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.

scholarly journals Audit logs to enforce document integrity in Skyline and Panorama

2020 ◽  
Vol 36 (15) ◽  
pp. 4366-4368
Author(s):  
Tobias Rohde ◽  
Rita Chupalov ◽  
Nicholas Shulman ◽  
Vagisha Sharma ◽  
Josh Eckels ◽  
...  
Keyword(s):  
User Interface ◽  
Graphical User Interface ◽  
Quantitative Data ◽  
Supplementary Information ◽  
Command Line ◽  
Supplementary Data ◽  
Spectrometry Method ◽  
Quantitative Data Analysis ◽  
User Actions ◽  
Web Repository

Abstract Summary Skyline is a Windows application for targeted mass spectrometry method creation and quantitative data analysis. Like most graphical user interface (GUI) tools, it has a complex user interface with many ways for users to edit their files which makes the task of logging user actions challenging and is the reason why audit logging of every change is not common in GUI tools. We present an object comparison-based approach to audit logging for Skyline that is extensible to other GUI tools. The new audit logging system keeps track of all document modifications made through the GUI or the command line and displays them in an interactive grid. The audit log can also be uploaded and viewed in Panorama, a web repository for Skyline documents that can be configured to only accept documents with a valid audit log, based on embedded hashes to protect log integrity. This makes workflows involving Skyline and Panorama more reproducible. Availability and implementation Skyline is freely available at https://skyline.ms. Supplementary information Supplementary data are available at Bioinformatics online.

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.

CoRC: the COPASI R Connector

2021 ◽  
Author(s):  
Jonas Förster ◽  
Frank T Bergmann ◽  
Jürgen Pahle
Keyword(s):  
Graphical User Interface ◽  
Academic Research ◽  
R Package ◽  
Supplementary Information ◽  
Command Line ◽  
Graphical Interface ◽  
Thought Process ◽  
Extensive Analysis ◽  
Command Line Tool ◽  
High Level

Abstract Motivation COPASI is a biochemical simulator and model analyzer which has found widespread use in academic research, teaching and beyond. One of COPASI’s strengths is its graphical user interface, and this is what most users work with. COPASI also provides a command-line tool. So far, an intuitive scripting interface that allows the creation and documentation of systems biology workflows was missing though. Results We have developed CoRC, the COPASI R Connector, an R package which provides a high-level scripting interface for COPASI. It closely mirrors the thought process of a (graphical interface) user and should therefore be very easy to use. This allows for complex workflows to be reproducibly scripted, utilizing COPASI’s powerful analytic toolset in combination with R’s extensive analysis and package ecosystem. Availability and implementation CoRC is a free and open-source R package, available via GitHub at https://jpahle.github.io/CoRC/ under the Artistic-2.0 license.   Supplementary information: We provide tutorial articles as well as several example scripts on the project’s website.

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 NanoPack: visualizing and processing long read sequencing data

2017 ◽  
Author(s):  
Wouter De Coster ◽  
Svenn D’Hert ◽  
Darrin T. Schultz ◽  
Marc Cruts ◽  
Christine Van Broeckhoven
Keyword(s):  
Web Service ◽  
Graphical User Interface ◽  
Source Code ◽  
Supplementary Information ◽  
Command Line ◽  
Sequencing Data ◽  
Link Type ◽  
Oxford Nanopore ◽  
Long Read ◽  
Oxford Nanopore Technologies

AbstractSummary: Here we describe NanoPack, a set of tools developed for visualization and processing of long read sequencing data from Oxford Nanopore Technologies and Pacific Biosciences.Availability and Implementation: The NanoPack tools are written in Python3 and released under the GNU GPL3.0 Licence. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are compatible with Linux, Mac OS and the MS Windows 10 subsystem for linux and are available as a graphical user interface, a web service at http://nanoplot.bioinf.be and command line tools.Contact:[email protected] information: Supplementary tables and figures are available at Bioinformatics online.

A Graphical User Interface (GUI) Testing Methodology

2010 ◽  
pp. 160-176
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 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 Development of graphical user interface for open source VLSI digital synthesis tool Qflow

2018 ◽  
Vol 7 (2) ◽  
pp. 710
Author(s):  
K. Sripath Roy ◽  
K. Abhiram ◽  
M. Arun Sumanth ◽  
Jaishree Jaishankar ◽  
P. Abhishek ◽  
...  
Keyword(s):  
User Interface ◽  
Open Source ◽  
Graphical User Interface ◽  
Source Code ◽  
Command Line ◽  
Simulation Process ◽  
Vlsi Technology ◽  
Synthesis Tool ◽  
Digital Synthesis ◽  
User Friendly

There are many tools that are used for simulation in the domain of VLSI technology but none of them are easily accessible. There is a need for Free and open source tools in this stream so as to make them accessible to everyone. There are efficient tools that already exist in open source in VLSI stream but are not used widely because of their command line user interface. Hence, creating a user friendly interface will help many developers and users to work easily. This paper deals with the idea to solve the above issue by creating a Graphical User Interface for the open source VLSI tool called QFlow. Qflow is a tool used in synthesizing a VLSI circuit from the Verilog source code. There are multiple tools integrated with this tool to assure the simulation process. It is a combination of many dependencies that are used for synthesis, placement, layout viewing and routing in a fabrication process. All the independent tools used for the Verilog code simulation are integrated onto a single platform. Qt is used for creating the cross-stage application.

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/.

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