Journal:From command-line bioinformatics to bioGUI
| Full article title | From command-line bioinformatics to bioGUI |
|---|---|
| Journal | PeerJ |
| Author(s) | Joppich, Markus; Zimmer, Ralf |
| Author affiliation(s) | Ludwig-Maximilians-Universität München |
| Primary contact | Email: joppich at bio dot ifi dot lmu dot de |
| Editors | Gillespie, Joseph |
| Year published | 2019 |
| Volume and issue | 7 |
| Page(s) | e8111 |
| DOI | 10.7717/peerj.8111 |
| ISSN | 2167-8359 |
| Distribution license | Creative Commons Attribution 4.0 International |
| Website | https://peerj.com/articles/8111/ |
| Download | https://peerj.com/articles/8111.pdf (PDF) |
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This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
Abstract
Bioinformatics is a highly interdisciplinary field providing informatics applications for scientists from many disciplines. Installing and starting applications on the command line (CL) is inconvenient and 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 more readily available to scientists, yielding a positive step toward more effective interdisciplinary work. With our bioGUI framework, we address two main problems of using CL bioinformatics applications. First, many tools work on UNIX-based systems only, while many scientists use Microsoft Windows. Second, scientists refrain from using CL tools, which, despite their reservations, 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.
Introduction
Supplemental information
- DOI 10.7717/peerj.8111/supp-1 - Survey questions on command-line tools and bioGUI: This is the original survey used to assess problems with current bioinformatics applications. (PDF)
- DOI 10.7717/peerj.8111/supp-2 - Answers on the survey on command-line tools and bioGUI: Each column represents a single participant. Questions are in rows. (XLXS)
Acknowledgements
We thank Luisa F. Jimenez-Soto and Gergely Csaba for their valuable input as well as for reviewing the manuscript. We thank the participants in our survey for their time. We thank the reviewers for their constructive feedback.
Authors’ contributions
Markus Joppich conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft. Ralf Zimmer conceived and designed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.
Funding
This work was supported by the Deutsche Forschungsgemeinschaft (Collaborative Research Centre SFB 1123-2/Z2). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Data availability
The bioGUI documentation is available here. In order to set up Windows Subsystem for Linux (required for using bioGUI on Windows), follow the steps documented here. bioGUI is open-source software. Releases and code are available on the GitHub project page. Additional software (cwl2biogui) is available here.
Competing interests
The authors declare that they have no competing interests.
References
Notes
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. We also added PMCID and DOI when they were missing from the original reference. The original article lists references alphabetically, but this version—by design—lists them in order of appearance.
