PipelineDog: a simple and flexible graphic pipeline construction and maintenance tool
Anbo Zhou1, Yeting Zhang1, Yazhou Sun2,3
1Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
Bioinformatics (Oxford, England)
|November 30, 2017
Summary
PipelineDog simplifies bioinformatics analysis by providing a user-friendly, web-based tool for rapid pipeline creation and management. This solution enhances reproducibility and accountability in research.
Area of Science:
- Bioinformatics
- Computational Biology
- Scientific Workflow Management
Background:
- Ad hoc analysis pipelines are crucial in bioinformatics research for prototyping.
- Existing pipeline management systems are often too complex for rapid prototyping and learning.
- A need exists for a lightweight, user-friendly, and flexible pipeline solution.
Purpose of the Study:
- To develop PipelineDog, a novel web-based integrated development environment for constructing and maintaining bioinformatics pipelines.
- To offer a user-friendly and flexible alternative to complex existing workflow engines.
- To enhance code reuse, sharing, reproducibility, and accountability in bioinformatics analyses.
Main Methods:
- Developed PipelineDog as a web-based integrated development environment (IDE).
- Implemented a modern web graphical user interface (GUI).
- Designed an easy-to-read/write script system and integrated an online repository.
Main Results:
- PipelineDog provides cross-platform compatibility, project management, code formatting, and error checking.
- The tool features an online repository for sharing pipelines, promoting reproducibility.
- Requires no software installation for most users, facilitating rapid adoption.
Conclusions:
- PipelineDog offers a lightweight, user-friendly, and flexible solution for rapid pipeline creation and management in bioinformatics.
- The web application enhances collaboration and reproducibility through its integrated online repository.
- Facilitates easier learning and adoption of pipeline concepts for researchers.
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