information from both T1 and T2 weighted structural MRI scans, both separately - using standard univariate VBM - and simultaneously, with multivariate analyses. Univariate VBM replicated predominantly bilateral changes in basal ganglia and insular regions in type 2 diabetes patients. On the other hand, multivariate analyses replicated key findings of univariate results, while also revealing the thalami as additional foci of pathology. While the presented algorithm must be further optimized, the proposed toolbox is the first implementation of multivariate statistics in SPM8 as a user-friendly toolbox, which shows great potential and is ready to be validated in other clinical cohorts and modalities.

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

PubMed Central

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 Security Association says, "whereas progress has been made in safety and health, the construction industry is still a high risk sector." Methods 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. Results 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. 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. PMID:22953194

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

PubMed

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.

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

PubMed

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.

Extending Inferential Group Analysis in Type 2 Diabetic Patients with Multivariate GLM Implemented in SPM8

PubMed Central

Ferreira, Fábio S.; Pereira, João M.S.; Duarte, João V.; Castelo-Branco, Miguel

2017-01-01

Background: Although voxel based morphometry studies are still the standard for analyzing brain structure, their dependence on massive univariate inferential methods is a limiting factor. A better understanding of brain pathologies can be achieved by applying inferential multivariate methods, which allow the study of multiple dependent variables, e.g. different imaging modalities of the same subject. Objective: Given the widespread use of SPM software in the brain imaging community, the main aim of this work is the implementation of massive multivariate inferential analysis as a toolbox in this software package. applied to the use of T1 and T2 structural data from diabetic patients and controls. This implementation was compared with the traditional ANCOVA in SPM and a similar multivariate GLM toolbox (MRM). Method: We implemented the new toolbox and tested it by investigating brain alterations on a cohort of twenty-eight type 2 diabetes patients and twenty-six matched healthy controls, using information from both T1 and T2 weighted structural MRI scans, both separately – using standard univariate VBM - and simultaneously, with multivariate analyses. Results: Univariate VBM replicated predominantly bilateral changes in basal ganglia and insular regions in type 2 diabetes patients. On the other hand, multivariate analyses replicated key findings of univariate results, while also revealing the thalami as additional foci of pathology. Conclusion: While the presented algorithm must be further optimized, the proposed toolbox is the first implementation of multivariate statistics in SPM8 as a user-friendly toolbox, which shows great potential and is ready to be validated in other clinical cohorts and modalities. PMID:28761571

GOCE User Toolbox and Tutorial

NASA Astrophysics Data System (ADS)

Knudsen, P.; Benveniste, J.

2011-07-01

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. GUT has been developed in a collaboration within the GUT Core Group. The GUT Core Group: S. Dinardo, D. Serpe, B.M. Lucas, R. Floberghagen, A. Horvath (ESA), O. Andersen, M. Herceg (DTU), M.-H. Rio, S. Mulet, G. Larnicol (CLS), J. Johannessen, L.Bertino (NERSC), H. Snaith, P. Challenor (NOC), K. Haines, D. Bretherton (NCEO), C. Hughes (POL), R.J. Bingham (NU), G. Balmino, S. Niemeijer, I. Price, L. Cornejo (S&T), M. Diament, I Panet (IPGP), C.C. Tscherning (KU), D. Stammer, F. Siegismund (UH), T. Gruber (TUM),

Turbo-Satori: a neurofeedback and brain-computer interface toolbox for real-time functional near-infrared spectroscopy.

PubMed

Lührs, Michael; Goebel, Rainer

2017-10-01

Turbo-Satori is a neurofeedback and brain-computer interface (BCI) toolbox for real-time functional near-infrared spectroscopy (fNIRS). It incorporates multiple pipelines from real-time preprocessing and analysis to neurofeedback and BCI applications. The toolbox is designed with a focus in usability, enabling a fast setup and execution of real-time experiments. Turbo-Satori uses an incremental recursive least-squares procedure for real-time general linear model calculation and support vector machine classifiers for advanced BCI applications. It communicates directly with common NIRx fNIRS hardware and was tested extensively ensuring that the calculations can be performed in real time without a significant change in calculation times for all sampling intervals during ongoing experiments of up to 6 h of recording. Enabling immediate access to advanced processing features also allows the use of this toolbox for students and nonexperts in the field of fNIRS data acquisition and processing. Flexible network interfaces allow third party stimulus applications to access the processed data and calculated statistics in real time so that this information can be easily incorporated in neurofeedback or BCI presentations.

HYDRORECESSION: A toolbox for streamflow recession analysis

NASA Astrophysics Data System (ADS)

Arciniega, S.

2015-12-01

Streamflow recession curves are hydrological signatures allowing to study the relationship between groundwater storage and baseflow and/or low flows at the catchment scale. Recent studies have showed that streamflow recession analysis can be quite sensitive to the combination of different models, extraction techniques and parameter estimation methods. In order to better characterize streamflow recession curves, new methodologies combining multiple approaches have been recommended. The HYDRORECESSION toolbox, presented here, is a Matlab graphical user interface developed to analyse streamflow recession time series with the support of different tools allowing to parameterize linear and nonlinear storage-outflow relationships through four of the most useful recession models (Maillet, Boussinesq, Coutagne and Wittenberg). The toolbox includes four parameter-fitting techniques (linear regression, lower envelope, data binning and mean squared error) and three different methods to extract hydrograph recessions segments (Vogel, Brutsaert and Aksoy). In addition, the toolbox has a module that separates the baseflow component from the observed hydrograph using the inverse reservoir algorithm. Potential applications provided by HYDRORECESSION include model parameter analysis, hydrological regionalization and classification, baseflow index estimates, catchment-scale recharge and low-flows modelling, among others. HYDRORECESSION is freely available for non-commercial and academic purposes.

Biological Parametric Mapping: A Statistical Toolbox for Multi-Modality Brain Image Analysis

PubMed Central

Casanova, Ramon; Ryali, Srikanth; Baer, Aaron; Laurienti, Paul J.; Burdette, Jonathan H.; Hayasaka, Satoru; Flowers, Lynn; Wood, Frank; Maldjian, Joseph A.

2006-01-01

In recent years multiple brain MR imaging modalities have emerged; however, analysis methodologies have mainly remained modality specific. In addition, when comparing across imaging modalities, most researchers have been forced to rely on simple region-of-interest type analyses, which do not allow the voxel-by-voxel comparisons necessary to answer more sophisticated neuroscience questions. To overcome these limitations, we developed a toolbox for multimodal image analysis called biological parametric mapping (BPM), based on a voxel-wise use of the general linear model. The BPM toolbox incorporates information obtained from other modalities as regressors in a voxel-wise analysis, thereby permitting investigation of more sophisticated hypotheses. The BPM toolbox has been developed in MATLAB with a user friendly interface for performing analyses, including voxel-wise multimodal correlation, ANCOVA, and multiple regression. It has a high degree of integration with the SPM (statistical parametric mapping) software relying on it for visualization and statistical inference. Furthermore, statistical inference for a correlation field, rather than a widely-used T-field, has been implemented in the correlation analysis for more accurate results. An example with in-vivo data is presented demonstrating the potential of the BPM methodology as a tool for multimodal image analysis. PMID:17070709

A novel toolbox for E. coli lysis monitoring.

PubMed

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

2017-01-01

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

NASA Tech Briefs, October 2005

NASA Technical Reports Server (NTRS)

2005-01-01

Topics covered include: Insect-Inspired Optical-Flow Navigation Sensors; Chemical Sensors Based on Optical Ring Resonators; A Broad-Band Phase-Contrast Wave-Front Sensor; Progress in Insect-Inspired Optical Navigation Sensors; Portable Airborne Laser System Measures Forest-Canopy Height; Deployable Wide-Aperture Array Antennas; Faster Evolution of More Multifunctional Logic Circuits; Video-Camera-Based Position-Measuring System; N-Type delta Doping of High-Purity Silicon Imaging Arrays; Avionics System Architecture Tool; Updated Chemical Kinetics and Sensitivity Analysis Code; Predicting Flutter and Forced Response in Turbomachinery; Upgrades of Two Computer Codes for Analysis of Turbomachinery; Program Facilitates CMMI Appraisals; Grid Visualization Tool; Program Computes Sound Pressures at Rocket Launches; Solar-System Ephemeris Toolbox; Data-Acquisition Software for PSP/TSP Wind-Tunnel Cameras; Corrosion-Prevention Capabilities of a Water-Borne, Silicone-Based, Primerless Coating; Sol-Gel Process for Making Pt-Ru Fuel-Cell Catalysts; Making Activated Carbon for Storing Gas; System Regulates the Water Contents of Fuel-Cell Streams; Five-Axis, Three-Magnetic-Bearing Dynamic Spin Rig; Modifications of Fabrication of Vibratory Microgyroscopes; Chamber for Growing and Observing Fungi; Electroporation System for Sterilizing Water; Thermoelectric Air/Soil Energy-Harvesting Device; Flexible Metal-Fabric Radiators; Actuated Hybrid Mirror Telescope; Optical Design of an Optical Communications Terminal; Algorithm for Identifying Erroneous Rain-Gauge Readings; Condition Assessment and End-of-Life Prediction System for Electric Machines and Their Loads; Lightweight Thermal Insulation for a Liquid-Oxygen Tank; Stellar Gyroscope for Determining Attitude of a Spacecraft; and Lifting Mechanism for the Mars Explorer Rover.

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

NASA Astrophysics Data System (ADS)

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 framework to assist decision makers at all levels - local, state, regional, and federal. Using Cleveland, Tennessee as an example, in this presentation, we illustrate how emerging cities could easily assess future land use scenario driven impacts on energy and environment utilizing such a capability.

Web-Based Model Visualization Tools to Aid in Model Optimization and Uncertainty Analysis

NASA Astrophysics Data System (ADS)

Alder, J.; van Griensven, A.; Meixner, T.

2003-12-01

Individuals applying hydrologic models have a need for a quick easy to use visualization tools to permit them to assess and understand model performance. We present here the Interactive Hydrologic Modeling (IHM) visualization toolbox. The IHM utilizes high-speed Internet access, the portability of the web and the increasing power of modern computers to provide an online toolbox for quick and easy model result visualization. This visualization interface allows for the interpretation and analysis of Monte-Carlo and batch model simulation results. Often times a given project will generate several thousands or even hundreds of thousands simulations. This large number of simulations creates a challenge for post-simulation analysis. IHM's goal is to try to solve this problem by loading all of the data into a database with a web interface that can dynamically generate graphs for the user according to their needs. IHM currently supports: a global samples statistics table (e.g. sum of squares error, sum of absolute differences etc.), top ten simulations table and graphs, graphs of an individual simulation using time step data, objective based dotty plots, threshold based parameter cumulative density function graphs (as used in the regional sensitivity analysis of Spear and Hornberger) and 2D error surface graphs of the parameter space. IHM is ideal for the simplest bucket model to the largest set of Monte-Carlo model simulations with a multi-dimensional parameter and model output space. By using a web interface, IHM offers the user complete flexibility in the sense that they can be anywhere in the world using any operating system. IHM can be a time saving and money saving alternative to spending time producing graphs or conducting analysis that may not be informative or being forced to purchase or use expensive and proprietary software. IHM is a simple, free, method of interpreting and analyzing batch model results, and is suitable for novice to expert hydrologic modelers.

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

PubMed

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

2015-03-01

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.

EEGLAB: an open source toolbox for analysis of single-trial EEG dynamics including independent component analysis.

PubMed

Delorme, Arnaud; Makeig, Scott

2004-03-15

We have developed a toolbox and graphic user interface, EEGLAB, running under the crossplatform MATLAB environment (The Mathworks, Inc.) for processing collections of single-trial and/or averaged EEG data of any number of channels. Available functions include EEG data, channel and event information importing, data visualization (scrolling, scalp map and dipole model plotting, plus multi-trial ERP-image plots), preprocessing (including artifact rejection, filtering, epoch selection, and averaging), independent component analysis (ICA) and time/frequency decompositions including channel and component cross-coherence supported by bootstrap statistical methods based on data resampling. EEGLAB functions are organized into three layers. Top-layer functions allow users to interact with the data through the graphic interface without needing to use MATLAB syntax. Menu options allow users to tune the behavior of EEGLAB to available memory. Middle-layer functions allow users to customize data processing using command history and interactive 'pop' functions. Experienced MATLAB users can use EEGLAB data structures and stand-alone signal processing functions to write custom and/or batch analysis scripts. Extensive function help and tutorial information are included. A 'plug-in' facility allows easy incorporation of new EEG modules into the main menu. EEGLAB is freely available (http://www.sccn.ucsd.edu/eeglab/) under the GNU public license for noncommercial use and open source development, together with sample data, user tutorial and extensive documentation.

ExoSOFT: Exoplanet Simple Orbit Fitting Toolbox

NASA Astrophysics Data System (ADS)

Mede, Kyle; Brandt, Timothy D.

2017-08-01

ExoSOFT provides orbital analysis of exoplanets and binary star systems. It fits any combination of astrometric and radial velocity data, and offers four parameter space exploration techniques, including MCMC. It is packaged with an automated set of post-processing and plotting routines to summarize results, and is suitable for performing orbital analysis during surveys with new radial velocity and direct imaging instruments.

Who Benefits from Postsecondary Occupational Education? Findings from the 1980s and 1990s. CCRC Brief Number 23

ERIC Educational Resources Information Center

Bailey, Thomas; Kienzl, Gregory; Marcotte, David

2004-01-01

Technological changes in the workplace have placed considerable pressure on the U.S. educational system to prepare students for increasingly skillbased occupations. Employers reward new hires for having the skills or credentials needed for their job, underscoring the importance of having either the requisite "tools in your toolbox," or some basic…

Action-based verification of RTCP-nets with CADP

NASA Astrophysics Data System (ADS)

Biernacki, Jerzy; Biernacka, Agnieszka; Szpyrka, Marcin

2015-12-01

The paper presents an RTCP-nets' (real-time coloured Petri nets) coverability graphs into Aldebaran format translation algorithm. The approach provides the possibility of automatic RTCP-nets verification using model checking techniques provided by the CADP toolbox. An actual fire alarm control panel system has been modelled and several of its crucial properties have been verified to demonstrate the usability of the approach.

Rapid Onboard Trajectory Design for Autonomous Spacecraft in Multibody Systems

NASA Astrophysics Data System (ADS)

Trumbauer, Eric Michael

This research develops automated, on-board trajectory planning algorithms in order to support current and new mission concepts. These include orbiter missions to Phobos or Deimos, Outer Planet Moon orbiters, and robotic and crewed missions to small bodies. The challenges stem from the limited on-board computing resources which restrict full trajectory optimization with guaranteed convergence in complex dynamical environments. The approach taken consists of leveraging pre-mission computations to create a large database of pre-computed orbits and arcs. Such a database is used to generate a discrete representation of the dynamics in the form of a directed graph, which acts to index these arcs. This allows the use of graph search algorithms on-board in order to provide good approximate solutions to the path planning problem. Coupled with robust differential correction and optimization techniques, this enables the determination of an efficient path between any boundary conditions with very little time and computing effort. Furthermore, the optimization methods developed here based on sequential convex programming are shown to have provable convergence properties, as well as generating feasible major iterates in case of a system interrupt -- a key requirement for on-board application. The outcome of this project is thus the development of an algorithmic framework which allows the deployment of this approach in a variety of specific mission contexts. Test cases related to missions of interest to NASA and JPL such as a Phobos orbiter and a Near Earth Asteroid interceptor are demonstrated, including the results of an implementation on the RAD750 flight processor. This method fills a gap in the toolbox being developed to create fully autonomous space exploration systems.

SWToolbox: A surface-water tool-box for statistical analysis of streamflow time series

USGS Publications Warehouse

Kiang, Julie E.; Flynn, Kate; Zhai, Tong; Hummel, Paul; Granato, Gregory

2018-03-07

This report is a user guide for the low-flow analysis methods provided with version 1.0 of the Surface Water Toolbox (SWToolbox) computer program. The software combines functionality from two software programs—U.S. Geological Survey (USGS) SWSTAT and U.S. Environmental Protection Agency (EPA) DFLOW. Both of these programs have been used primarily for computation of critical low-flow statistics. The main analysis methods are the computation of hydrologic frequency statistics such as the 7-day minimum flow that occurs on average only once every 10 years (7Q10), computation of design flows including biologically based flows, and computation of flow-duration curves and duration hydrographs. Other annual, monthly, and seasonal statistics can also be computed. The interface facilitates retrieval of streamflow discharge data from the USGS National Water Information System and outputs text reports for a record of the analysis. Tools for graphing data and screening tests are available to assist the analyst in conducting the analysis.

a Hadoop-Based Distributed Framework for Efficient Managing and Processing Big Remote Sensing Images

NASA Astrophysics Data System (ADS)

Wang, C.; Hu, F.; Hu, X.; Zhao, S.; Wen, W.; Yang, C.

2015-07-01

Various sensors from airborne and satellite platforms are producing large volumes of remote sensing images for mapping, environmental monitoring, disaster management, military intelligence, and others. However, it is challenging to efficiently storage, query and process such big data due to the data- and computing- intensive issues. In this paper, a Hadoop-based framework is proposed to manage and process the big remote sensing data in a distributed and parallel manner. Especially, remote sensing data can be directly fetched from other data platforms into the Hadoop Distributed File System (HDFS). The Orfeo toolbox, a ready-to-use tool for large image processing, is integrated into MapReduce to provide affluent image processing operations. With the integration of HDFS, Orfeo toolbox and MapReduce, these remote sensing images can be directly processed in parallel in a scalable computing environment. The experiment results show that the proposed framework can efficiently manage and process such big remote sensing data.

Toolbox No. 2: Expanding the Role of Foster Parents in Achieving Permanency. Toolboxes for Permanency.

ERIC Educational Resources Information Center

Dougherty, Susan

Noting that over the last decade, the role of a foster parent has evolved from temporary caregiver to essential part of a professional team in determining the best long-term plan for children in their care, this guide focuses on practical ways in which best child welfare practice can be incorporated into the recruitment, training, and support of…

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

Simple tool for the rapid, automated quantification of glacier advance/retreat observations using multiple methods

NASA Astrophysics Data System (ADS)

Lea, J.

2017-12-01

The quantification of glacier change is a key variable within glacier monitoring, with the method used potentially being crucial to ensuring that data can be appropriately compared with environmental data. The topic and timescales of study (e.g. land/marine terminating environments; sub-annual/decadal/centennial/millennial timescales) often mean that different methods are more suitable for different problems. However, depending on the GIS/coding expertise of the user, some methods can potentially be time consuming to undertake, making large-scale studies problematic. In addition, examples exist where different users have nominally applied the same methods in different studies, though with minor methodological inconsistencies in their approach. In turn, this will have implications for data homogeneity where regional/global datasets may be constructed. Here, I present a simple toolbox scripted in a Matlab® environment that requires only glacier margin and glacier centreline data to quantify glacier length, glacier change between observations, rate of change, in addition to other metrics. The toolbox includes the option to apply the established centreline or curvilinear box methods, or a new method: the variable box method - designed for tidewater margins where box width is defined as the total width of the individual terminus observation. The toolbox is extremely flexible, and has the option to be applied as either Matlab® functions within user scripts, or via a graphical user interface (GUI) for those unfamiliar with a coding environment. In both instances, there is potential to apply the methods quickly to large datasets (100s-1000s of glaciers, with potentially similar numbers of observations each), thus ensuring large scale methodological consistency (and therefore data homogeneity) and allowing regional/global scale analyses to be achievable for those with limited GIS/coding experience. The toolbox has been evaluated against idealised scenarios demonstrating its accuracy, while feedback from undergraduate students who have trialled the toolbox is that it is intuitive and simple to use. When released, the toolbox will be free and open source allowing users to potentially modify, improve and expand upon the current version.

A tool for NDVI time series extraction from wide-swath remotely sensed images

NASA Astrophysics Data System (ADS)

Li, Zhishan; Shi, Runhe; Zhou, Cong

2015-09-01

Normalized Difference Vegetation Index (NDVI) is one of the most widely used indicators for monitoring the vegetation coverage in land surface. The time series features of NDVI are capable of reflecting dynamic changes of various ecosystems. Calculating NDVI via Moderate Resolution Imaging Spectrometer (MODIS) and other wide-swath remotely sensed images provides an important way to monitor the spatial and temporal characteristics of large-scale NDVI. However, difficulties are still existed for ecologists to extract such information correctly and efficiently because of the problems in several professional processes on the original remote sensing images including radiometric calibration, geometric correction, multiple data composition and curve smoothing. In this study, we developed an efficient and convenient online toolbox for non-remote sensing professionals who want to extract NDVI time series with a friendly graphic user interface. It is based on Java Web and Web GIS technically. Moreover, Struts, Spring and Hibernate frameworks (SSH) are integrated in the system for the purpose of easy maintenance and expansion. Latitude, longitude and time period are the key inputs that users need to provide, and the NDVI time series are calculated automatically.

Data distribution service-based interoperability framework for smart grid testbed infrastructure

DOE PAGES

Youssef, Tarek A.; Elsayed, Ahmed T.; Mohammed, Osama A.

2016-03-02

This study presents the design and implementation of a communication and control infrastructure for smart grid operation. The proposed infrastructure enhances the reliability of the measurements and control network. The advantages of utilizing the data-centric over message-centric communication approach are discussed in the context of smart grid applications. The data distribution service (DDS) is used to implement a data-centric common data bus for the smart grid. This common data bus improves the communication reliability, enabling distributed control and smart load management. These enhancements are achieved by avoiding a single point of failure while enabling peer-to-peer communication and an automatic discoverymore » feature for dynamic participating nodes. The infrastructure and ideas presented in this paper were implemented and tested on the smart grid testbed. A toolbox and application programing interface for the testbed infrastructure are developed in order to facilitate interoperability and remote access to the testbed. This interface allows control, monitoring, and performing of experiments remotely. Furthermore, it could be used to integrate multidisciplinary testbeds to study complex cyber-physical systems (CPS).« less

A novel Laser Ion Mobility Spectrometer

NASA Astrophysics Data System (ADS)

Göbel, J.; Kessler, M.; Langmeier, A.

2009-05-01

IMS is a well know technology within the range of security based applications. Its main advantages lie in the simplicity of measurement, along with a fast and sensitive detection method. Contemporary technology often fails due to interference substances, in conjunction with saturation effects and a low dynamic detection range. High throughput facilities, such as airports, require the analysis of many samples at low detection limits within a very short timeframe. High detection reliability is a requirement for safe and secure operation. In our present work we developed a laser based ion-mobility-sensor which shows several advantages over known IMS sensor technology. The goal of our research was to increase the sensitivity compared to the range of 63Ni based instruments. This was achieved with an optimised geometric drift tube design and a pulsed UV laser system at an efficient intensity. In this intensity range multi-photon ionisation is possible, which leads to higher selectivity in the ion-formation process itself. After high speed capturing of detection samples, a custom designed pattern recognition software toolbox provides reliable auto-detection capability with a learning algorithm and a graphical user interface.

Spacecraft Orbit Anomaly Representation Using Thrust-Fourier-Coefficients with Orbit Determination Toolbox

NASA Astrophysics Data System (ADS)

Ko, H.; Scheeres, D.

2014-09-01

Representing spacecraft orbit anomalies between two separate states is a challenging but an important problem in achieving space situational awareness for an active spacecraft. Incorporation of such a capability could play an essential role in analyzing satellite behaviors as well as trajectory estimation of the space object. A general way to deal with the anomaly problem is to add an estimated perturbing acceleration such as dynamic model compensation (DMC) into an orbit determination process based on pre- and post-anomaly tracking data. It is a time-consuming numerical process to find valid coefficients to compensate for unknown dynamics for the anomaly. Even if the orbit determination filter with DMC can crudely estimate an unknown acceleration, this approach does not consider any fundamental element of the unknown dynamics for a given anomaly. In this paper, a new way of representing a spacecraft anomaly using an interpolation technique with the Thrust-Fourier-Coefficients (TFCs) is introduced and several anomaly cases are studied using this interpolation method. It provides a very efficient way of reconstructing the fundamental elements of the dynamics for a given spacecraft anomaly. Any maneuver performed by a satellite transitioning between two arbitrary orbital states can be represented as an equivalent maneuver using an interpolation technique with the TFCs. Given unconnected orbit states between two epochs due to a spacecraft anomaly, it is possible to obtain a unique control law using the TFCs that is able to generate the desired secular behavior for the given orbital changes. This interpolation technique can capture the fundamental elements of combined unmodeled anomaly events. The interpolated orbit trajectory, using the TFCs compensating for a given anomaly, can be used to improve the quality of orbit fits through the anomaly period and therefore help to obtain a good orbit determination solution after the anomaly. Orbit Determination Toolbox (ODTBX) is modified to adapt this technique in order to verify the performance of this interpolation approach. Spacecraft anomaly cases are based on either single or multiple low or high thrust maneuvers and the unknown thrust accelerations are recovered and compared with the true thrust acceleration. The advantage of this approach is to easily append TFCs and its dynamics to the pre-built ODTBX, which enables us to blend post-anomaly tracking data to improve the performance of the interpolation representation in the absence of detailed information about a maneuver. It allows us to improve space situational awareness in the areas of uncertainty propagation, anomaly characterization and track correlation.

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies.

PubMed

O'Grady, John; Schwender, Jörg; Shachar-Hill, Yair; Morgan, John A

2012-03-01

For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

Measuring vigilance decrement using computer vision assisted eye tracking in dynamic naturalistic environments.

PubMed

Bodala, Indu P; Abbasi, Nida I; Yu Sun; Bezerianos, Anastasios; Al-Nashash, Hasan; Thakor, Nitish V

2017-07-01

Eye tracking offers a practical solution for monitoring cognitive performance in real world tasks. However, eye tracking in dynamic environments is difficult due to high spatial and temporal variation of stimuli, needing further and thorough investigation. In this paper, we study the possibility of developing a novel computer vision assisted eye tracking analysis by using fixations. Eye movement data is obtained from a long duration naturalistic driving experiment. Source invariant feature transform (SIFT) algorithm was implemented using VLFeat toolbox to identify multiple areas of interest (AOIs). A new measure called `fixation score' was defined to understand the dynamics of fixation position between the target AOI and the non target AOIs. Fixation score is maximum when the subjects focus on the target AOI and diminishes when they gaze at the non-target AOIs. Statistically significant negative correlation was found between fixation score and reaction time data (r =-0.2253 and p<;0.05). This implies that with vigilance decrement, the fixation score decreases due to visual attention shifting away from the target objects resulting in an increase in the reaction time.

TRENTOOL: A Matlab open source toolbox to analyse information flow in time series data with transfer entropy

PubMed Central

2011-01-01

Background Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. Results In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. Conclusions TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox. PMID:22098775

Evaluation of an educational "toolbox" for improving nursing staff competence and psychosocial work environment in elderly care: results of a prospective, non-randomized controlled intervention.

PubMed

Arnetz, J E; Hasson, H

2007-07-01

Lack of professional development opportunities among nursing staff is a major concern in elderly care and has been associated with work dissatisfaction and staff turnover. There is a lack of prospective, controlled studies evaluating the effects of educational interventions on nursing competence and work satisfaction. The aim of this study was to evaluate the possible effects of an educational "toolbox" intervention on nursing staff ratings of their competence, psychosocial work environment and overall work satisfaction. The study was a prospective, non-randomized, controlled intervention. Nursing staff in two municipal elderly care organizations in western Sweden. In an initial questionnaire survey, nursing staff in the intervention municipality described several areas in which they felt a need for competence development. Measurement instruments and educational materials for improving staff knowledge and work practices were then collated by researchers and managers in a "toolbox." Nursing staff ratings of their competence and work were measured pre and post-intervention by questionnaire. Staff ratings in the intervention municipality were compared to staff ratings in the reference municipality, where no toolbox was introduced. Nursing staff ratings of their competence and psychosocial work environment, including overall work satisfaction, improved significantly over time in the intervention municipality, compared to the reference group. Both competence and work environment ratings were largely unchanged among reference municipality staff. Multivariate analysis revealed a significant interaction effect between municipalities over time for nursing staff ratings of participation, leadership, performance feedback and skills' development. Staff ratings for these four scales improved significantly in the intervention municipality as compared to the reference municipality. Compared to a reference municipality, nursing staff ratings of their competence and the psychosocial work environment improved in the municipality where the toolbox was introduced.

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

PubMed

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.

TRENTOOL: a Matlab open source toolbox to analyse information flow in time series data with transfer entropy.

PubMed

Lindner, Michael; Vicente, Raul; Priesemann, Viola; Wibral, Michael

2011-11-18

Transfer entropy (TE) is a measure for the detection of directed interactions. Transfer entropy is an information theoretic implementation of Wiener's principle of observational causality. It offers an approach to the detection of neuronal interactions that is free of an explicit model of the interactions. Hence, it offers the power to analyze linear and nonlinear interactions alike. This allows for example the comprehensive analysis of directed interactions in neural networks at various levels of description. Here we present the open-source MATLAB toolbox TRENTOOL that allows the user to handle the considerable complexity of this measure and to validate the obtained results using non-parametrical statistical testing. We demonstrate the use of the toolbox and the performance of the algorithm on simulated data with nonlinear (quadratic) coupling and on local field potentials (LFP) recorded from the retina and the optic tectum of the turtle (Pseudemys scripta elegans) where a neuronal one-way connection is likely present. In simulated data TE detected information flow in the simulated direction reliably with false positives not exceeding the rates expected under the null hypothesis. In the LFP data we found directed interactions from the retina to the tectum, despite the complicated signal transformations between these stages. No false positive interactions in the reverse directions were detected. TRENTOOL is an implementation of transfer entropy and mutual information analysis that aims to support the user in the application of this information theoretic measure. TRENTOOL is implemented as a MATLAB toolbox and available under an open source license (GPL v3). For the use with neural data TRENTOOL seamlessly integrates with the popular FieldTrip toolbox.

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

PubMed

Hilbink, Mirrian A H W; Ouwens, Marielle M T J; Burgers, Jako S; Kool, Rudolf B

2014-03-19

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, implementation, revision, and evaluation. All relevant guideline organizations in the Netherlands were approached to prioritize the topics. We sent out a questionnaire and discussed the results at an invitational conference. Based on consensus, twelve topics were selected for the development of new tools. Subsequently, working groups were composed for the development of the tools. After development of the tools, their draft versions were pilot tested in 40 guideline projects. Based on the results of the pilot tests, the tools were refined and their final versions were presented. The vast majority of organizations involved in pilot testing of the tools reported satisfaction with using the tools. Guideline experts involved in pilot testing of the tools proposed a variety of suggestions for the implementation of the tools. The tools are available in Dutch and in English at a web-based platform on guideline development and implementation (http://www.ha-ring.nl). A collaborative approach was used for the development and evaluation of a toolbox for development, implementation, revision, and evaluation of guidelines. This approach yielded a potentially powerful toolbox for improving the quality and implementation of Dutch clinical guidelines. Collaboration between guideline organizations within this project led to stronger linkages, which is useful for enhancing coordination of guideline development and implementation and preventing duplication of efforts. Use of the toolbox could improve quality standards in the Netherlands, and might facilitate the development of high-quality guidelines in other countries as well.

Earth Girl Volcano: An Interactive Casual Game about Complex Volcanic Hazards

NASA Astrophysics Data System (ADS)

Kerlow, I.

2017-12-01

Earth Girl Volcano is an interactive casual strategy game for disaster preparedness. The project is designed for mainstream audiences, particularly for children, as an engaging and fun way to learn about volcano hazards, monitoring, and mitigation strategies. The game is deceptively simple but it provides a toolbox to address practically all volcanic hazards ranging from gas and ash fall to pyroclastic flows, lava and lahars. This presentation shows the basic dynamic to explore the area, assess the risk, choose the best-suited tools and execute a mitigation strategy within the available budget. This game is a real-time simulation of a crowd evacuation that allows players to intervene before and during the disaster.

A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

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

Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.

In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sedimentmore » for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.« less

A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

PubMed

Yu, Zheng; Krause, Sascha M B; Beck, David A C; Chistoserdova, Ludmila

2016-01-01

In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.

A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

DOE PAGES

Yu, Zheng; Krause, Sascha M. B.; Beck, David A. C.; ...

2016-06-15

In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sedimentmore » for a few decades and have identified a number of species genetically equipped for this activity. We have also identified cooccurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. Furthermore, these findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.« less

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

PubMed

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.

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

PubMed

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.

III. NIH Toolbox Cognition Battery (CB): measuring episodic memory.

PubMed

Bauer, Patricia J; Dikmen, Sureyya S; Heaton, Robert K; Mungas, Dan; Slotkin, Jerry; Beaumont, Jennifer L

2013-08-01

One of the most significant domains of cognition is episodic memory, which allows for rapid acquisition and long-term storage of new information. For purposes of the NIH Toolbox, we devised a new test of episodic memory. The nonverbal NIH Toolbox Picture Sequence Memory Test (TPSMT) requires participants to reproduce the order of an arbitrarily ordered sequence of pictures presented on a computer. To adjust for ability, sequence length varies from 6 to 15 pictures. Multiple trials are administered to increase reliability. Pediatric data from the validation study revealed the TPSMT to be sensitive to age-related changes. The task also has high test-retest reliability and promising construct validity. Steps to further increase the sensitivity of the instrument to individual and age-related variability are described. © 2013 The Society for Research in Child Development, Inc.

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

PubMed

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/).

Ideas Exchange: How Do You Use NASPE's Teacher Toolbox to Enhance Professional Activities with Students, Sport or Physical Education Lessons, Faculty Wellness Classes or Community Programs?

ERIC Educational Resources Information Center

Simpkins, Mary Ann; McNeill, Shane; Dieckman, Dale; Sissom, Mark; LoBianco, Judy; Lund, Jackie; Barney, David C.; Manson, Mara; Silva, Betsy

2009-01-01

NASPE's Teacher Toolbox is an instructional resource site which provides educators with a wide variety of teaching tools that focus on physical activity. This service is provided by NASPE to support instructional activities as well as promote quality programs. New monthly issues support NASPE's mission to enhance knowledge, improve professional…

Motion Simulation in the Environment for Auditory Research

DTIC Science & Technology

2011-08-01

Toolbox, Centre for Digital Music , Queen Mary University of London, 2009. http://www.isophonics.net/content/spatial-audio- matlab-toolbox (accessed July 27...this work. 46 Student Bio I studied Music Technology at Northwestern University, graduating as valedictorian of the School of... Music in 2008. In 2009, I was awarded the Gates Cambridge Scholarship to fund a postgraduate degree at the University of Cambridge. I read for a

DETECT: Detection of Events in Continuous Time Toolbox: User’s Guide, Examples, and Function Reference Documentation

DTIC Science & Technology

2013-06-01

benefitting from rapid, automated discrimination of specific predefined signals , and is free-standing (requiring no other plugins or packages). The...previously labeled dataset, and comparing two labeled datasets. 15. SUBJECT TERMS Artifact, signal detection, EEG, MATLAB, toolbox 16. SECURITY... CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18. NUMBER OF PAGES 56 19a. NAME OF RESPONSIBLE PERSON W. David Hairston a. REPORT

Development of a Dependency Theory Toolbox for Database Design.

DTIC Science & Technology

1987-12-01

published algorithms and theorems , and hand simulating these algorithms can be a tedious and error prone chore. Additionally, since the process of...to design and study relational databases exists in the form of published algorithms and theorems . However, hand simulating these algorithms can be a...published algorithms and theorems . Hand simulating these algorithms can be a tedious and error prone chore. Therefore, a toolbox of algorithms and

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

PubMed Central

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. PMID:24782741

Citizen Science Air Monitoring in the Ironbound Community ...

EPA Pesticide Factsheets

The Environmental Protection Agency’s (EPA) mission is to protect human health and the environment. To move toward achieving this goal, EPA is facilitating identification of potential environmental concerns, particularly in vulnerable communities. This includes actively supporting citizen science projects and providing communities with the information and assistance they need to conduct their own air pollution monitoring efforts. The Air Sensor Toolbox for Citizen Scientists1 was developed as a resource to meet stakeholder needs. Examples of materials developed for the Toolbox and ultimately pilot tested in the Ironbound Community in Newark, New Jersey are reported here. The Air Sensor Toolbox for Citizen Scientists is designed as an online resource that provides information and guidance on new, low-cost compact technologies used for measuring air quality. The Toolbox features resources developed by EPA researchers that can be used by citizens to effectively collect, analyze, interpret, and communicate air quality data. The resources include information about sampling methods, how to calibrate and validate monitors, options for measuring air quality, data interpretation guidelines, and low-cost sensor performance information. This Regional Applied Research Effort (RARE) project provided an opportunity for the Office of Research and Development (ORD) to work collaboratively with EPA Region 2 to provide the Ironbound Community with a “Toolbox” specific for c