Journal article

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

Peter Georgeson, Anna Syme, Clare Sloggett, Jessica Chung, Harriet Dashnow, Michael Milton, Andrew Lonsdale, David Powell, Torsten Seemann, Bernard Pope

GIGASCIENCE | OXFORD UNIV PRESS | Published : 2019

Abstract

BACKGROUND: Bioinformatics software tools are often created ad hoc, frequently by people without extensive training in software development. In particular, for beginners, the barrier to entry in bioinformatics software development is high, especially if they want to adopt good programming practices. Even experienced developers do not always follow best practices. This results in the proliferation of poorer-quality bioinformatics software, leading to limited scalability and inefficient use of resources; lack of reproducibility, usability, adaptability, and interoperability; and erroneous or inaccurate results. FINDINGS: We have developed Bionitio, a tool that automates the process of starting..

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Grants

Funding Acknowledgements

B.P. is supported by a Victorian Health and Medical Research Fellowship. H.D. is supported by an Australian Government Research Training Program (RTP) Scholarship, an Australian Genomics Health Alliance top up scholarship, and a Murdoch Children's Research Institute top up scholarship. A.L. is supported by an Australian Government Research Training Program (RTP) Scholarship. P.G. is supported by an Australian Government Research Training Program (RTP) scholarship.