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

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Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software.

Peter Georgeson^1,2, Anna Syme^1,3, Clare Sloggett¹

¹Melbourne Bioinformatics, The University of Melbourne, 187 Grattan Street, Carlton, Victoria, Australia 3053.

|September 24, 2019

Summary

This summary is machine-generated.

Bioinformatics software development is challenging for beginners. Bionitio is a new tool that automates project setup, promoting best practices and improving software quality for researchers.

Keywords:

best practices bioinformatics software development training

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Area of Science:

Bioinformatics
Computational Biology
Software Engineering

Background:

Bioinformatics software is often developed ad hoc, leading to poor quality, limited scalability, and reproducibility issues.
Beginners face a high barrier to entry in bioinformatics software development, hindering the adoption of best practices.
Even experienced developers may not consistently follow best practices, exacerbating software quality problems.

Purpose of the Study:

To automate the creation of new bioinformatics software projects.
To ensure new projects adhere to recommended software development best practices from the outset.
To provide a learning aid for bioinformatics programmers and a template for new tools.

Main Methods:

Development of Bionitio, a command-line tool.
Automation of project scaffolding in 12 programming languages.
Inclusion of features such as argument parsing, error handling, testing, documentation, and containerization.

Main Results:

Bionitio generates functional, well-structured bioinformatics software projects with a single command.
The generated projects serve as working examples and templates for new tool development.
Key software engineering best practices are automatically incorporated into new projects.

Conclusions:

Bionitio lowers the barrier to entry for bioinformatics software development.
It facilitates the adoption of good programming practices, leading to higher-quality tools.
The tool benefits both developers and users through improved usability and consistency.