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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

How to test bioinformatics software?

Amir Hossein Kamali^1,2, Eleni Giannoulatou^1,3, Tsong Yueh Chen⁴

¹Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

Biophysical Reviews

|May 17, 2017

Summary

This summary is machine-generated.

This study reviews software testing methods for bioinformatics, highlighting challenges in verifying computational results and generating test cases. It explores adapting software testing for systems biology and genomic medicine.

Keywords:

Automated testing Bioinformatics Cloud-based testing Quality assurance Software testing

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Area of Science:

Bioinformatics
Computational Biology
Biophysics

Background:

Bioinformatics applies computational, mathematical, and statistical methods to biological and medical problems.
Bioinformatics tools are crucial for computational simulation and large-scale data analysis across biophysics.
Ensuring the reliability of bioinformatics software requires rigorous testing, which is often challenging due to output verification difficulties.

Purpose of the Study:

To review fundamental concepts and advanced techniques in software testing.
To discuss the adaptation and application of software testing methodologies within bioinformatics.
To provide specific examples from systems biology and genomic medicine.

Main Methods:

Systematic review of software testing principles.
Analysis of existing literature on bioinformatics software validation.
Case study examples from systems biology and genomic medicine.

Main Results:

Identified significant challenges in systematically testing bioinformatics programs.
Highlighted the critical need for robust verification and validation of scientific software.
Demonstrated the applicability of software testing methodologies in specialized bioinformatics fields.

Conclusions:

Software testing is essential for reliable bioinformatics research.
Adapting software testing practices is crucial for advancing systems biology and genomic medicine.
Further research is needed to develop specialized testing strategies for bioinformatics tools.