scholarly journals Visualizing and comparing circular genomes using the CGView family of tools

2017 ◽  
Vol 20 (4) ◽  
pp. 1576-1582 ◽  
Author(s):  
Paul Stothard ◽  
Jason R Grant ◽  
Gary Van Domselaar
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Ease Of Use ◽  
Current Development ◽  
Genome Maps ◽  
Circular Genome ◽  
Genome Viewer ◽  
Genome Features ◽  
Sequence Characteristics

Abstract Graphical genome maps are widely used to assess genome features and sequence characteristics. The CGView (Circular Genome Viewer) software family is a popular collection of tools for generating genome maps for bacteria, organelles and viruses. In this review, we describe the capabilities of the original CGView program along with those of subsequent companion applications, including the CGView Server and the CGView Comparison Tool. We also discuss GView, a graphical user interface-enabled rewrite of CGView, and the GView Server, which offers several integrated analyses for identifying shared or unique genome regions relative to a collection of comparison genomes. We conclude with some remarks about our current development efforts related to CGView aimed at adding new functionality while increasing ease of use.

Mobile Based Security and Control System Using Python s60

2011 ◽  
Vol 403-408 ◽  
pp. 511-515
Author(s):  
Arun Raveendran ◽  
Jency K. Joy
Keyword(s):  
Control System ◽  
User Interface ◽  
Mobile Phones ◽  
Graphical User Interface ◽  
Ease Of Use ◽  
Home Appliances ◽  
Control Signals ◽  
Control Devices ◽  
Ubiquitous Access ◽  
And Control

This paper proposes a mobile phone based security and control system for home appliances through SMS/Bluetooth. It focuses on controlling home appliances remotely, and providing security with good graphical user interface. The system uses GSM technology, providing ubiquitous access to the system for security and automated appliance control from anywhere around the globe. The system provides security against intrusion using a smarter digital lock which notifies owners in case of an unauthorized via SMS message, as well as facilitates both short and long-range device control using Bluetooth or SMS technology. Rather than a conventional method of sending an SMS message to control devices, a graphical user interface is designed using Python S60 language for ease of use. The control signals in the form of SMS messages are encrypted and restricted to unique mobile phones or SIM cards for improved security.

scholarly journals A tool for precise calculation of organ doses in voxelised geometries using GAMOS/Geant4 with a graphical user interface

2021 ◽  
Vol 27 (1) ◽  
pp. 31-40
Author(s):  
Pedro Arce Dubois ◽  
Nguyen Thi Phuong Thao ◽  
Nguyen Thien Trung ◽  
Juan Diego Azcona ◽  
Pedro-Borja Aguilar-Redondo
Keyword(s):  
Monte Carlo ◽  
User Interface ◽  
Graphical User Interface ◽  
Dose Calculation ◽  
Medical Personnel ◽  
Ease Of Use ◽  
Simulation Code ◽  
Organ Doses ◽  
Precise Calculation ◽  
Parallel Geometry

Abstract Introduction: The limit of the method of calculating organ doses using voxelised phantoms with a Monte Carlo simulation code is that dose calculation errors in the boundaries of the organs are especially relevant for thin, small or complex geometries. In this report, we describe a tool that helps overcome this problem, accurately calculating organ doses by applying the “parallel geometry” utility feature of Geant4 through the GAMOS framework. Methods and methods: We have tried to simplify the use of this tool by automatically processing the different DICOM image modalities (CT, PT, ST, NM), and by including the automatic conversion of the structures found in a DICOM RTSTRUCT file into Geant4 volumes that build the parallel geometry. For Nuclear Medicine applications, the DICOM PT, ST or NM images are converted into probabilities of generation of primary particles in each voxel, and the DICOM CT images into materials and material densities. For radiotherapy treatments, the DICOM RTPlan or RTIonPlan may also be used, hence the user only needs to describe the accelerator geometry. We also provide a Graphical User Interface for ease of use by for inexperienced users in Monte Carlo. Results: We have tested the functionality of the tool with an I-131 thyroid cancer treatment, and obtained the expected energy deposition and dose differences, given that the particle source, geometry and structures are defined. Conclusions: In summary, we provide an easy-to-use tool to calculate, with high accuracy, organ doses, taking into account their exact geometry as painted by the medical personnel on a voxelised phantom.

scholarly journals artMAP: a user-friendly tool for mapping EMS-induced mutations in Arabidopsis

2018 ◽  
Author(s):  
Peter Javorka ◽  
Vivek Raxwal ◽  
Jan Najvarek ◽  
Karel Riha
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Source Code ◽  
Ease Of Use ◽  
Sequencing Data ◽  
Induced Mutations ◽  
Mouse Click ◽  
User Friendly ◽  
Paired End Sequencing ◽  
Mapping By Sequencing

AbstractMapping-by-sequencing is a rapid method for identifying both natural as well as induced variations in the genome. However, it requires extensive bioinformatics expertise along with the computational infrastructure to analyze the sequencing data and these requirements have limited its widespread adoption. In the current study, we develop an easy to use tool, artMAP, to discover ethyl methanesulfonate (EMS) induced mutations in the Arabidopsis genome. The artMAP pipeline consists of well-established tools including TrimGalore, BWA, BEDTools, SAMtools, and SnpEff which were integrated in a Docker container. artMAP provides a graphical user interface and can be run on a regular laptop and desktop, thereby limiting the bioinformatics expertise required. artMAP can process input sequencing files generated from single or paired-end sequencing. The results of the analysis are presented in interactive graphs which display the annotation details of each mutation. Due to its ease of use, artMAP made the identification of EMS-induced mutations in Arabidopsis possible with only a few mouse click. The source code of artMAP is available on Github (https://github.com/RihaLab/artMAP).

GRAPHICAL USER INTERFACE FOR ASSESSING SUSTAINABILITY BY USING FUZZY LOGIC: A CASE STUDY ON HOLLOW FIBER MEMBRANE MODULE

2015 ◽  
Vol 76 (1) ◽  
Author(s):  
Salwa Mahmood ◽  
Abdul Rahman Hemdi ◽  
Muhamad Zameri Mat Saman ◽  
Noordin Mohd Yusof
Keyword(s):  
Fuzzy Logic ◽  
User Interface ◽  
Product Development ◽  
Graphical User Interface ◽  
Product Life Cycle ◽  
Hollow Fiber Membrane ◽  
Ease Of Use ◽  
Raw Material ◽  
Two Phases

An important consideration during product development is the sustainability level of a product. Thus, several tools and methods have been developed to assess product sustainability. However, most of current tools focus only on the environmental element without considering two important sustainability elements such economic and social elements. Other tools are limited to the cradle-to-gate system boundary, which covers two phases of the product life cycle from raw material extraction to the end of the manufacturing stage. Users need to understand the mathematical calculations and tools needed to achieve this purpose. Hence, this paper developed a comprehensive method for assessing the sustainability of product development considering all sustainability elements from cradle-to-grave. A graphical user interface (GUI) was developed for ease of use from the structured methodology. The developed GUI was embedded with the fuzzy logic calculation under the Matlab GUI platform with codes and callback functions by using fuzzy linguistics. The GUI presented is a user friendly assessment since users no need to understand the mathematical equation embedded. A product was selected as a case study to demonstrate the use of the GUI. The sustainability level of a product can be monitored via the GUI to enable further product sustainability improvement.

Development of a Web-Based Interactive Compressible Flow Solver

2005 ◽  
Author(s):  
H. Eletem ◽  
F. Young ◽  
K. Aung
Keyword(s):  
User Interface ◽  
Compressible Flow ◽  
Programming Language ◽  
Graphical User Interface ◽  
Mechanical Engineering ◽  
Software Tool ◽  
Ease Of Use ◽  
Web Based ◽  
Flow Solver ◽  
Java Programming

Compressible flow is an important subject in aerospace and mechanical engineering disciplines. This paper describes the development of a web-base interactive compressible flow solver using Java programming language. The main objective of the solver is to provide students with a software tool than can be used in the compressible flow course offered in the Department of Mechanical Engineering at Lamar University. The solver has a graphical user interface (GUI) for ease of use and interactivity. The solver was developed with the intention of free distribution to the educational community and other interested users.

HOW TO USE CROP GROWTH MODEL WOFOST FOR FORECASTING GROWTH AND YIELD OF A CROP

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
LAL SINGH ◽  
PARMEET SINGH ◽  
RAIHANA HABIB KANTH ◽  
PURUSHOTAM SINGH ◽  
SABIA AKHTER ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Input Data ◽  
Growth And Yield ◽  
Weather Data ◽  
Data Sets ◽  
Crop Growth Model ◽  
Control Center ◽  
Field Crops ◽  
Crop Calendar

WOFOST version 7.1.3 is a computer model that simulates the growth and production of annual field crops. All the run options are operational through a graphical user interface named WOFOST Control Center version 1.8 (WCC). WCC facilitates selecting the production level, and input data sets on crop, soil, weather, crop calendar, hydrological field conditions, soil fertility parameters and the output options. The files with crop, soil and weather data are explained, as well as the run files and the output files. A general overview is given of the development and the applications of the model. Its underlying concepts are discussed briefly.

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