User Full Control Research Articles

A Matlab-based finite-difference solver for the Poisson problem with mixed Dirichlet–Neumann boundary conditions

A Matlab-based finite-difference numerical solver for the Poisson equation for a rectangle and a disk in two dimensions, and a spherical domain in three dimensions, is presented. The solver is optimized for handling an arbitrary combination of Dirichlet and Neumann boundary conditions, and allows for full user control of mesh refinement. The solver routines utilize effective and parallelized sparse vector and matrix operations. Computations exhibit high speeds, numerical stability with respect to mesh size and mesh refinement, and acceptable error values even on desktop computers. Program summaryProgram title: FDMRP 1.0Catalogue identifier: AENQ_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENQ_v1_0.htmlProgram obtainable from: CPC Program Library, Queen’s University, Belfast, N. IrelandLicensing provisions: GNU General Public License v3.0No. of lines in distributed program, including test data, etc.: 102793No. of bytes in distributed program, including test data, etc.: 369378Distribution format: tar.gzProgramming language: Matlab 2010a.Computer: PC, Macintosh.Operating system: Windows, OSX, Linux.RAM: 8GB (8,589,934,592 bytes)Classification: 4.3.Nature of problem: To solve the Poisson problem in a standard domain with “patchy surface”-type (strongly heterogeneous) Neumann/Dirichlet boundary conditions.Solution method: Finite difference with mesh refinement.Restrictions: Spherical domain in 3D; rectangular domain or a disk in 2D.Unusual features: Choice between mldivide/iterative solver for the solution of large system of linear algebraic equations that arise. Full user control of Neumann/Dirichlet boundary conditions and mesh refinement.Running time: Depending on the number of points taken and the geometry of the domain, the routine may take from less than a second to several hours to execute.

An Open-Source Engine for the Processing of Electron Backscatter Patterns: EBSD-Image

An open source software package dedicated to processing stored electron backscatter patterns is presented. The package gives users full control over the type and order of operations that are performed on electron backscatter diffraction (EBSD) patterns as well as the results obtained. The current version of EBSD-Image (www.ebsd-image.org) offers a flexible and structured interface to calculate various quality metrics over large datasets. It includes unique features such as practical file formats for storing diffraction patterns and analysis results, stitching of mappings with automatic reorganization of their diffraction patterns, and routines for processing data on a distributed computer grid. Implementations of the algorithms used in the software are described and benchmarked using simulated diffraction patterns. Using those simulated EBSD patterns, the detection of Kikuchi bands in EBSD-Image was found to be comparable to commercially available EBSD systems. In addition, 24 quality metrics were evaluated based on the ability to assess the level of deformation in two samples (copper and iron) deformed using 220 grit SiC grinding paper. Fourteen metrics were able to properly measure the deformation gradient of the samples.

BISMA - Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences

BackgroundBisulfite sequencing is a popular method to analyze DNA methylation patterns at high resolution. A region of interest is targeted by PCR and about 20-50 subcloned DNA molecules are usually analyzed, to determine the methylation status at single CpG sites and molecule resolution.ResultsThe BISMA (Bisulfite Sequencing DNA Methylation Analysis) software for analysis of primary bisulfite sequencing data implements sequencing data extraction and enhanced data processing, quality controls, analysis and presentation of the methylation state. It uses an improved strategy for detection of clonal molecules and accurate CpG site detection and it supports for the first time analysis of repetitive sequences.ConclusionsBISMA works highly automated but still provides the user full control over all steps of the analysis. The BISMA software is freely available as an online tool for academic purposes for the analysis of bisulfite sequencing data from both unique and repetitive sequences http://biochem.jacobs-university.de/BDPC/BISMA/.

Interactive reflection editing

Effective digital content creation tools must be both efficient in the interactions they provide but also allow full user control. There may be occasions, when art direction requires changes that contradict physical laws. In particular, it is known that physical correctness of reflections for the human observer is hard to assess. For many centuries, traditional artists have exploited this fact to depict reflections that lie outside the realm of physical possibility. However, a system that gives explicit control of this effect to digital artists has not yet been described. This paper introduces a system that transforms physically correct reflections into art-directed reflections, as specified by reflection constraints . The system introduces a taxonomy of reflection editing operations, using an intuitive user interface, that works directly on the reflecting surfaces with real-time visual feedback using a GPU. A user study shows how such a system can allow users to quickly manipulate reflections according to an art direction task.

“Glyco‐peakfinder” – de novo composition analysis of glycoconjugates

Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, the lack of robust, dependable, and freely available software for the (semi-) automatic annotation of mass spectra is still a severe bottleneck that hampers their rapid interpretation. In this article the "Glyco-Peakfinder" web-service is described allowing de novo determination of glycan compositions from their mass signals. Starting from a basic set of mandatory masses of glycan components, the calculation can be performed without any knowledge concerning the biological background of the sample or the fragmentation technique used. "Glyco-Peakfinder" assigns all types of fragment ions including monosaccharide cross-ring cleavage products and multiply charged ions. It provides full user control to handle modified glycans (persubstituted molecules, reducing-end modifications, glycoconjugates) and ion types. The formula applied to calculate the fragment masses and an outline of the implemented algorithm are discussed. A systematic evaluation of the dependence of all factors influencing the computation time revealed strikingly different impact of the individual calculation steps. To provide access to known carbohydrate structures a "composition search" in the open access database GLYCOSCIENCES.de can be performed. The service is available at the URL: www.eurocarbdb.org/applications/ms-tools.

Design and control of a mobile hyper-redundant urban search and rescue robot

In this work we introduce a new concept of a search and rescue robotic system that is composed of a hyper-redundant robot (HRR) which is mounted on a mobile base. This system is capable not only of inspecting areas reachable by the mobile base, but also of inspecting unreachable areas such as small cracks and pipes, using the camera and sensors mounted on its end-effector. The HRR is composed of 14 actuated, serially chained, d.o.f. which have been designed for compactness, yet each is strong enough to support the entire robot structure. The low-level control system of the robot incorporates 14 embedded mini-circuit boards implementing a low number of wires and highspeed, I2C data bus technology. The high-level control algorithms implement kinematic methods to perform on-line motion control both in a global coordinate frame and in the camera coordinate frame for which a camera is mounted on the robot end-effector. The user interface allows the user full and easy control and interpretation of the data received from the camera. All the components of the system are hose-able as required by search and rescue regulations. Finally, we describe the integration of all the above-mentioned components in a complete operational mobile hyper-redundant search and rescue robotic system. This system has been deployed and tested in several search and rescue training scenarios.

Objective Evaluation of Three-dimensional Image Registration Algorithms – Tools for Optimization and Evaluation

The registration of medical volume data sets plays an important role when different images or modalities are used during computer-assisted surgical procedures. Nevertheless, it is often questionable how robust and accurate the underlying algorithms really are. Therefore, the goal is to foster the establishment of methods for an objective evaluation. To reliably calculate the accuracy of registration algorithms, a reference transformation must be known. Due to the unknown perfect registration for real clinical data, the simulation of realistic data and successive affine transformations are employed. The simulation is based on models of the respective imaging modality where the dominant physical effects are taken into account. This gives the user full control over all simulation and transformation parameters. Finally, suitable quality measures are applied which allow a systematic evaluation of image registration accuracy by comparing the known theoretical result and the transformation calculated by the algorithm under investigation. During the development of a new registration algorithm, the presented method proved to be a very valuable tool for optimization and evaluation of registration accuracy, since it allows objective numerical comparison of the calculated results. The presented method can be used during the development of algorithms for optimization and for quantitative comparison of different registration schemes. The respective software tool can automatically generate and transform simulated but realistic data. Employing suitable numerical quality measures, an objective evaluation of registration results can be easily obtained. Still, the validity of the relatively simple models has to be verified to draw reliable conclusions with respect to real data.

Analysis of fungal fruiting patterns at the Dawyck Botanic Garden

Since 1994 data on fungal fruiting have been gathered in the Dawyck Botanic Garden outside Edinburgh, including that for eight plots within a 7.5 ha wood, which has been left unmanaged in order to investigate relationships amongst fungal succession, habitat characteristics and local weather patterns. The climatic data are provided by a small meteorological station situated on site. To handle nearly 4000 entries of data so far collected a computer database was constructed. This assists querying of the information so that changes in fungal communities and patterns of succession can be observed, and the relevant data extracted for further analysis. To aid in this analysis, and to give the user full control over editing, updating and querying the database, a special computer program was compiled. Analysis of the database records revealed that the currently known Dawyck fungal community comprises over 620 different taxa, and the species list increases every year. Although some species of mycorrhizal fungi showed high specificity towards their preferred host either at species (e.g. Lactarius blennius with beech, Lactarius quietus with oak, Russula fellea and Russula mairei with beech), or at genus level (e.g. Suillus spp. with Pinaceae), some other common fungi (e.g. of the genus Amanita) were found to have very wide host ranges. In addition, unusual mycorrhizal associations have also been recorded. A lime tree ( Tilia), which is supposedly primarily endomycorrhizal, has been found regularly associated with Russula cyanoxantha, Russula parazurea, Russula pectinata and Inocybe fastigiata. Many common Scottish fungi were found to be associated with introduced exotic trees, which is illustrated on the example of Pseudotsuga menziesii (Douglas Fir). The software created utilises the Microsoft Office suite of programs. Microsoft Access was used to construct the database, and Microsoft Excel was used for statistical investigations. The software was programmed using Microsoft Visual Basic, and provided a means of extracting the necessary data stored in Access and controlling the formulae used in Excel for their analysis. The recorded seasonal patterns of fungal fruiting was successfully described by a simulation mathematical model comprising differential and algebraic equations. This model may now be used as a submodel within more complex models describing terrestrial ecosystem processes. Examples of model simulations and sensitivity analysis are given and implications for future research discussed.

Multiobjective optimization of combinatorial libraries.

Combinatorial chemistry and high-throughput screening have caused a fundamental shift in the way chemists contemplate experiments. Designing a combinatorial library is a controversial art that involves a heterogeneous mix of chemistry, mathematics, economics, experience, and intuition. Although there seems to be little agreement as to what constitutes an ideal library, one thing is certain: only one property or measure seldom defines the quality of the design. In most real-world applications, a good experiment requires the simultaneous optimization of several, often conflicting, design objectives, some of which may be vague and uncertain. In this paper, we discuss a class of algorithms for subset selection rooted in the principles of multiobjective optimization. Our approach is to employ an objective function that encodes all of the desired selection criteria, and then use a simulated annealing or evolutionary approach to identify the optimal (or a nearly optimal) subset from among the vast number of possibilities. Many design criteria can be accommodated, including diversity, similarity to known actives, predicted activity and/or selectivity determined by quantitative structure-activity relationship (QSAR) models or receptor binding models, enforcement of certain property distributions, reagent cost and availability, and many others. The method is robust, convergent, and extensible, offers the user full control over the relative significance of the various objectives in the final design, and permits the simultaneous selection of compounds from multiple libraries in full- or sparse-array format.

Multiobjective optimization of combinatorial libraries

Combinatorial chemistry and high-throughput screening have caused a fundamental shift in the way chemists contemplate experiments. Designing a combinatorial library is a controversial art that involves a heterogeneous mix of chemistry, mathematics, economics, experience, and intuition. Although there seems to be little agreement as to what constitutes an ideal library, one thing is certain: Only one property or measure seldom defines the quality of the design. In most real-world applications, a good experiment requires the simultaneous optimization of several, often conflicting, design objectives, some of which may be vague and uncertain. In this paper, we discuss a class of algorithms for subset selection rooted in the principles of multiobjective optimization. Our approach is to employ an objective function that encodes all of the desired selection criteria, and then use a simulated annealing or evolutionary approach to identify the optimal (or a nearly optimal) subset from among the vast number of pos sibilities. Many design criteria can be accommodated, including diversity, similarity to known actives, predicted activity and/or selectivity determined by quantitative structure-activity relationship (QSAR) models or receptor binding models, enforcement of certain property distributions, reagent cost and availability, and many others. The method is robust, convergent, and extensible, offers the user full control over the relative significance of the various objectives in the final design, and permits the simultaneous selection of compounds from multiple libraries in full- or sparse-array format.

Multiobjective optimization of combinatorial libraries.

Combinatorial chemistry and high-throughput screening have caused a fundamental shift in the way chemists contemplate experiments. Designing a combinatorial library is a controversial art that involves a heterogeneous mix of chemistry, mathematics, economics, experience, and intuition. Although there seems to be little agreement as to what constitutes an ideal library, one thing is certain: only one property or measure seldom defines the quality of the design. In most real-world applications, a good experiment requires the simultaneous optimization of several, often conflicting, design objectives, some of which may be vague and uncertain. In this paper, we discuss a class of algorithms for subset selection rooted in the principles of multiobjective optimization. Our approach is to employ an objective function that encodes all of the desired selection criteria, and then use a simulated annealing or evolutionary approach to identify the optimal (or a nearly optimal) subset from among the vast number of possibilities. Many design criteria can be accommodated, including diversity, similarity to known actives, predicted activity and/or selectivity determined by quantitative structure-activity relationship (QSAR) models or receptor binding models, enforcement of certain property distributions, reagent cost and availability, and many others. The method is robust, convergent, and extensible, offers the user full control over the relative significance of the various objectives in the final design, and permits the simultaneous selection of compounds from multiple libraries in full- or sparse-array format.

XIMDISP—A Visualization Tool to Aid Structure Determination from Electron Microscope Images

The display of digitized electron microscope images on a computer screen is a crucial first step in the computation of macromolecular structures. It is also essential to be able to visualize the final computed density map in a way that reveals its shape in three dimensions. Ximdisp is an X-windows based, menu-driven computer program that forms the core of the MRC image processing package. Raw electron microscope images, Fourier transforms, and computed density maps may all be displayed in a variety of ways with a choice of colour representations suitable for manuscript illustration purposes. It gives the user full interactive control over its many functions with clear, simple menus, labels, and editable dialogue boxes. Ximdisp plays a part in single-particle analysis with a straightforward particle selection procedure, in processing 2D crystal and electron diffraction data with extended lattice refinement, and in the analysis of helical structures with filament straightening and interactive Fourier transform display of automatically rotated, padded, and floated particles. The role of Ximdisp in all of these analyses and the most effective ways in which it can be used to display images are described.

A Potential Vorticity-Based Study of the Role of Diabatic Heating and Friction in a Numerically Simulated Baroclinic Cyclone

Abstract A particularly intense case of western Atlantic baroclinic cyclogenesis was investigated in this study. Specifically, the roles of latent heat of condensation and surface friction were examined from the potential vorticity or “PV thinking” perspective. The methodology used for this study involves three key components: 1) a full-physics mesoscale model, which provides a continuous and dynamically consistent dataset and provides full user control over physical processes; 2) a partitioned PV integration, which temporally integrates the accumulation of PV due to various physical processes in the model's Eulerian framework: and 3) the piecewise inversion method of Davis and Emanuel, which calculates the balanced wind and mass field associated with particular PV anomalies. Potential vorticity features obtained through the partitioned integration technique were inverted to yield their direct contributions to the total circulation. In addition, sensitivity studies were carried out to determine the overal...

Gamma spectrum analysis including NAA with SAMPO for windows

SAMPO for Windows is a high performance gamma spectrum analysis program. All the measurement, analysis and NAA phases can be done either under full interactive user control or user defined tasks can be used for automated measurement and analysis sequences including control of MCAs and sample changers. High resolution gamma-ray spectroscopy together with the possibility to resolve complex multiplets with high accuracy makesSAMPO very suitable for INAA. On the other hand, the possibility to automate analysis sequences allows its use effectively also in all routine NAA measurements.

Application Of An Expert System Shell In The Preliminary Design Of Offshore Supply Vessels

This paper presents the application of expert system programming in preliminary ship design with particular emphasis on offshore supply vessels. Instead of using one of the conventional programming expert system languages, the system is developed using an expert system shell, Leonardo. The design program is written in such a way that it is user friendly as well as giving the user full control over the progress of the design. The algorithms developed in this system are based on extensive research on existing offshore supply vessels.

Use of a graphical user interface approach for digital and physical simulation in power systems control education: application to an HVDC transmission system model

The authors present the design of a laboratory with software and hardware structures for digital and physical simulation in the area of power systems control education. The hardware structure includes a physically based model of the power system. The software structure includes a special man-machine interface designed with a graphical user interface approach. This interface allows the user full control over the simulation and provides facilities for the study of the response of the simulated system. This approach is illustrated with the design of a control system for a physically based high-voltage DC transmission system model. >

A workbench for digital control systems

A toolbox for developing applications for debugging, tuning, and field-testing digital control systems is described. It is primarily intended for the programmer responsible for the coding of the control software, and it provides a diagnostic environment in which this custom software will run. The operator workbench, i.e. the facility the control specialist uses actually to set up and test a system once the custom software has been generated, is also described. It comprises a commissioning utility, which manages a menu-assisted choice of predefined control structures and algorithms, and a multitasking run-time module, which gives the user full interactive control over the evolution of the control system, and the monitoring of its behavior. Underlying the structure of the run-time module is the concept of Petri nets, which describe in a natural way the concurrent and event-related activities of the control system, the interactive user interface, and the monitoring/data-logging utilities. The highly modular structure of the environment makes it equally well suited for simulating the behavior of an entire control system or for tuning an algorithm to a real-world process.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Contab—A program for connection table generation from linear input

Abstract The FORTRAN program CONTAB generates a redundant connection table from a linear alphanumerical input stream with full user control of the numbering of the molecule. Stereocenters are automatically detected. The alternative configurations are presented and the user is asked for his choice.

A Macintosh Hypercard stack for calculation of thermodynamically-corrected buffer recipes.

This paper describes a stack for the Apple Macintosh Hypercard environment that facilitates the calculation of a set of thermodynamically-corrected pH buffers. Presented in the familiar Macintosh mouse-based environment, the program allows comprehensive buffer design and gives the user full control of buffer species, temperature, ionic strength, pH and choice of counter-ion to maintain the ionic strength at a fixed value. Addition of new buffers to the stack is straightforward and the recipes that are generated, including the weights of the various components, can be displayed on the screen or saved to a disk file for subsequent printing.

RINGS — a general program to build ring systems

RINGS is a computer program for the general and rapid construction of ring skeletons. Prestored molecules are connected together by various operations, such as joining along one bond, fusion of one or more bonds, spiro joining, and carbon-bridge building. RINGS uses full 3D molecular structure information from the outset and offers the user full control of all geometrical features at each step of construction. The program is user-friendly, with a graphical man-machine interface (PLOT10-compatible) and extensive checking for possible input errors.