ANISOtime: Traveltime Computation Software for Laterally Homogeneous, Transversely Isotropic, Spherical Media

2021 ◽  
Author(s):  
Kensuke Konishi ◽  
Anselme F. E. Borgeaud ◽  
Kenji Kawai ◽  
Robert J. Geller
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Software Package ◽  
Transversely Isotropic ◽  
Earth Model ◽  
Spherically Symmetric ◽  
Command Line ◽  
Command Line Interface ◽  
Software Packages ◽  
Cross Platform

Abstract Software packages for computing seismic traveltimes and raypaths in an isotropic, spherically symmetric, Earth model are well known and widely used. However, even though the theory for transversely isotropic (TI), spherically symmetric, models has been known since the late 1960s, readily available programs for traveltime calculations are restricted to isotropic models. We have developed a new software package, ANISOtime, for computing seismic traveltimes and raypaths in laterally homogeneous, TI, spherical media. This package calculates traveltime tables for both immediate and subsequent use. ANISOtime has both graphical user interface and command-line interface modes. The package is available for free public download. As it offers cross-platform compatibility through Java 8, it runs on Windows, macOS, Unix, and Linux.

scholarly journals ESTUDO DA USABILIDADE NAS INTERFACES HOMEM-MÁQUINA

e-xacta ◽  
2013 ◽  
Vol 6 (2) ◽  
pp. 93
Author(s):  
Felipe Francisco Ramos de Oliveira ◽  
Marlon Marques Ferreira ◽  
Alexandre Furst
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Command Line ◽  
Natural User Interface ◽  
Command Line Interface ◽  
Technological Differences

<p align="justify">Este artigo documenta e analisa o processo de evolução das principais interfaces homem-máquina, com enfoque na usabilidade, e as diferenças tecnológicas entre elas. A pesquisa desempenhada para elaboração deste documento procura, também, experimentar o desempenho das interfaces CLI (Command Line Interface), GUI (Graphical User Interface) e NUI (Natural User Interface) por meio de um experimento de usabilidade que aborde as três interfaces em um único objetivo e permita o recolhimento de dados para avaliação.</p><p align="justify">Abstract</p><p align="justify">This article documents and analyzes the evolution of the main man-machine interfaces, with a focus on usability and technological differences between them. The research carried out for the preparation of this document also seeks to experience the performance of interfaces CLI (Command Line Interface) GUI (Graphical User Interface) and NUI (Natural User Interface) through an experiment that addresses the usability of three interfaces on a single goal and allow the collection of data for evaluation.</p>

scholarly journals omicplotR: visualizing omic datasets as compositions

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Daniel J. Giguere ◽  
Jean M. Macklaim ◽  
Brandon Y. Lieng ◽  
Gregory B. Gloor
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
High Throughput Sequencing ◽  
Principal Component ◽  
Visual Exploration ◽  
Command Line ◽  
Sequencing Data ◽  
Software Packages ◽  
High Throughput Sequencing Data ◽  
Differential Abundance Analysis

Abstract Background Differential abundance analysis is widely used with high-throughput sequencing data to compare gene abundance or expression between groups of samples. Many software packages exist for this purpose, but each uses a unique set of statistical assumptions to solve problems on a case-by-case basis. These software packages are typically difficult to use for researchers without command-line skills, and software that does offer a graphical user interface do not use a compositionally valid method. Results omicplotR facilitates visual exploration of omic datasets for researchers with and without prior scripting knowledge. Reproducible visualizations include principal component analysis, hierarchical clustering, MA plots and effect plots. We demonstrate the functionality of omicplotR using a publicly available metatranscriptome dataset. Conclusions omicplotR provides a graphical user interface to explore sequence count data using generalizable compositional methods, facilitating visualization for investigators without command-line experience.

scholarly journals SraTailor: GUI software for visualizing high-throughput sequence read archives

2014 ◽  
Author(s):  
Shinya Oki ◽  
Kazumitsu Maehara ◽  
Yasuyuki Ohkawa ◽  
Chikara Meno
Keyword(s):  
User Interface ◽  
Data Processing ◽  
High Throughput ◽  
Graphical User Interface ◽  
Software Package ◽  
Sequence Data ◽  
Command Line ◽  
Accession Number ◽  
Wide Range

Raw high-throughput sequence data are deposited in public databases as SRAs (Sequence Read Archives) and are publically available to every researcher. However, in order to graphically visualize the sequence data of interest, the corresponding SRAs must be downloaded and converted into BigWig format through complicated command-line processing. This task requires users to possess skill with script languages and sequence data processing, a requirement that prevents a wide range of biologists from exploiting SRAs. To address these challenges, we developed SraTailor, a GUI (Graphical User Interface) software package that automatically converts an SRA into a BigWig-formatted file. Simplicity of use is one of the most notable features of SraTailor: entering an accession number of an SRA and clicking the mouse are the only steps required in order to obtain BigWig-formatted files and to graphically visualize the extents of reads at given loci. SraTailor is also able to make peak calls and files of other formats, and the software also accepts various command-line-like options. Therefore, this software makes SRAs fully exploitable by a wide range of biologists. SraTailor is freely available at http://www.dev.med.kyushu-u.ac.jp/sra_tailor/.

scholarly journals From command-line bioinformatics to bioGUI

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e8111 ◽  
Author(s):  
Markus Joppich ◽  
Ralf Zimmer
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Command Line ◽  
Command Line Interface ◽  
Interdisciplinary Work ◽  
Interdisciplinary Field ◽  
Bioinformatics Tools ◽  
One Step ◽  
Microsoft Windows

Bioinformatics is a highly interdisciplinary field providing (bioinformatics) applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is inconvenient and/or inefficient for many scientists. Nonetheless, most methods are implemented with a command-line interface only. Providing a graphical user interface (GUI) for bioinformatics applications is one step toward routinely making CL-only applications available to more scientists and, thus, toward a more effective interdisciplinary work. With our bioGUI framework we address two main problems of using CL bioinformatics applications: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools which, however, could well support them in their research. With bioGUI install modules and templates, installing and using CL tools is made possible for most scientists—even on Windows, due to bioGUI’s support for Windows Subsystem for Linux. In addition, bioGUI templates can easily be created, making the bioGUI framework highly rewarding for developers. From the bioGUI repository it is possible to download, install and use bioinformatics tools with just a few clicks.

scholarly journals PENERAPAN PROJECT BASED LEARNING UNTUK MENINGKATKAN AKTIVITAS DAN KOMPETENSI INSTALASI SISTEM OPERASI BERBASIS GUI DAN CLI PADA SISWA KELAS X TKJ DI SMK N 1 SAWIT

2019 ◽  
Vol 2 (3) ◽  
Author(s):  
Pinasti Nur Handayaningtyas ◽  
Basori Basori ◽  
A.G Tamrin
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Project Based Learning ◽  
Command Line ◽  
Command Line Interface

<p>Penelitian ini bertujuan untuk mengetahui apakah penerapan project   based learning dapat meningkatkan aktivitas dan kompetensi belajar siswa dalam Instalasi Sistem Operasi Berbasis GUI ( Graphical User Interface) dan CLI ( Command Line Interface)  kelas X TKJ SMK N 1 Sawit. Penelitian ini menggunakan metode Penelitian Tindakan Kelas (PTK) yang dilaksanakan sebanyak dua siklus dimana masing – masing siklus dilakukan dengan empat tahapan, yaitu : (1) tindakan perencanaan; (2) tindakan pelaksanaan; (3) tindakan observasi; dan (4) refleksi. Subjek penelitian adalah siswa kelas X TKJ 3 di SMK N 1 Sawit sebanyak 34 siswa. Penelitian ini dilaksanakan dengan kolaborasi antara peneliti, guru, observer dan melibatkan partisipasi siswa. Teknik pengumpulan data menggunakan lembar observasi, wawancara, instrumen tes dan teknik analisis data. Berdasarkan hasil penelitian, dapat disimpulkan bahwa penerapan project   based learning dapat meningkatkan aktivitas dan kompetensi instalasi sistem operasi berbasis GUI dan CLI. Hal ini terbukti dari fakta – fakta hasil sebagai berikut : (1) Aktivitas siswa dalam mengikuti pembelajaran mengalami peningkatan pada pra siklus sebesar 32,35% menjadi 58,82% pada siklus I dan pada siklus II meningkat menjadi 82,35%. (2) Kompetensi siswa dalam pembelajaran terdisi dari 3 ranah yaitu masing – masing ranah meengalami peningkatan sebagai berikut : (a) Ranah Kognitif  dari pra siklus sebesar 11,76% menjadi 26,47% pada siklus I dan siklus II meningkat menjadi sebesar 47,05%. (b) Ranah Afektif dari pra siklus sebesar 32,35% menjadi 53,29% pada siklus I dan pada siklus II meningkat menjadi sebesar 76,47%. (c) Ranah Psikomotorik dari pra siklus sebesar 44,11% menjadi 79,41% pada siklus I dan pada siklus II meningkat menjadi 82,35%.</p><div><p><strong> Kata kunci :</strong> Project   based learning, Aktivitas dan Kompetensi, Instalasi Sistem Operasi Berbasis GUI (Graphical User Interface) dan CLI ( Command Line Interface</p></div>

scholarly journals PENGEMBANGAN APLIKASI INFORMATION GATHERING MENGGUNAKAN METODE HYBRID SCAN BERBASIS GRAPHICAL USER INTERFACE

2021 ◽  
Vol 4 (1) ◽  
pp. 44-48
Author(s):  
Mardhani Riasetiawan ◽  
Akas Wisnuaji ◽  
Dedy Hariyadi ◽  
Tri Febrianto
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Application Programming Interface ◽  
Information Gathering ◽  
Command Line ◽  
Command Line Interface ◽  
Application Programming ◽  
Programming Interface

Sebagian analis keamanan sistem dan jaringan komputer menyatakan aplikasi atau alat bantu pengujian berbasis Command-line Interface (CLI) sangat mempermudah pekerjaan. Namun, tidak banyak aplikasi tersebut tidak komprehensif baik cara menganalisis maupun hasil laporannya. Laporan pada proses pengujian keamanan sistem dan jaringan komputer diharapkan minimal terdiri dari dua tipe, yaitu keperluan manajemen dan tim teknis. Tulisan ini diusulkan pengembangan aplikasi atau alat bantu pengujian keamanan sistem dan jaringan komputer yang komprehensif dan memiliki laporan yang memudahkan tim manajemen dan tim teknis. Pada pengembangan ini menggunakan bahasa pemrograman Python dengan module TKInter untuk menghasilkan aplikasi berbasis Graphical User Interface (GUI). Dengan menggunakan aplikasi GUI harapannya dapat digunakan oleh siapapun. Fokus pengembangan aplikasi ini yaitu pada tahapan Information Gathering yang menggunakan metode Hybrid Scan,yaitu: Passive dan Active. Passive Scan menggunakan 11 Application Programming Interface (API) sedangkan Active Scan menggunakan Socket Module Python dan berberapa aplikasi native yang berjalan di GNU/Linux.

A New Paradigm for Ship Design Calculations

2015 ◽  
Author(s):  
Stephen M. Hollister
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Ship Design ◽  
New Paradigm ◽  
New Model ◽  
Analysis Tools ◽  
Cross Platform ◽  
Open Code ◽  
Design Calculations ◽  
Interactive Graphical User Interface

A new model for ship design calculations is presented that separates the graphical user interface (GUI) from the calculations (CALC). Design programs can now be defined as more than one interactive graphical user interface tied to one calculation. Several different GUIs can be created for one CALC engine and one GUI can be created to launch several CALC engines in sequence. The GUI of choice is a spreadsheet due to its availability, programmable customization, powerful analysis tools, cross-platform capability, and open code environment.

scholarly journals UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

2021 ◽  
Vol 9 ◽  
Author(s):  
Caio Ribeiro ◽  
Lucas Oliveira ◽  
Romina Batista ◽  
Marcos De Sousa
Keyword(s):  
Best Practices ◽  
Software Package ◽  
Phylogenetic Trees ◽  
Computational Analysis ◽  
Data Matrix ◽  
Command Line ◽  
Command Line Interface ◽  
Ultraconserved Elements ◽  
Research Software ◽  
Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

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