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 d2Dplot: 2D X-ray diffraction data processing and analysis for through-the-substrate microdiffraction

2019 ◽  
Vol 52 (2) ◽  
pp. 478-484 ◽  
Author(s):  
Oriol Vallcorba ◽  
Jordi Rius
Keyword(s):  
User Interface ◽  
Data Processing ◽  
Graphical User Interface ◽  
Background Subtraction ◽  
Phase Identification ◽  
Command Line ◽  
X Ray Diffraction ◽  
X Ray ◽  
Fast Phase ◽  
Compound Database

The d2Dplot computer program provides a set of tools for the visualization, processing and analysis of 2D X-ray diffraction (2DXRD) data. Among the operations available there are the sum/subtraction of 2DXRD images, conversion to 1D data (powder pattern), azimuthal plotting, calibration of instrumental parameters, background subtraction and a command-line mode to run operations inside data processing pipelines. The graphical user interface allows easy use of the program. It also includes two main features: (i) the possibility of creating a user compound database to help in the fast phase identification of similar samples, and (ii) a detailed peak analysis routine for the application of the through-the-substrate microdiffraction methodology.

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 DolphinNext: A graphical user interface for creating, deploying and executing Nextflow pipelines

2019 ◽  
Author(s):  
Onur Yukselen ◽  
Osman Turkyilmaz ◽  
Ahmet Rasit Ozturk ◽  
Manuel Garber ◽  
Alper Kucukural
Keyword(s):  
User Interface ◽  
Data Processing ◽  
Programming Languages ◽  
High Throughput ◽  
High Performance ◽  
Scientific Discovery ◽  
Biological Research ◽  
Wide Range ◽  
The Face ◽  
Economic Constraints

ABSTRACTThe emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) are transforming biological research. The dramatic increase in the volume of data makes analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for a highly-parallel, flexible, portable, and reproducible data processing frameworks. Flexibility ensures that pipelines can support a variety of applications without requiring one-off modifications. Portability ensures that users can leverage computationally available resources and work within economic constraints. Reproducibility warrants credibility to the results and is particularly challenging in the face of the sheer volume of data and the complexity of processing pipelines that vary widely between users.Several platforms currently exist for the design and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, these platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, Nextflow was implemented to simplify portable, scalable, and reproducible scientific pipelines using containers. We have used Nextflow capabilities as leverage and developed a user interface, DolphinNext, for creating, deploying, and executing complex Nextflow pipelines for high throughput data processing. The guiding principle of DolphinNext is to facilitate the building and deployment of complex pipelines using a modular approach implemented in a graphical interface. DolphinNext provides: 1. A drag and drop user interface that abstracts pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. A user interface to monitor pipeline execution that allows the re-initiation of pipelines at intermediate steps 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Seamless portability to distributed computational environments such as high-performance clusters or cloud computing environments.

GEView (Gene Expression View) Tool for Intuitive and High Accessible Visualization of Expression Data for Non-Programmer Biologists

2020 ◽  
pp. 580-592
Author(s):  
Libi Hertzberg ◽  
Assif Yitzhaky ◽  
Metsada Pasmanik-Chor
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
User Interface ◽  
High Throughput ◽  
Graphical User Interface ◽  
Differential Expression Analysis ◽  
Biological Data ◽  
Expression Data ◽  
Batch Correction ◽  
User Friendly

This article describes how the last decade has been characterized by the production of huge amounts of different types of biological data. Following that, a flood of bioinformatics tools have been published. However, many of these tools are commercial, or require computational skills. In addition, not all tools provide intuitive and highly accessible visualization of the results. The authors have developed GEView (Gene Expression View), which is a free, user-friendly tool harboring several existing algorithms and statistical methods for the analysis of high-throughput gene, microRNA or protein expression data. It can be used to perform basic analysis such as quality control, outlier detection, batch correction and differential expression analysis, through a single intuitive graphical user interface. GEView is unique in its simplicity and highly accessible visualization it provides. Together with its basic and intuitive functionality it allows Bio-Medical scientists with no computational skills to independently analyze and visualize high-throughput data produced in their own labs.

A MATLAB graphical user interface program for tomographic viscometer data processing

2005 ◽  
Vol 47 (1) ◽  
pp. 59-67 ◽  
Author(s):  
Young Jin Choi ◽  
Kathryn L. McCarthy ◽  
Michael J. McCarthy
Keyword(s):  
User Interface ◽  
Data Processing ◽  
Graphical User Interface

scholarly journals BioSANS: A Software Package for Symbolic and Numeric Biological Simulation

2021 ◽  
Author(s):  
Erickson Fajiculay ◽  
Chao-Ping Hsu
Keyword(s):  
Parameter Estimation ◽  
User Interface ◽  
Systems Biology ◽  
Graphical User Interface ◽  
Software Package ◽  
Input Method ◽  
Biochemical Systems ◽  
Kinetics And Dynamics ◽  
Systems Biology Markup Language ◽  
Biological Simulation

Modeling biochemical systems can provide insights into behaviors that are difficult to observe or understand. It requires software, programming, and understanding of the system to build a model and study it. Softwares exist for such systems biology modeling, but most support only certain types of modeling tasks. Desirable features including ease in preparing input, symbolic or analytical computation, parameter estimation, graphical user interface, and systems biology markup language (SBML) support are not seen concurrently in one software package. In this study, we developed a python-based software that supports these features, with both deterministic and stochastic propagations. The software can be used by graphical user interface, command line, or as a python import. We also developed a semi-programmable and intuitively easy topology input method for the biochemical reactions. We tested the software with semantic and stochastic SBML test cases. Tests on symbolic solution and parameter estimation were also included. The software we developed is reliable, well performing, convenient to use, and compliant with most of the SBML tests. So far it is the only systems biology software that supports symbolic, deterministic, and stochastic modeling in one package that also features parameter estimation and SBML support. This work offers a comprehensive set of tools and allows for better availability and accessibility for studying kinetics and dynamics in biochemical systems.

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.

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