Desktop Program Research Articles

New perspectives in hardmetal abrasion simulation

The response of tungsten carbide hardmetals with differing binder chemistries and carbide grain sizes to a traversing diamond indenter under load has been investigated in two principal regimes; single pass traverses and a multi-pass regime intended to simulate two-body abrasion experienced when the hardmetal is worn by a hard, high crushing strength abradant. The two-body regime is intended to simulate in-field degradation modes witnessed when a non-compliant counterface is present. The multi-pass test is achieved by a desktop computer program which generates pre-set spatial distributions to define the lateral position of the individual abrasion events with the scratches generated accumulating as a model of an abrasion process. Surfaces (and pre-polished sub-surface sections) were analysed using SEM, optical relocation profilometry, x-ray energy dispersive analysis (EDS) and ion beam milling (FIB). By these means, physical and chemical changes could be analysed; namely surface and sub-surface grain micro-cracking, pluckout, debris generation and re-embedment, grain and binder plasticity and surface oxidation. A comparison is also made between the results of this evaluation and the microstructural mechanisms that occur in standardised macroscopic laboratory abrasion tests including ASTM G65 and ASTM B611.

RNA Secondary Structure Prediction.

In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by John Wiley & Sons, Inc.

The method of formation of the status of personality understanding based on the content analysis

The approach is proposed to developing an information system of determining the psychological state of personalities based on the five personality dispositions (extraversion/introversion, amiability, integrity, neuroticism, openness to experience), which is based on the content analysis of the Internet resources where users leave their mark (social networks, forums, chats, etc.). In general, to form the status of psychological state of a personality based on the content analysis, it is necessary to solve four problems. First, it is necessary to collect content from various sources from the Internet. Then it is necessary to process it at the initial level (remove the tags, auxilary words, signs, special symbols, hyperlinks, pictures, etc. from the text). Then the content is filtered (to identify spam, detect duplication, format the content, etc.) and sorted out (comments to the comments, likes, posts) according to the statistics over a specific period. The last stage is conducting the content analysis of collected information, which is categorized by the stop-words (markers). To determine the psychological dispositions of a personality we implemented the developed method of the search and analysis of the marked words in the English and Ukrainian languages. We used the Potter stemming, lemmatising and the modified Potter stemming for the Ukrainian texts, designed by the authors. The tables of correlation between the marked words and psychological dispositions were developed. The information system is created for determining the psychological state of personality, based on the developed approach and the methods of the content processing. The system operates by analyzing the messages from the users in a social network based on the traits of the Big Five. The system is designed in the form of a desktop program, which is the Internet service at the same time, and allows analyzing the psychological state of a particular user of a social network by his/her messages. All collected results are stored in the database. The results are displayed in the form of percent ratio for each trait, the number of tweets, as well as the most frequently used words related to these traits. Potential users of such systems are consulting and marketing companies. The collected and analyzed information on users may be used in hiring or promotion of products/services. Automated compilation of the personality models of users is helpful for social networks and Web services. It improves the quality and efficiency of context advertising, referral systems, recommendations and dating services. The in-depth knowledge of the audience is crucial for business and recruiting. The approbation of functioning of the constructed system was conducted. The results of the work of the system are satisfactory. Such an information system is recommended to use for searching employees for certain positions. Automated analysis of messages of users in a social network to form the status of psychological state of a personality based on the content analysis significantly reduces the time of finding a potentially promising employee among those applied taking into account his/her psychological portrait for a specific position.

Rocket Science in a Virtual World

As a partner college of Greenwich University, Bromley College run Foundation Degrees in Software Development and Network Computing, and as part the programme, students complete a major Software Development project in year 1 and 2. The academic year 2014-15has a combined post 18 student cohort of 25 male and 1 female. Within the group there are two students with learning need statements, one for Dyslexia the other with Pervasive Learning Disorder. The theme for the year’s project is Rocket Science, where students are required to produce a desktop program capable of modelling the flight of a single stage rocket and this case study sets out to describe the delivery learning requirements.In education, virtual worlds provide unique learning opportunities, for accurate/real contexts and activities for experiential learning, simulation, modelling of complex scenarios, social interaction, that may not be experienced in other learning modalities (Atkinson, 2009).

СТАТИСТИЧНИЙ ПОРІВНЯЛЬНИЙ МІЖГРУПОВИЙ АНАЛІЗ ПОЄДНАННЯ ГЕНОТИПІВ

An important consequence of informatization of medical professionals is to decrease the number of diagnostic errors, large long-term calculations, to improve the accuracy of calculations.<p>The program was designed to make calculations and statistical analysis of the genotypes’ combination for the institution «Reference Centerfor Molecular Diagnostics of Ministry of Public Health of Ukraine».<br />The program provides the creation of desktop program complex for statistics calculations on a personal computer of doctor. Modern methods and tools for development of information systems were described to create program.</p>

WHATIF: An open-source desktop application for extraction and management of the incidental findings from next-generation sequencing variant data

BackgroundIdentification and evaluation of incidental findings in patients following whole exome (WGS) or whole genome sequencing (WGS) is challenging for both practicing physicians and researchers. The American College of Medical Genetics and Genomics (ACMG) recently recommended a list of reportable incidental genetic findings. However, no informatics tools are currently available to support evaluation of incidental findings in next-generation sequencing data. MethodsThe Wisconsin Hierarchical Analysis Tool for Incidental Findings (WHATIF), was developed as a stand-alone Windows-based desktop executable, to support the interactive analysis of incidental findings in the context of the ACMG recommendations. WHATIF integrates the European Bioinformatics Institute Variant Effect Predictor (VEP) tool for biological interpretation and the National Center for Biotechnology Information ClinVar tool for clinical interpretation. ResultsAn open-source desktop program was created to annotate incidental findings and present the results with a user-friendly interface. Further, a meaningful index (WHATIF Index) was devised for each gene to facilitate ranking of the relative importance of the variants and estimate the potential workload associated with further evaluation of the variants. Our WHATIF application is available at: http://tinyurl.com/WHATIF-SOFTWARE ConclusionsThe WHATIF application offers a user-friendly interface and allows users to investigate the extracted variant information efficiently and intuitively while always accessing the up to date information on variants via application programming interfaces (API) connections. WHATIF׳s highly flexible design and straightforward implementation aids users in customizing the source code to meet their own special needs.

Aplicación web para el análisis y diseño de estructuras

“Cloud computing” describes an innovative use of computing resources that are delivered as a service over a network, typically Internet. Today, structure analysis that requires high performance calculation has not been fully “migrated” to the Internet environment, structural software is usually developed as a desktop program against the current trend of the computer market. In this paper, the architecture of a structural analysis web application will be presented. This application, which would be a package of web services as SaaS (Software as a Service), will consist of 4 modules: a 3D modeler, a structural analysis solver, a structural design solver and a graphic documentation render. Also, current tools to develop this service as cloud application will be presented. Finally, a preliminary version of the CAD module, which generates graphical output as DXF format, is developed.

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is an established method for the interrogation of protein conformation and dynamics. While the data analysis challenge of HDX-MS has been addressed by a number of software packages, new computational tools are needed to keep pace with the improved methods and throughput of this technique. To address these needs, we report an integrated desktop program titled HDX Workbench, which facilitates automation, management, visualization, and statistical cross-comparison of large HDX data sets. Using the software, validated data analysis can be achieved at the rate of generation. The application is available at the project home page http://hdx.florida.scripps.edu .

Illuminator, a desktop program for mutation detection using short-read clonal sequencing

Current methods for sequencing clonal populations of DNA molecules yield several gigabases of data per day, typically comprising reads of <100 nt. Such datasets permit widespread genome resequencing and transcriptome analysis or other quantitative tasks. However, this huge capacity can also be harnessed for the resequencing of smaller (gene-sized) target regions, through the simultaneous parallel analysis of multiple subjects, using sample “tagging” or “indexing”. These methods promise to have a huge impact on diagnostic mutation analysis and candidate gene testing. Here we describe a software package developed for such studies, offering the ability to resolve pooled samples carrying barcode tags and to align reads to a reference sequence using a mutation-tolerant process. The program, Illuminator, can identify rare sequence variants, including insertions and deletions, and permits interactive data analysis on standard desktop computers. It facilitates the effective analysis of targeted clonal sequencer data without dedicated computational infrastructure or specialized training.

Morphometric approach to geomorphologic characteristics of Zeytinli Stream basin

Abstract In this study, the numeric data of the Zeytinli stream Basin's, which is located on the Kaz (Mt. Ida) Mountain massif in the North of Edremit Gulf, elevation - area - volume statistics, elevation levels, hypsographic curve values, profile series, drainage type, length and longitudinal profiles, bed slope values, bifurcation ratio, drainage density and frequency, SL index, stream size gradient, and asymmetry factors considered thalweg reconstructions was formed by using ArcGIS Desktop program with the help of numeric integration method. In these applications 1:25.000 scale topographic maps were based. In addition to this, all the analysis, calculations and evaluations were conducted in computers, too. The aim of the study is to search of the geomorphological evolution and development which is occured in the river basin via analysis and calculation. The other aim of the study is to expose the characteristics of displacement – development by making table, graphic and maps with the gathered data of analysis and calculation. In the conclusion of the study, it is shown that the effects of the different denudational process and tectonic activity have a big role in the formation of geomorphological characteristics of Zeytinli Stream Basin.

GeneScreen: a program for high-throughput mutation detection in DNA sequence electropherograms

BackgroundWhile massively parallel DNA sequencing methods continue to evolve rapidly, the benchmark technique for detection and verification of rare (particularly disease-causing) sequence variants remains four-colour dye-terminator sequencing by capillary electrophoresis....

Integration and visualization of systems biology data in context of the genome

BackgroundHigh-density tiling arrays and new sequencing technologies are generating rapidly increasing volumes of transcriptome and protein-DNA interaction data. Visualization and exploration of this data is critical to understanding the regulatory logic encoded in the genome by which the cell dynamically affects its physiology and interacts with its environment.ResultsThe Gaggle Genome Browser is a cross-platform desktop program for interactively visualizing high-throughput data in the context of the genome. Important features include dynamic panning and zooming, keyword search and open interoperability through the Gaggle framework. Users may bookmark locations on the genome with descriptive annotations and share these bookmarks with other users. The program handles large sets of user-generated data using an in-process database and leverages the facilities of SQL and the R environment for importing and manipulating data.A key aspect of the Gaggle Genome Browser is interoperability. By connecting to the Gaggle framework, the genome browser joins a suite of interconnected bioinformatics tools for analysis and visualization with connectivity to major public repositories of sequences, interactions and pathways. To this flexible environment for exploring and combining data, the Gaggle Genome Browser adds the ability to visualize diverse types of data in relation to its coordinates on the genome.ConclusionsGenomic coordinates function as a common key by which disparate biological data types can be related to one another. In the Gaggle Genome Browser, heterogeneous data are joined by their location on the genome to create information-rich visualizations yielding insight into genome organization, transcription and its regulation and, ultimately, a better understanding of the mechanisms that enable the cell to dynamically respond to its environment.

Optimistic Proteins Structure Classification and Identification Using Software tool –Approach

There are different bioinformatics tools available over the internet for free of cost whomever wishes to use them.The number of software products growing constantly, as software developers working in the life science are constantly updating and producing useful applications.CLC Protein Workbench is a user-friendly desktop program featuring a number of unique and innovative bioinformatics tools for supporting advanced biochemistry lab research. CLC Protein Workbench is fully integrated across these platforms and fully compatible with all other programs from CLC bio. In this paper with the help of software tool and with different methods to identify proteins structures with analysis and design are performed. The full text of the article is not available in the cache. Kindly refer the IJCA digital library at www.ijcaonline.org for the complete article. In case, you face problems while downloading the full-text, please send a mail to editor at editor@ijcaonline.org

An Interactive Desktop Computer Program for Simulating Nanometer Scale Surface Pattern Formation

AbstractNanometer-scale patterns may form as one or more chemical components deposit on a solid substrate. This self-assembly process can be described by a set of nonlinear integral-differential diffusion equations accounting for two opposing factors: phase separation to minimizing Gibb's free energy in individual surface phases and reduction in phase boundaries to minimize surface energy created by phase separation. I here present a desktop computer program that allows us to interactively simulate self-assembly of nanometer-scale surface patterns. In particular, this program provides a convenient tool for studying the effects of temperature variations and preexisting patterns on the self-assembly process. Computer simulations show that an increase in temperature may enlarge pattern sizes and can eventually lead to the disappearance of the patterns.

A tribute to Victor A. McKusick

A tribute to Victor A. McKusick

The use of a commercial remote desktop program in the delineation of target volumes in radiotherapy

Recent guidance from the Royal College of Radiologists suggests that there should be close collaboration between oncologists and radiologists in target volume determination. However, the guidance also states that there may be practical difficulties in achieving this. To ameliorate some of these difficulties, we have implemented a readily available remote desktop package, Microsoft NetMeeting, in conjunction with a commercial virtual simulation package, ProSoma. This allows radiologists to conference easily with oncologists on a particular patient, as the full functionality of the virtual simulator is available simultaneously to both parties. We have found that this solution is eminently practical and increases the amount of interaction between oncologists and radiologists during target volume definition.

GSEA-P: a desktop application for Gene Set Enrichment Analysis

Gene Set Enrichment Analysis (GSEA) is a computational method that assesses whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states. We report the availability of a new version of the Java based software (GSEA-P 2.0) that represents a major improvement on the previous release through the addition of a leading edge analysis component, seamless integration with the Molecular Signature Database (MSigDB) and an embedded browser that allows users to search for gene sets and map them to a variety of microarray platform formats. This functionality makes it possible for users to directly import gene sets from MSigDB for analysis with GSEA. We have also improved the visualizations in GSEA-P 2.0 and added links to a new form of concise gene set annotations called Gene Set Cards. These additions, as well as other improvements suggested by over 3500 users who have downloaded the software over the past year have been incorporated into this new release of the GSEA-P Java desktop program. GSEA-P 2.0 is freely available for academic and commercial users and can be downloaded from http://www.broad.mit.edu/GSEA

DVD Based Electronic Pulser

This paper describes the design, construction, and testing of a digital versatile disc (DVD) based electronic pulser system (DVDEPS). Such a device is used to generate pulse streams for simulation of both gamma and neutron detector systems. The DVDEPS reproduces a random pulse stream of a full high purity germanium (HPGe) spectrum as well as a digital pulse stream representing the output of a neutron multiplicity detector. The exchangeable DVD media contains over an hour of data for both detector systems and can contain an arbitrary gamma spectrum and neutron pulse stream. The data is written to the DVD using a desktop computer program from either real or simulated spectra. The targeted use of the DVDEPS is authentication or validation of monitoring equipment for non-proliferation purposes, but it is also of general use in a variety of situations. The DVD based pulser combines the storage capacity and simplicity of DVD technology with commonly available electronic components to build a relatively inexpensive yet highly capable testing instrument

RunMC—an object-oriented analysis framework for Monte Carlo simulation of high-energy particle collisions

RunMC is an object-oriented framework aimed to generate and to analyse high-energy collisions of elementary particles using Monte Carlo simulations. This package, being based on C++ adopted by CERN as the main programming language for the LHC experiments, provides a common interface to different Monte Carlo models using modern physics libraries. Physics calculations (projects) can easily be loaded and saved as external modules. This simplifies the development of complicated calculations for high-energy physics in large collaborations. This desktop program is open-source licensed and is available on the LINUX and Windows/Cygwin platforms. Program summary Title of program: RunMC version 3.3 Catalogue identifier: ADWH Program summary URL: http://cpc.cs.qub.ac.uk/summaries/ADWH Program obtainable from:CPC Program Library, Queen's University of Belfast, N. Ireland Computer: x86, SGI, Sun Microsystems Operating system: Linux, Windows/Cygwin Memory required: 32 Mbytes No. of bits in a word: 32 No. of processors used: 1 Parallelized?: No No of lines in distributed program, including test data, etc.: ≈ 1 000 000 No of bytes in distributed program, including test data, etc.: 22 464 383 Distribution format: tar.gz Typical running time: 0.004–0.01 s per event Programming language used: C/C++, Fortran, Java, bash Program requirements: g77, g++, make, X11, Java JRE1.4 and higher Nature of the physical problem: Simulation of high-energy collisions of elementary particles Method of solution: Monte Carlo method External libraries: CLHEP, ROOT, CERNLIB with PDFLIB

Acquisition of high-resolution digital images in video microscopy: automated image mosaicking on a desktop microcomputer.

For the digital processing of microscopical images, mosaicking is a prerequisite if the specimen is larger than the camera field at the necessary magnification. This study investigates the possibilities and limitations of fully automated mosaicking on a desktop computer. Cross-correlation-based frame registration was performed with high reliability if the video frames were edge-enhanced before matched filtering, and also in a reasonable time since the search for matches was restricted to pairs of consecutive frames. An environment for routine mosaicking was developed and implemented in a widely used desktop image-processing program. The software developed during this study has been released to the public domain.