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Updated: Oct 1, 2025

Using the Open-Source MALDI TOF-MS IDBac Pipeline for Analysis of Microbial Protein and Specialized Metabolite Data

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Software testing in microbial bioinformatics: a call to action.

Boas C L van der Putten^1,2, C I Mendes³, Brooke M Talbot⁴

¹Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, the Netherlands.

Microbial Genomics

|March 8, 2022

Summary

This summary is machine-generated.

Implementing software testing in microbial bioinformatics is crucial for research reproducibility and sustainability. This study offers seven practical recommendations and resources to help researchers adopt these essential validation practices.

Keywords:

computational biology continuous integration software testing

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Area of Science:

Bioinformatics
Computational Biology
Microbial Genomics

Background:

Computational algorithms are vital in scientific research, with community efforts to improve code development and distribution standards.
Despite progress, software sustainability and reproducibility remain significant challenges due to infrequent adoption of software testing.
Validation through rigorous software testing is not yet a widespread practice in scientific research.

Purpose of the Study:

To provide actionable recommendations for implementing software testing in microbial bioinformatics research.
To address the ongoing issues of sustainability and reproducibility in computational research.
To guide researchers in adopting best practices for code validation.

Main Methods:

Development of seven key recommendations based on practical experience.
Leveraging insights from a collaborative hackathon preceding the American Society for Microbiology Next Generation Sequencing (ASM NGS) 2020 conference.
Creation of a publicly accessible repository with testing examples and guidelines.

Main Results:

Seven concrete recommendations for integrating software testing into microbial bioinformatics workflows.
A curated repository offering practical examples and guidance for software testing implementation.
Enhanced understanding of the importance and methods for ensuring code quality and reliability.

Conclusions:

Software testing is essential for ensuring the sustainability and reproducibility of microbial bioinformatics research.
The presented recommendations and resources can facilitate the adoption of software testing practices among researchers.
Proactive implementation of software testing will improve the overall quality and reliability of computational research in microbiology.