381,896 research outputs found

    pde2path - A Matlab package for continuation and bifurcation in 2D elliptic systems

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    pde2path is a free and easy to use Matlab continuation/bifurcation package for elliptic systems of PDEs with arbitrary many components, on general two dimensional domains, and with rather general boundary conditions. The package is based on the FEM of the Matlab pdetoolbox, and is explained by a number of examples, including Bratu's problem, the Schnakenberg model, Rayleigh-Benard convection, and von Karman plate equations. These serve as templates to study new problems, for which the user has to provide, via Matlab function files, a description of the geometry, the boundary conditions, the coefficients of the PDE, and a rough initial guess of a solution. The basic algorithm is a one parameter arclength continuation with optional bifurcation detection and branch-switching. Stability calculations, error control and mesh-handling, and some elementary time-integration for the associated parabolic problem are also supported. The continuation, branch-switching, plotting etc are performed via Matlab command-line function calls guided by the AUTO style. The software can be downloaded from www.staff.uni-oldenburg.de/hannes.uecker/pde2path, where also an online documentation of the software is provided such that in this paper we focus more on the mathematics and the example systems

    STOCHSIMGPU Parallel stochastic simulation for the Systems\ud Biology Toolbox 2 for MATLAB

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    Motivation: The importance of stochasticity in biological systems is becoming increasingly recognised and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU which 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.\ud \ud Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM), and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user’s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2

    Design and Control of a Flight-Style AUV with Hovering Capability

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    The small flight-style Delphin AUV is designed to evaluate the performance of a long range survey AUV with the additional capability to hover and manoeuvre at slow speed. Delphin’s hull form is based on a scaled version of Autosub6000, and in addition to the main thruster and control surfaces at the rear of the vehicle, Delphin is equipped with four rim driven tunnel thrusters. In order to reduce the development cycle time, Delphin was designed to use commercial-off-the-shelf (COTS) sensors and thrusters interfaced to a standard PC motherboard running the control software within the MS Windows environment. To further simplify the development, the autonomy system uses the State-Flow Toolbox within the Matlab/Simulink environment. While the autonomy software is running, image processing routines are used for obstacle avoidance and target tracking, within the commercial Scorpion Vision software. This runs as a parallel thread and passes results to Matlab via the TCP/IP communication protocol. The COTS based development approach has proved effective. However, a powerful PC is required to effectively run Matlab and Simulink, and, due to the nature of the Windows environment, it is impossible to run the control in hard real-time. The autonomy system will be recoded to run under the Matlab Windows Real-Time Windows Target in the near future. Experimental results are used to demonstrating the performance and current capabilities of the vehicle are presented

    MetaboLab - advanced NMR data processing and analysis for metabolomics

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    Background\ud Despite wide-spread use of Nuclear Magnetic Resonance (NMR) in metabolomics for the analysis of biological samples there is a lack of graphically driven, publicly available software to process large one and two-dimensional NMR data sets for statistical analysis.\ud \ud Results\ud Here we present MetaboLab, a MATLAB based software package that facilitates NMR data processing by providing automated algorithms for processing series of spectra in a reproducible fashion. A graphical user interface provides easy access to all steps of data processing via a script builder to generate MATLAB scripts, providing an option to alter code manually. The analysis of two-dimensional spectra (1H,13C-HSQC spectra) is facilitated by the use of a spectral library derived from publicly available databases which can be extended readily. The software allows to display specific metabolites in small regions of interest where signals can be picked. To facilitate the analysis of series of two-dimensional spectra, different spectra can be overlaid and assignments can be transferred between spectra. The software includes mechanisms to account for overlapping signals by highlighting neighboring and ambiguous assignments.\ud \ud Conclusions\ud The MetaboLab software is an integrated software package for NMR data processing and analysis, closely linked to the previously developed NMRLab software. It includes tools for batch processing and gives access to a wealth of algorithms available in the MATLAB framework. Algorithms within MetaboLab help to optimize the flow of metabolomics data preparation for statistical analysis. The combination of an intuitive graphical user interface along with advanced data processing algorithms facilitates the use of MetaboLab in a broader metabolomics context.\ud \u

    Some control design experiments with HIFOO

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    A new MATLAB package called HIFOO was recently proposed for H-infinity fixed-order controller design. This document illustrates how some standard controller design examples can be solved with this software

    Alternative method for the metrological characterization of spur gears in the sub-millimeter range using optical equipment

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    The aim of this work is to develop a software that allows the inspection of spur gear manufactured in the sub-millimeter range. The measurements are made using a digital optical machine and using an analysis proprietary software implemented in Matlab®, which is able to handle images, captured using the digital optical machine. The software allows to evaluate the profile and pitch deviations as establish in the ISO/TR 10064-1:1992 standar
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