Graphical Windows Research Articles

Development and evaluation of an automatic software for management zone delineation

The lack of availability of user-friendly and automatic software for management zone delineation is limiting the adoption of site-specific management practices. Several procedures for management zone delineation have been proposed, but they commonly require the use of different software, or advanced GIS and statistical skills of users, which limit their adoption. This study proposes a user-friendly and automatic software that would integrate all steps in order to delineate management zones and make prescription files. The software includes importation of different input data layers, re-projection and resizing data in a common grid size. An integrative index was proposed for the selection of the optimal number of zones after clustering analysis. Users are guided by graphical windows showing intermediate results. Also, additional automatic post-processing techniques to improve size, shape and fragmentation of delineated zones are available. The final step allows generation of the ESRI Shapefile required to make variable rate prescriptions by zone with minimal user intervention. The performance of the approach was evaluated for management zone delineation using single and multiple layers of data by comparing with Management Zone Analyst software, and the improvement of the approach in the selection of the optimal number of zones and reducing zone-fragmentation was shown. The software design includes a simple graphical user interface and requires minimal user intervention in order to assist the end-user. The main contribution of this work was the successful development of this automatic user-friendly solution that includes all the necessary steps for management zone delineation and prescription file generation.

Generating Electric Current by Bioartificial Photosynthesis.

Abundant solar energy can be a sustainable source of energy. This chapter highlights recent advancements, challenges, and future scenarios in bioartificial photosynthesis, which is a new subset of bioelectrochemical systems (BESs) and technologies. BES technologies exploit the catalytic interactions between biological moieties and electrodes. At the nexus of BES and photovoltaics, this review focuses on light-harvesting technologies based on bioartificial photosynthesis. Such technologies are promising because electrical energy is generated from sunlight and water without the need for additional organic feedstock. This review focuses on photosynthetic electron generation and transfer and compares the current status of bioartificial photosynthesis with other artificial systems that mimic the chemistry of photosynthetic energy transformation.The fundamental principles and the operation of functional units of bioartificial photosynthesis are addressed. Selected photobioelectrochemical systems employed to obtain light-driven electric currents from photosynthetic organisms are presented. The achievable current output and theoretical maxima are revisited by conceptualizing operational and process window techniques. Factors affecting overall photocurrent efficiency, performance limitations, and scaleup bottlenecks are highlighted in view of enhancing the energy conversion efficiency of photobioelectrochemical systems. To finish, the challenges associated with bioartificial photosynthetic technologies are outlined. Graphical Abstract Operational window for (bio-)artificial photosynthesis. Green circle in the upper right corner: development objective for research and engineering efforts.

GUI Based Control System Analysis using PID Controller for Education

PID control strategy should be understood as a huge part in the education oriented on process control. Application of suitable GUI windows software can contribute in the increase of education quality and providing a better understanding of PID control through as it provides a user friendly environment which is suitable and comfortable for teaching, learning and training application. This paper present the PID control system analysis by explaining the PID controller three-term parameters, PID control types and structure, and PID tuning approach using Ziegler-Nichols and manual tuning method (in both s-domain and z-domain) with the help of simulation and Graphical User Interface GUI windows based on MATLAB. This software package is targeted for engineering students and practicing engineers.

PyGrav, a Python-based program for handling and processing relative gravity data

pyGrav is a Python-based open-source software dedicated to the complete processing of relative-gravity data. It is particularly suited for time-lapse gravity surveys where high precision is sought. Its purpose is to bind together single-task processing codes in a user-friendly interface for handy and fast treatment of raw gravity data from many stations of a network. The intuitive object-based implementation allows to easily integrate additional functions (reading/writing routines, processing schemes, data plots) related to the appropriate object (a station, a loop, or a survey). This makes pyGrav an evolving tool. Raw data can be corrected for tides and air pressure effects. The data selection step features a double table-plot graphical window with either manual or automatic selection according to specific thresholds on data channels (tilts, gravity values, gravity standard deviation, duration of measurements, etc.). Instrumental drifts and gravity residuals are obtained by least square analysis of the dataset. This first step leads to the gravity simple differences between a reference point and any point of the network. When different repetitions of the network are done, the software computes then the gravity double differences and associated errors. The program has been tested on two specific case studies: a large dataset acquired for the study of water storage changes on a small catchment in West Africa, and a dataset operated and processed by several different users for geothermal studies in northern Alsace, France. In both cases, pyGrav proved to be an efficient and easy-to-use solution for the effective processing of relative-gravity data.

Modelling and Simulation of MEMS based Sensors for Microbotics

In this age of automation, where robotics play a very important role in all fields particularly in medicine, there are many tasks performed which are inaccessible to humanoid robots. Here the major pushback is the size of the inaccessible micro parts. This is where Microbotics, which is a field of miniaturized robotics whose characteristic dimensions are usually less than 0.1mm, would be a choice. Currently research is on in modeling and designing reliable mesoscopic devices which can overcome the size limitation of humanoid robots. Today miniaturization is a tool of interest not alone because of the size aspect but also due to the capabilities such as sensitivity selectivity and specificity. This work focuses on the design of sensor with necessary aspect dimension in the graphics window followed by meshing with suitable mesh and simulation of different microsensors which are capable to operate individually as a microbot along with some associated mechatronics, or these features can be accumulated to frame a bot of great capabilities. The results proposed in the paper are simulated using COMSOL MULTIPHYSICS package.

R2MLwiN: A Package to RunMLwiNfrom withinR

R2MLwiN is a new package designed to run the multilevel modeling software program MLwiN from within the R environment. It allows for a large range of models to be specified which take account of a multilevel structure, including continuous, binary, proportion, count, ordinal and nominal responses for data structures which are nested, cross-classified and/or exhibit multiple membership. Estimation is available via iterative generalized least squares (IGLS), which yields maximum likelihood estimates, and also via Markov chain Monte Carlo (MCMC) estimation for Bayesian inference. As well as employing MLwiN's own MCMC engine, users can request that MLwiN write BUGS model, data and initial values statements for use with WinBUGS or OpenBUGS (which R2MLwiN automatically calls via rbugs), employing IGLS starting values from MLwiN. Users can also take advantage of MLwiN's graphical user interface: for example to specify models and inspect plots via its interactive equations and graphics windows. R2MLwiN is supported by a large number of examples, reproducing all the analyses conducted in MLwiN's IGLS and MCMC manuals.

Geographic Information System-based tools in environmental management

The authors reviewed existing modelling platforms as part of a large study of water and pollution pathways through catchments in Ireland (Irish EPA Pathways project). Worldwide, work on producing catchment management tools (CMTs) has been underway for some time and some of the tools identified here date from as early as 1989. Some of the management problems and model conceptualisations have not changed very much but now there is a stronger emphasis on water quality and more concern about a wider range of contaminants. What has changed substantially is the use of Geographical Information System and Graphical Windows interfaces as technologies supporting a wider practical use of these tools. This review of existing CMTs identified three systems which would be candidates if a CMT had to be deployed immediately in Ireland. All have a rigid catchment model structure and lack the flexibility to include any new scientific information or flow-path conceptualisation that may emerge. The same modelling structure is used for all parts of the catchment, with spatial variation represented by parameter variation only and not variation in model structure. They also have rigid graphical user interfaces which cannot be tailored to match any specific requirements that may emerge from the pathways end-user workshops. Thus a CMT with a more flexible and accessible modelling structure is required if the results of current research are to be incorporated.

Geographic Information System-based tools in environmental management

The authors reviewed existing modelling platforms as part of a large study of water and pollution pathways through catchments in Ireland (Irish EPA Pathways project). Worldwide, work on producing catchment management tools (CMTs) has been underway for some time and some of the tools identified here date from as early as 1989. Some of the management problems and model conceptualisations have not changed very much but now there is a stronger emphasis on water quality and more concern about a wider range of contaminants. What has changed substantially is the use of Geographical Information System and Graphical Windows interfaces as technologies supporting a wider practical use of these tools. This review of existing CMTs identified three systems which would be candidates if a CMT had to be deployed immediately in Ireland. All have a rigid catchment model structure and lack the flexibility to include any new scientific information or flow-path conceptualisation that may emerge. The same modelling structure is...

SU-E-T-595: Design of a Graphical User Interface for An In-House Monte Carlo Based Treatment Planning System: Planning and Contouring Tools

Purpose: An in-house Monte Carlo based treatment planning system (MC TPS) has been developed for modulated electron radiation therapy (MERT). Our preliminary MERT planning experience called for a more user friendly graphical user interface. The current work aimed to design graphical windows and tools to facilitate the contouring and planning process. Methods: Our In-house GUI MC TPS is built on a set of EGS4 user codes namely MCPLAN and MCBEAM in addition to an in-house optimization code, which was named as MCOPTIM. Patient virtual phantom is constructed using the tomographic images in DICOM format exported from clinical treatment planning systems (TPS). Treatment target volumes and critical structures were usually contoured on clinical TPS and then sent as a structure set file. In our GUI program we developed a visualization tool to allow the planner to visualize the DICOM images and delineate the various structures. We implemented an option in our code for automatic contouring of the patient body and lungs. We also created an interface window displaying a three dimensional representation of the target and also showing a graphical representation of the treatment beams. Results: The new GUI features helped streamline the planning process. The implemented contouring option eliminated themore » need for performing this step on clinical TPS. The auto detection option for contouring the outer patient body and lungs was tested on patient CTs and it was shown to be accurate as compared to that of clinical TPS. The three dimensional representation of the target and the beams allows better selection of the gantry, collimator and couch angles. Conclusion: An in-house GUI program has been developed for more efficient MERT planning. The application of aiding tools implemented in the program is time saving and gives better control of the planning process.« less

Bubble fountain with wandering black hole

Programming assignments with graphics elements may be used to spark student interest and enthusiasm, especially in early courses. We have created a sequence of CS I labs, built on the ACM Java Library, which culminates in a Bubble Fountain with Wandering Black Hole, where a particle emitter spews colorful bubbles that bounce around the graphics window while a larger black circle, also bouncing around the window, consumes any particles that cross its path. This assignment requires that students extend an oval class (GOval) from the graphics library. The following is the class hierarchy: • circle: an oval that has same width and height, always • smart-circle: a circle that knows where it is relative to the edges of its graphics window (canvas) • moving-circle: a smart-circle with its own displacement that knows how to move inside its window, bouncing against the boundaries • particle: a moving-circle with a built-in lifetime. When the lifetime expires, the object is removed from the canvas.

Abstract 5142: COSMIC: Exploring the world's knowledge of somatic mutations in cancer.

Abstract COSMIC, the Catalogue Of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk/), is the world's largest database of curated somatic mutations. The current version (v62, Nov 2012) has over a million mutations across 800000 samples from 15327 peer-reviewd publications, online data portals such as TCGA, ICGC, the IARC p53 database and the Cancer Genome Project (CGP) at the Sanger Institute, UK. The project aims to build a comprehensive catalogue of somatic mutations prioritized by the Cancer Gene Census (http://cancer.sanger.ac.uk/cancergenome/projects/census/), allowing users to explore correlations between cancer phenotypes and mutant genotypes. At present, a full distribution of somatic mutations have been curated across 116 known cancer genes and 169 gene fusion pairs. A focus on cancer genomes has recently emerged from the rapid expansion of whole genome/exome resequencing, as shown by our "COSMIC Genomes" website (http://cancer.sanger.ac.uk/cancergenome/projects/studies/), already comprising over 4500 tumours across a variety of cancer types. There are a number of ways to examine the data within COSMIC. A newly released website provides an intuitive interface for users to scrutinize the data through numerous filters, including mutation types, histology and tissue types. This is supplimented with statistical summaries presented in many graphs and charts. The website includes a COSMIC genome browser for views across combined cancer genomes, including all mutation types in one graphical window. Many other resources are designed for bioinformatic access including a Biomart, and FTP downloads in a variety of formats (ftp://ftp.sanger.ac.uk/pub/CGP/cosmic/). We actively seek to integrate with the wider bioinformatics community and are integrated within the UCSC and Ensembl genome browsers. COSMIC both documents mutation trends in known cancer genes, and combines distributed information to allow substantial mining of these data for discovery of novel correlations. COSMIC can aid discovery of novel recurrence patterns between variants, genes and tissues in different mutant genotypes and cancer phenotypes. The most frequently mutated gene in COSMIC (v62, Nov 2012), is JAK2 with the p.V617F mutation observed in 36% of all blood cancers examined. This is followed by TP53 with a variety of truncating mutations observed at a total frequency of 29.7%, and KRAS, found mutated in 21% of cancers, most frequently p.G12D in pancreatic tumours. Focusing particularly on the 4571 whole genomes, the most mutated gene is unsurprisingly TP53 at 27.57% (followed by TTN, MUC16, PIK3CA, CSMD3). Many techniques may identify putative novel cancer genes outside the cancer gene census. For instance, in Lung cancer the most mutated genes (correcting for CDS length) are TPTE, FAM5C, CDH10 and KEAP1. The rapid combination of increasingly large datasets in COSMIC ensure its future relevance in discovery of new trends in cancer genetics. Citation Format: Kenric Leung, Chai Yin Kok, Rebecca Shepherd, John Gamble, Mingming Jia, Sally Bamford, Sari Ward, Charlotte Cole, David Beare, Nidhi Bindal, Prasad Gunasekaran, Jon Teague, Simon A. Forbes, Michael R. Stratton, Peter Campbell. COSMIC: Exploring the world's knowledge of somatic mutations in cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5142. doi:10.1158/1538-7445.AM2013-5142

Architecture of Noninvasive Real Time Visual Monitoring System for Dial Type Measuring Instrument

Noninvasive real time visual monitoring systems are more demanding in the field of automation because of their high reliability, robustness, fast execution time, portability, and flexibility. In this paper, a novel architecture of detection algorithm has been developed to identify the geometrical and statistical features of position of the pointer's image from the captured image of indicating type meters in real time. In our view, a real time visual monitoring system has the following stages: 1) image acquisition; 2) image pre-processing; 3) segmentation; 4) feature extraction; 5) feature matching; and 6) display of result into graphical user interface window along with controlling decision. The geometrical, statistical, and wavelet-based image features were used to recognize the indicated value using feature matching algorithm. Also, the system controller compares the recognized value with the set value of parameters and if, it is found beyond the specified limit, it generates various alarms and controlling or tripping signals for the final control elements.

Simulation Tool for the Visualization of EM Wave Reflection and Refraction

This papers presents a simulation tool that can be helpful in teaching the concepts related to the reflection and refraction of electromagnetic waves incident on a planar interface between two dielectric media. It is implemented in MATLAB This tool provides a very flexible graphical interface, with multiple viewing formats for static images or animations. It presents an easy-to-use graphical interface that allows the analysis of any pair of dielectric/conducting media at any incidence angle with linear TE or TM polarization, as well as circular polarization. Different viewing modes, which can be simultaneously presented in a single window, plus the graphical tools already available in all MATLAB graphical windows, provide a simple and efficient interactive environment for the visualization and understanding of the EM reflection phenomena. The implementation of the simulation tool uses an analytical formulation instead of a numerical formulation, providing fast calculations for any modifications in the geometry.

Multilevel DC-Link Inverter and Control Algorithm to Overcome the PV Partial Shading

This letter presents for the first time the application of multilevel dc-link inverter to overcome the problem of partial shading of individual photovoltaic (PV) sources which are connected in series. The “PV permutation algorithm,” as a new method, is developed for the control of the inverter so as to extract the maximum power form each PV source under partial shading and to deliver all that power to the load. The algorithm is based on combination of the direct pulsewidth modulation, the sequential permutation PV sources, and the output generation to control the multilevel dc-link inverter. The algorithm is applied successfully to a seven-level inverter with separate maximum power point tracking algorithm for each PV source and under nonuniform irradiance (partial shading). Digital processing unit F28335 eZdsp is used to control the PV system in the real-time mode, and MATLAB-Simulink real-time data exchange is employed to display the extracted power and to control the system parameters via a designed graphical user interface window. The implementation and experimental results are presented.

Event Display for the Visualization of CMS Events

During the last year the CMS experiment engaged in consolidation of its existing event display programs. The core of the new system is based on the Fireworks event display program which was by-design directly integrated with the CMS Event Data Model (EDM) and the light version of the software framework (FWLite). The Event Visualization Environment (EVE) of the ROOT framework is used to manage a consistent set of 3D and 2D views, selection, user-feedback and user-interaction with the graphics windows; several EVE components were developed by CMS in collaboration with the ROOT project. In event display operation simple plugins are registered into the system to perform conversion from EDM collections into their visual representations which are then managed by the application. Full event navigation and filtering as well as collection-level filtering is supported. The same data-extraction principle can also be applied when Fireworks will eventually operate as a service within the full software framework.

TempNet: a method to display statistical parsimony networks for heterochronous DNA sequence data

Summary1. Heterochronous data have been used to study demographic changes in epidemiology and ancient DNA studies, revolutionizing our understanding of complex evolutionary processes such as invasions, migrations and responses to drugs or climate change. While there are sophisticated applications based on Markov‐Chain Monte Carlo or Approximate Bayesian Computation to study these processes through time, summarizing the raw genetic data in an intuitively meaningful graphic can be challenging, most notably if identical haplotypes are present at different points in time.2. We present temporal networks, an attractive way to display and summarize relationships within the heterochronous data so commonly used in ancient DNA or epidemiological research. TempNet is a user‐friendly R script that creates journal‐quality figures from genetic data in standard formats (FASTA, CLUSTAL, etc.). These figures are customizable and interactive within the R graphics window. Using three examples, we demonstrate that TempNet can deal with standard‐sized datasets, as well as datasets of hundreds of sequences from fast‐evolving organisms.3. Temporal networks are flexible ways to illustrate genetic relationships through time. Furthermore, this approach is not limited to time‐stamped data, but can also be used for different data partitioning strategies, such as spatial or phenotypic groupings. The R script presented here will be useful in illustrating complex genetic relationships between groups.

웹 환경에서의 입체적 가시화를 위한 3-D 가상현실 기법의 적용

In this paper, our effort to apply 3-D Virtual Reality system for stereoscopic visualization of mesh data on the web is briefly described. This study is an extension of our previous and on-going research efforts to develop an automatic grid generation program specialized for wing mesh, named as eGWing. The program is developed by using JAVA programming language, and it can be used either as an application program on a local computer or as an applet in the network environment. In this research advancing layer method(ALM) augmented by elliptic smoothing method is used for the structured grid generation. And to achieve a stereoscopic viewing capability, two graphic windows are used to render its own viewing image for the left and right eye respectively. These two windows are merged into one image using 3D monitor and the viewers can see the mesh data visualization results with stereoscopic depth effects by using polarizing glasses. In this paper three dimensional mesh data visualization with stereoscopic technique combined with 3D monitor is demonstrated, and the current achievement would be a good start-up for further development of low-cost high-quality stereoscopic mesh data visualization system which can be shared by many users through the web.

The digitize Package: Extracting Numerical Data from Scatterplots

I present the small R package digitize, designed to extract data from scatterplots with a simple method and suited to small datasets. I present an application of this method to the ex- traction of data from a graph whose source is not available. The package digitize, that I present here, allows a user to load a graphical file of a scatterplot (with the help of the read.jpeg function of the ReadImages package) in the graphical window of R, and to use the locator function to calibrate and extract the data. Calibration is done by setting four reference points on the original graph axis, two for the x values and two for the y values. The use of four points for cal- ibration is justified by the fact that it makes calibra- tions on the axis possible, as y data are not taken into account for calibration of the x axis, and vice versa. This is useful when working on data that are not available in digital form, e.g. when integrating old papers in meta-analyses. Several commercial or free software packages allow a user to extract data from a plot in image format, among which we can cite PlotDigitizer (http://plotdigitizer.sourceforge. net/) or the commercial package GraphClick (http: //www.arizona-software.ch/graphclick/). While these programs are powerful and quite ergonomic, for some lightweight use, one may want to load the graph directly into R, and as a result get the data di- rectly in R format. This paper presents a rapid dig- itization of a scatterplot and subsequent statistical analysis of the data. As an example, we will use the data presented by Jacques Monod in a seminal mi- crobiology paper (Monod, 1949). The original paper presents the growth rate (in terms of divisions per hour) of the bacterium Es- cherichia coli in media of increasing glucose concen- tration. Such a hyperbolic relationship is best repre- sented by the equation

KMeyeDB: a graphical database of mutations in genes that cause eye diseases

KMeyeDB (http://mutview.dmb.med.keio.ac.jp/) is a database of human gene mutations that cause eye diseases. We have substantially enriched the amount of data in the database, which now contains information about the mutations of 167 human genes causing eye-related diseases including retinitis pigmentosa, cone-rod dystrophy, night blindness, Oguchi disease, Stargardt disease, macular degeneration, Leber congenital amaurosis, corneal dystrophy, cataract, glaucoma, retinoblastoma, Bardet-Biedl syndrome, and Usher syndrome. KMeyeDB is operated using the database software MutationView, which deals with various characters of mutations, gene structure, protein functional domains, and polymerase chain reaction (PCR) primers, as well as clinical data for each case. Users can access the database using an ordinary Internet browser with smooth user-interface, without user registration. The results are displayed on the graphical windows together with statistical calculations. All mutations and associated data have been collected from published articles. Careful data analysis with KMeyeDB revealed many interesting features regarding the mutations in 167 genes that cause 326 different types of eye diseases. Some genes are involved in multiple types of eye diseases, whereas several eye diseases are caused by different mutations in one gene.

Classical item and test analysis with graphics: The ViSta-CITA program

Current advances in test development theory have mostly been influenced by item response theory. Notwithstanding this, classical test theory still plays a major part in the development of tests for applied educational and behavioral research. This article describes ViSta-CITA, a computer program that implements a set of classical item and test analysis methods that incorporate innovative graphics whose aim is to provide deeper insight into analysis results. Such an aim is achieved through the SpreadPlot, a graphical method designed to display multiple, simultaneous, interactive views of the analysis results. It behaves on a dynamic basis, so that users' changes (e.g., selecting a subset of items) are automatically updated in the graphical windows showing the analysis results. Moreover, ViSta-CITA is freely available, and its code is open to modifications or additions by the user. Features such as these constitute useful tools for research and teaching purposes related to test development.