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Related Experiment Video

Updated: Jan 12, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

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Nextpie: a web-based reporting tool and database for reproducible nextflow pipelines.

Bishwa Ghimire^1,2,3, Nicholas Booth^3,4, Tapio Lönnberg^3,4

¹Medicity Research Laboratory, University of Turku, Turku, 20520, Finland.

Bioinformatics Advances

|November 3, 2025

Summary

This summary is machine-generated.

Nextpie is a web-based tool that aggregates and visualizes Nextflow pipeline resource usage data from scattered log files. This enhances the optimization and reproducibility of complex genomic data analyses.

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Area of Science:

Bioinformatics
Computational Biology
Genomic Data Analysis

Background:

High-throughput genomic data analysis relies on complex bioinformatic pipelines.
Workflow management tools like Nextflow automate these pipelines.
Managing and parsing scattered Nextflow log files for resource usage is cumbersome.

Purpose of the Study:

To develop a centralized solution for managing Nextflow pipeline resource usage data.
To facilitate optimization and improve reproducibility of Nextflow-based analyses.
To provide an accessible overview of pipeline performance.

Main Methods:

Developed Nextpie, a web-based tool with a relational database.
Integrated Nextflow log data aggregation into the database.
Implemented reporting and interactive visualization features for resource usage.

Main Results:

Nextpie centralizes comprehensive resource usage information for Nextflow pipelines.
The tool accelerates data analysis and interactive visualization of pipeline performance.
Provides an easily comprehensible overview of pipeline resource utilization.

Conclusions:

Nextpie simplifies the management of Nextflow pipeline resource data.
The tool aids in optimizing pipeline performance and enhancing reproducibility.
Nextpie is available on GitHub with documentation and example data.