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Related Experiment Video

Updated: May 1, 2026

The Replica Set Method: A High-throughput Approach to Quantitatively Measure Caenorhabditis elegans Lifespan

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Published on: June 29, 2018

Bashing irreproducibility with shournal.

Tycho Kirchner¹, Konstantin Riege¹, Steve Hoffmann²

¹Computational Biology Group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.

Scientific Reports

|February 28, 2024

Summary

We developed shournal, a tool that automatically records shell commands and file events for computational scientists. This enables easy tracking of data provenance and generation for reproducible research.

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Last Updated: May 1, 2026

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Area of Science:

Computational Science
Bioinformatics
Data Science

Background:

The Linux shell is crucial for computational scientists.
Manual documentation of shell command usage is time-consuming and prone to errors.
Existing tools for command logging have integration or overhead issues.

Purpose of the Study:

Introduce shournal, a novel tool for automatic shell command and file event recording.
Enable detailed tracking of data provenance and processing steps.
Facilitate the generation of comprehensive project reports.

Main Methods:

shournal integrates tightly with the Linux shell.
It automatically records shell commands and associated file system events.
Data is retrieved directly from the Linux kernel for low-overhead monitoring of process trees.

Main Results:

shournal provides a reliable method to trace how files were generated and processed.
It allows for the creation of detailed, automated reports for entire project directories.
The tool operates with low overhead by leveraging kernel-level data.

Conclusions:

shournal significantly enhances reproducibility in computational workflows.
It offers a seamless and efficient solution for documenting shell-based data analysis.
This tool empowers scientists to manage and report on complex projects effectively.