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Related Experiment Video

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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From command-line bioinformatics to bioGUI.

Markus Joppich1, Ralf Zimmer1

  • 1Department of Informatics, Ludwig-Maximilians-Universität München, Munich, Germany.

Peerj
|November 28, 2019
PubMed
Summary
This summary is machine-generated.

The bioGUI framework simplifies bioinformatics tool usage by providing graphical interfaces, making command-line applications accessible to more scientists, including Windows users. This enhances interdisciplinary research by overcoming installation and usability barriers.

Keywords:
BioinformaticsBioinformatics toolCommand-line InterfaceCross-platformGraphical user interfaceOpen-sourceSoftware accessibilityWindowsWindows subsystem for Linux

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Software Development

Background:

  • Bioinformatics tools are crucial for interdisciplinary research but often require command-line (CL) usage, posing a barrier for many scientists.
  • Most bioinformatics methods are exclusively available via CL interfaces, limiting their accessibility and adoption.
  • Scientists, particularly those using Microsoft Windows, face challenges installing and utilizing UNIX-based bioinformatics applications.

Purpose of the Study:

  • To develop a framework (bioGUI) that simplifies the installation and use of command-line bioinformatics applications.
  • To bridge the accessibility gap for bioinformatics tools, enabling wider adoption across scientific disciplines.
  • To provide a user-friendly interface for bioinformatics software, reducing the technical hurdles for researchers.

Main Methods:

  • Development of the bioGUI framework featuring install modules and templates.
  • Integration of support for Windows Subsystem for Linux (WSL) to enable use on Windows systems.
  • Creation of a repository for downloading, installing, and executing bioinformatics tools through a graphical user interface (GUI).

Main Results:

  • The bioGUI framework successfully enables the installation and use of CL bioinformatics tools, even on Windows.
  • bioGUI templates facilitate easy creation, making the framework developer-friendly.
  • Users can download, install, and utilize bioinformatics tools with minimal effort via the bioGUI repository.

Conclusions:

  • The bioGUI framework significantly enhances the accessibility of command-line bioinformatics tools for a broader scientific audience.
  • By offering a GUI and Windows compatibility, bioGUI promotes more effective interdisciplinary collaboration and research.
  • The framework lowers the barrier to entry for using powerful bioinformatics methods, fostering wider scientific application.