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 From command-line bioinformatics to bioGUI

2018 ◽  
Author(s):  
Markus Joppich ◽  
Ralf Zimmer
Keyword(s):  
Command Line ◽  
Interdisciplinary Work ◽  
Bioinformatic Tools ◽  
Interdisciplinary Field ◽  
Bioinformatics Tools ◽  
One Step ◽  
Microsoft Windows

Bioinformatics is a highly interdisciplinary field providing applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is a problem for many scientists, nonetheless, most methods are implemented with a CL interface only. Providing a GUI for bioinformatics applications is one step towards routinely making CL-only applications available to more scientists, and, thus towards a more effective interdisciplinary work. We identified two main problems for conveniently using CL bioinformatic tools: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using command-line tools which, however, could well support them in their research. Both issues are addressed by bioGUI. The bioGUI framework provides easy means to make CL tools available for most scientists, especially making use of Windows Subsystem for Linux, which provides a native Ubuntu bash on Windows. In addition, bioGUI templates are easily created (automatically), making this framework highly rewarding for developers. The bioGUI repository allows to install and use bioinformatics tools with just a few clicks.

scholarly journals From command-line bioinformatics to bioGUI

2018 ◽  
Author(s):  
Markus Joppich ◽  
Ralf Zimmer
Keyword(s):  
Command Line ◽  
Interdisciplinary Work ◽  
Bioinformatic Tools ◽  
Interdisciplinary Field ◽  
Bioinformatics Tools ◽  
One Step ◽  
Microsoft Windows

Bioinformatics is a highly interdisciplinary field providing applications for scientists from many disciplines. Installing and starting applications on the command-line (CL) is a problem for many scientists, nonetheless, most methods are implemented with a CL interface only. Providing a GUI for bioinformatics applications is one step towards routinely making CL-only applications available to more scientists, and, thus towards a more effective interdisciplinary work. We identified two main problems for conveniently using CL bioinformatic tools: First, many tools work on UNIX-systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using command-line tools which, however, could well support them in their research. Both issues are addressed by bioGUI. The bioGUI framework provides easy means to make CL tools available for most scientists, especially making use of Windows Subsystem for Linux, which provides a native Ubuntu bash on Windows. In addition, bioGUI templates are easily created (automatically), making this framework highly rewarding for developers. The bioGUI repository allows to install and use bioinformatics tools with just a few clicks.

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 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.

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 Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

2015 ◽  
Vol 14 ◽  
pp. CIN.S26470 ◽  
Author(s):  
Richard P. Finney ◽  
Qing-Rong Chen ◽  
Cu V. Nguyen ◽  
Chih Hao Hsu ◽  
Chunhua Yan ◽  
...  
Keyword(s):  
Graphical User Interface ◽  
Reference Genome ◽  
Source Code ◽  
Software Tool ◽  
Command Line ◽  
Sequencing Data ◽  
Genome Data ◽  
Command Line Tool ◽  
Portable Software ◽  
Microsoft Windows

The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application can run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview . The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview .

A Graphical User Interface (GUI) Testing Methodology

2009 ◽  
pp. 3037-3054
Author(s):  
Zafar Singhera ◽  
Ellis Horowitz ◽  
Abad Shah
Keyword(s):  
User Interface ◽  
Software Testing ◽  
Graphical User Interface ◽  
Command Line ◽  
Multiple Sources ◽  
Gui Testing ◽  
Organization And Management ◽  
Testing Techniques ◽  
The Creation ◽  
Test Suites

Software testing in general and graphical user interface (GUI) testing in particular is one of the major challenges in the lifecycle of any software system. GUI testing is inherently more difficult than the traditional and command-line interface testing. Some of the factors that make GUI testing different from the traditional software testing and significantly more difficult are: a large number of objects, different look and feel of objects, many parameters associated with each object, progressive disclosure, complex inputs from multiple sources, and graphical outputs. The existing testing techniques for the creation and management of test suites need to be adapted/enhanced for GUIs, and new testing techniques are desired to make the creation and management of test suites more efficient and effective. In this article, a methodology is proposed to create test suites for a GUI. The proposed methodology organizes the testing activity into various levels. The tests created at a particular level can be reused at higher levels. This methodology extends the notion of modularity and reusability to the testing phase. The organization and management of the created test suites resembles closely to the structure of the GUI under test.

scholarly journals GenCoF: a graphical user interface to rapidly remove human genome contaminants from metagenomic datasets

2018 ◽  
Vol 35 (13) ◽  
pp. 2318-2319 ◽  
Author(s):  
Matthew D Czajkowski ◽  
Daniel P Vance ◽  
Steven A Frese ◽  
Giorgio Casaburi
Keyword(s):  
User Interface ◽  
Human Genome ◽  
Graphical User Interface ◽  
Supplementary Information ◽  
Metagenomic Sequencing ◽  
Command Line ◽  
Shotgun Metagenomic Sequencing ◽  
Human Genomic ◽  
Quality Filtering ◽  
Analytical Time

Abstract Summary The removal of human genomic reads from shotgun metagenomic sequencing is a critical step in protecting subject privacy. Freely available tools addressing this issue require advanced programing knowledge or are limited by analytical time and data load due to their server-based nature. Here, we compared the most cited tools for host-DNA removal using synthetic and real metagenomic datasets. Then, we integrated the most efficient pipeline in a graphical user interface to make these tools available without command line use. This interface, GenCoF, rapidly removes human genome contaminants from metagenomic datasets. Additionally, the tool offers quality-filtering, data reduction and interactive modification of any parameter in order to customize the analysis. GenCoF offers both quality and host-associated filtering in a non-commercial, freely available tool in a local, interactive and easy-to-use interface. Availability and implementation GenCoF is freely available (under a GPL license) for Mac OS and Linux at https://github.com/MattCzajkowski/GenCoF. Supplementary information Supplementary data are available at Bioinformatics online.

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