Interactive Graphics Software Research Articles

The FIR Filter Design based on Genetic Algorithm

Especially, in the signal and image processing
 fields of electronics, filters are most often used parts. Also, rapid advances
 in digital systems have expanded the use of digital filters. Therefore, it is
 very important to understand and learn the filters and calculation of their
 coefficients. Thus, in this work, interactive graphical user interface software
 which can be used for educational purposes and also accessible via the Internet
 is designed in the MATLAB environment. 
 In the software, genetic algorithm, which is one of the popular methods
 in recent years, is used for designing the Finite Impulse Response (FIR)
 filters. In this program, when the parameters of filter, which will be
 designed, are entered by the user, the coefficients are obtained from genetic
 algorithms, and many features of the filter are presented numerically and
 graphically. Thus, the FIR filter design can easily be carried out for
 practical or educational purposes using the software. Further, the superiority
 of the genetic algorithm over the classical design in this field has been shown
 by comparing the obtained filter coefficients for both methods.

StatsX v2.0: the interactive graphical software for population statistics on X-STR

StatsX (Statistics for X-STR) v2.0 is developed to facilitate the workflow for analysis of population data on X-chromosomal short tandem repeat (X-STR) marker. The interactive graphical and installable software can estimate allele/haplotype frequencies from female, male, and pooled samples and calculate forensic parameters by importing a single file. In addition, it is able to filter out the invalid raw data and export a series of pre-formatted Arlequin input files that are directly used for testing the significance of the Hardy-Weinberg equilibrium (HWE), linkage disequilibrium (LD), and gender differentiation. As expected, all results of frequencies and forensic parameters can be saved as EXCEL workbooks and also plotted as bar or line graphs. Further, full concordance was obtained by recalculating frequencies and forensic parameters with other established software from a published Han Chinese population.

DExSI: a new tool for the rapid quantitation of 13C-labelled metabolites detected by GC-MS.

SummaryStable isotope directed metabolomics is increasingly being used to measure metabolic fluxes in microbial, plant and animal cells. Incorporation of 13C/15N isotopes into a wide range of metabolites is typically determined using gas chromatography-mass spectrometry (GC/MS) or other hyphenated mass spectrometry approaches. The DExSI (Data Extraction for Stable Isotope-labelled metabolites) pipeline is an interactive graphical software package which can be used to rapidly quantitate isotopologues for a wide variety of metabolites detected by GC/MS. DExSI performs automated metabolite annotation, mass and positional isotopomer abundance determination and natural isotope abundance correction. It provides a range of output options and is suitable for high throughput analyses.Availability and implementationDExSI is available for non-commercial use from: https://github.com/DExSI/DExSI/. For Microsoft Windows 7 or higher (64-bit).Supplementary information Supplementary data are available at Bioinformatics online.

Double Orthogonal Projection of Four-Dimensional Objects onto Two Perpendicular Three-Dimensional Spaces

A method of visualization of four-dimensional objects using a double orthogonal parallel projection onto two orthogonal three-dimensional spaces is proposed. A synthetic approach, with the use of basic descriptive geometry tools of Monge’s projection in interactive 3D graphical software, is taken. Descriptive constructions of projections of points, lines, planes and three-dimensional spaces are shown. Methods of measuring true lengths of segments and rotating projections of objects into the modeling space are described. The focus lies on improving the spatial ability and understanding of the four-dimensional space. An example of a construction is carried out on a model of tesseract. All the constructions are analogies of constructions in Monge’s projection of a three-dimensional space. With advantages of interactive computer graphics, the constructions are easy to perform, and objects are easy to manipulate with.

Eliciting Dirichlet and Gaussian copula prior distributions for multinomial models

In this paper, we propose novel methods of quantifying expert opinion about prior distributions for multinomial models. Two different multivariate priors are elicited using median and quartile assessments of the multinomial probabilities. First, we start by eliciting a univariate beta distribution for the probability of each category. Then we elicit the hyperparameters of the Dirichlet distribution, as a tractable conjugate prior, from those of the univariate betas through various forms of reconciliation using least-squares techniques. However, a multivariate copula function will give a more flexible correlation structure between multinomial parameters if it is used as their multivariate prior distribution. So, second, we use beta marginal distributions to construct a Gaussian copula as a multivariate normal distribution function that binds these marginals and expresses the dependence structure between them. The proposed method elicits a positive-definite correlation matrix of this Gaussian copula. The two proposed methods are designed to be used through interactive graphical software written in Java.

Second-Year Integrative Project for Computer and Software Engineering Students at Polytechnique Montréal

In 2005, Polytechnique Montréal introduced project-based learning (PBL) in its curriculum. The second-year integrative project for computer and software engineering students is software-oriented, as the main goal is to develop an interactive graphical software application. Students are given a software requirements specification (SRS), which details every feature the application must comply to. The students must then implement these features, starting from a provided framework, and various common software libraries. The main technical concepts integrated in the project are software design patterns, computer graphics, unit testing, and user interface design. Students are also provided with tools to put into practice project management concepts such as scope management, time management, cost management, and risk management. The second-year project is also a good opportunity for students to develop their non-technical skills, such as collaboration, communication and critical thinking.

RNA-Pareto: interactive analysis of Pareto-optimal RNA sequence-structure alignments

Incorporating secondary structure information into the alignment process improves the quality of RNA sequence alignments. Instead of using fixed weighting parameters, sequence and structure components can be treated as different objectives and optimized simultaneously. The result is not a single, but a Pareto-set of equally optimal solutions, which all represent different possible weighting parameters. We now provide the interactive graphical software tool RNA-Pareto, which allows a direct inspection of all feasible results to the pairwise RNA sequence-structure alignment problem and greatly facilitates the exploration of the optimal solution set.

Eliciting Dirichlet and Connor–Mosimann prior distributions for multinomial models

This paper addresses the task of eliciting an informative prior distribution for multinomial models. We first introduce a method of eliciting univariate beta distributions for the probability of each category, conditional on the probabilities of other categories. Two different forms of multivariate prior are derived from the elicited beta distributions. First, we determine the hyperparameters of a Dirichlet distribution by reconciling the assessed parameters of the univariate beta conditional distributions. Although the Dirichlet distribution is the standard conjugate prior distribution for multinomial models, it is not flexible enough to represent a broad range of prior information. Second, we use the beta distributions to determine the parameters of a Connor–Mosimann distribution, which is a generalization of a Dirichlet distribution and is also a conjugate prior for multinomial models. It has a larger number of parameters than the standard Dirichlet distribution and hence a more flexible structure. The elicitation methods are designed to be used with the aid of interactive graphical user-friendly software.

TorsionAnalyzer: exploring conformational space

Molecular conformations are used in a wide range of virtual screening applications to represent the conformational flexibility of a molecule. As the underlying conformational model has a major influence on the results of these applications, a closer insight into the conformational space of molecules is very important. We developed a new interactive graphical software tool for conformation analysis called TorsionAnalyzer. The tool uses a predefined set of over 450 SMARTS patterns to analyze the torsion angles of an input conformation. Each pattern describes a torsion angle and is associated with frequency histograms derived from CSD [1] and PDB [2] data. For each pattern a list of allowed torsion angles was automatically derived from the torsion histograms. Rotatable bonds of a conformation are colored according to their classification into usual, borderline and unusual torsion angles, using the list of allowed angles from the corresponding patterns. This allows the user to see at a glance if one of the torsion angles of an examined conformation is out of the ordinary. The TorsionAnalyzer supports easy modification of the existing SMARTS patterns as well as the preparation and storage of different sets of patterns for different sets of molecules.

LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons

BackgroundLong terminal repeat (LTR) retrotransposons are a class of eukaryotic mobile elements characterized by a distinctive sequence similarity-based structure. Hence they are well suited for computational identification. Current software allows for a comprehensive genome-wide de novo detection of such elements. The obvious next step is the classification of newly detected candidates resulting in (super-)families. Such a de novo classification approach based on sequence-based clustering of transposon features has been proposed before, resulting in a preliminary assignment of candidates to families as a basis for subsequent manual refinement. However, such a classification workflow is typically split across a heterogeneous set of glue scripts and generic software (for example, spreadsheets), making it tedious for a human expert to inspect, curate and export the putative families produced by the workflow.ResultsWe have developed LTRsift, an interactive graphical software tool for semi-automatic postprocessing of de novo predicted LTR retrotransposon annotations. Its user-friendly interface offers customizable filtering and classification functionality, displaying the putative candidate groups, their members and their internal structure in a hierarchical fashion. To ease manual work, it also supports graphical user interface-driven reassignment, splitting and further annotation of candidates. Export of grouped candidate sets in standard formats is possible. In two case studies, we demonstrate how LTRsift can be employed in the context of a genome-wide LTR retrotransposon survey effort.ConclusionsLTRsift is a useful and convenient tool for semi-automated classification of newly detected LTR retrotransposons based on their internal features. Its efficient implementation allows for convenient and seamless filtering and classification in an integrated environment. Developed for life scientists, it is helpful in postprocessing and refining the output of software for predicting LTR retrotransposons up to the stage of preparing full-length reference sequence libraries. The LTRsift software is freely available at http://www.zbh.uni-hamburg.de/LTRsift under an open-source license.

A common sense approach to peak picking in two-, three-, and four-dimensional spectra using automatic computer analysis of contour diagrams

The analysis of multidimensional NMR spectra has been a challenging problem since the earliest two-dimensional experiments were reported as stacked plots (I). The first step in analysis involves obtaining a list of chemical-shift coordinates for the cross peaks. Initially, simple programs were used to generate contour plots of twodimensional NMR data, which were analyzed manually. As the utility and versatility of multidimensional NMR spectroscopy grew, several automated methods of peak picking have been developed. This Communication describes a new peak-picking algorithm which is based on contour diagrams and designed for the automated interpretation of higher dimensional 3D and 4D spectra. The oldest and most robust method of analysis is the manual interpretation of 2D contour plots. The strength of manual peak picking results from the relative ease with which the human eye can discriminate real peaks from artifacts and noise. As the proteins studied have become larger, the number of spectra to be analyzed and the number of cross peaks within a spectrum have increased dramatically, with the result that significantly more time and energy are required for the tedious manual peakpicking step. Interactive graphics software, which dynamically maintains a list of peak positions, has to some extent helped with this time-consuming step, particularly with regard to bookkeeping. Although more time will be saved with the automation of peak picking, manual inspection of spectra with an interactive graphics program will always be necessary to verify and edit automated results. Approaches to automated peak picking can be divided into three types: (a) thresholdbased methods; (b) multiplet-symmetry-based methods; and (c) peak-shape-based methods. The simplest automated peak-picking algorithm is based primarily on the intensity of local extrema exceeding a threshold value (2). Uninteresting regions of the spectrum, such as tl noise ridges, are defined to avoid selecting peaks along these artifacts. Since some real peaks have very low intensities, the threshold must be set close to the noise level, which unfortunately results in a very large number of local extrema being picked due to the noise. Thus, by itself the threshold method fails by selecting too many or too few peaks, but is ideally suited as a filter for more sophisticated methods.

IPlots eXtreme: next-generation interactive graphics design and implementation of modern interactive graphics

Interactive graphics provide a very important tool that facilitates the process of exploratory data and model analysis which is a crucial step in real-world applied statistics. Only a very limited set of software exists that provides truly interactive graphics for data analysis, partially because it is not easy to implement. Very often specialized software is created to offer graphics for a particular problem, but many fundamental plots are omitted since it is not considered new research. In this paper we discuss a general framework that allows to create interactive graphics software on a sound foundation that offers consistent user interface, fast prototyping of new plots and extensibility to support interactive models. In addition, we also discuss one implementation of the general framework: iPlots eXtreme—next-generation interactive graphics for analysis of large data in R. It provides most fundamental plot types and allows new interactive plots to be created. The implementation raises interactive graphics performance to an entirely new level. We will discuss briefly several methods that allowed us to achieve this goal and illustrate the use of advanced programmability features in conjunction with R.

From Strange to Impossible: Interactive Attractor Music

Starting with a short overview of fractal music, the essay presents the development and technical aspects of a mid-1990s project for interactive algorithmic music that was based directly on interactive fractal graphics software. Several kinds of impossibility are discussed in relation to the music created by this system and generally to nonlinear attractor music.

Redundant Reactions of Indeterminate Beams by Principle of Quasi Work

A new methodology for determining redundant reactions of beams is presented in this paper. This methodology is based on the principle of quasi work, which is a powerful pseudoenergy theorem deduced from Tellegen's theorem. It takes topography of a structural system as a variable in addition to the variables involved in conventional energy methods, variational principles, and finite element methods. The concept of topologically similar system lies at the heart of the principle of quasi work. This concept is explored for beams to define topologically similar beams and topologically equivalent beams. The principle of quasi work is validated for beams and subsequently used for determining redundant reactions of indeterminate and continuous beams. Further, a unique concept of reference beam is developed. Equation of deflection curve of this reference beam is used to solve redundant reactions of indeterminate beams. This methodology has an advantage of calculating redundant reactions mostly by simple multiplications without any integrations or differentiations and does not require any prior knowledge of writing bending moment expressions. The method is illustrated through examples. It is possible to develop an interactive graphic computer package for calculating reactions of indeterminate beams.

Numerical Continuation of Bifurcations of Limit Cycles in MATLAB

${\rm CL\_MATCONT}$ and MATCONT are MATLAB continuation packages for the interactive numerical study of a range of parameterized nonlinear dynamical systems, in particular ODEs. MATCONT is an interactive graphical package and ${\rm CL\_MATCONT}$ is a commandline version. Both packages allow us to compute curves of equilibria, limit points, Hopf points, limit cycles, flip, fold, and torus bifurcation points of limit cycles. We discuss computational details of the continuation of limit cycles and flip, fold, and torus bifurcations of limit cycles in MATCONT and ${\rm CL\_MATCONT}$ using orthogonal collocation. Instead of the more commonly used fully extended systems we use minimally extended systems. We further describe the use of the MATLAB sparse matrix routines and the initialization and adaptation of the bordering vectors that are essential in minimally extended systems. Finally, we compare the use of the minimally and the fully extended systems in the MATLAB environment.

Automatic generation of numerical control part programs using object-oriented software

This paper presents an automatic approach to the generation of numerical control (NC) part programs for a specified manufacturing process plan. Generation of NC part programs for a specified process plan is a tedious task, especially when there are repetitive sequences of operations. The interactive graphics software developed in the present work simultaneously generates manual part programs. Three modules of the present software separately create an interactive process plan and NC code for point-to-point operations, straight-cut operations and contouring operations. Outputs of the present software are shown with examples.

Visualizing diffusion tensor mr images using streamtubes and streamsurfaces

We present a new method for visualizing 3D volumetric diffusion tensor MR images. We distinguish between linear anisotropy and planar anisotropy and represent values in the two regimes using streamtubes and streamsurfaces, respectively. Streamtubes represent structures with primarily linear diffusion, typically fiber tracts; streamtube direction correlates with tract orientation. The cross-sectional shape and color of each streamtube represent additional information from the diffusion tensor at each point. Streamsurfaces represent structures in which diffusion is primarily planar. Our algorithm chooses a very small representative subset of the streamtubes and streamsurfaces for display. We describe the set of metrics used for the culling process, which reduces visual clutter and improves interactivity. We also generate anatomical landmarks to identify the locations of such structures as the eyes, skull surface, and ventricles. The final models are complex surface geometries that can be imported into many interactive graphics software environments. We describe a virtual environment to interact with these models. Expert feedback from doctors studying changes in white-matter structures after gamma-knife capsulotomy and preoperative planning for brain tumor surgery shows that streamtubes correlate well with major neural structures, the 2D section and geometric landmarks are important in understanding the visualization, and the stereo and interactivity from the virtual environment aid in understanding the complex geometric models.

Discrete dynamics lab: tools for investigating cellular automata and discrete dynamical networks

DDLab is interactive graphics software for creating and visualizing discrete dynamical networks, and studying their behavior in terms of both space‐time patterns and basins of attraction. The networks can range from cellular automata to random Boolean networks. This article provides some general background, and gives the flavor of DDLab with a range of examples. Further details can be found at www.ddlab.comwww.ddlab.com

Real-time hybrid adaptive fuzzy control of a SCARA robot

This paper presents the design, development and implementation of a Hybrid Adaptive Fuzzy Controller (HAFC) suitable for real-time industrial applications. The developed HAFC consists of a weighted combination of the Direct Adaptive Fuzzy Controller (DAFC) and Indirect Adaptive Fuzzy Controller (IAFC) and a gradually activated supervisory controller. The unique feature of the HAFC is that no mathematical models of the plant are required and the proposed controller is able to adaptively estimate the bound functions on-line, which are required for the determination of the supervisory controller. The supervisor controller in the sense that all signals are bounded guarantees global stability of the closed-loop system. The approach of rapid prototyping is employed to implement the HAFC so as to control a Selectively Compliance Assembly Robot Arm (SCARA) Robot in real time. Simulink, an interactive graphical software for simulating dynamic systems, is used to model, simulate and analyse the dynamic system. Once encouraging system performances are achieved, the HAFC is implemented in real-time through Real-Time Workshop (RTW). RTW generates C-codes from the Simulink block diagrams and in turn, the generated codes (object codes) are downloaded to the Texas Instruments TMS320C31 floating-point processor, together with the supporting files, for execution. The performance of the HAFC was found to be superior and it matches favourably the simulation results.

Java-based graphical user interface for the MRUI quantitation package.

This article describes the Java-based version of the magnetic resonance user interface (MRUI) quantitation package. This package allows MR spectroscopists to easily perform time-domain analysis of in vivo MR spectroscopy data. We show that the Java programming language is very well suited for developing highly interactive graphical software applications such as the MRUI software. We have also established that MR quantitation algorithms, programmed in other languages, can easily be embedded into the Java-based MRUI by using the Java native interface (JNI). This new graphical user interface (GUI) has been conceived for the processing of large data sets and uses prior knowledge data-bases to make interactive quantitation algorithms more userfriendly.