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. 2016;4(1):e44.
doi: 10.5334/jors.35. Epub 2016 Nov 29.

Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

Michael R Crusoe  1 , C Titus Brown  2
Affiliations

Walking the Talk: Adopting and Adapting Sustainable Scientific Software Development processes in a Small Biology Lab

Michael R Crusoe et al. J Open Res Softw. 2016.

Abstract

The khmer software project provides both research and production functionality for largescale nucleic-acid sequence analysis. The software implements several novel data structures and algorithms that perform data pre-fltering for common bioinformatics tasks, including sequence mapping and de novo assembly. Development is driven by a small lab with one full-time developer (MRC), as well as several graduate students and a professor (CTB) who contribute regularly to research features. Here we describe our efforts to bring better design, testing, and more open development to the khmer software project as of version 1.1. The khmer software is developed openly at http://github.com/dib-lab/khmer/.

Keywords: WSSSPE; k-mer.

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References

    1. Brown CT. BIGDATA: Small: DA: DCM: Low-memory streaming prefilters for biological sequencing data. 2012 http://www.ged.msu.edu/downloads/2012-bigdata-nsf.pdf.
    1. Brown CT, Howe A, Zhang Q, Pyrkosz A, Brom TH. A reference-free algorithm for computational normalization of shotgun sequencing data. review at PLoS One. 2012 Jul; Preprint at http://arxiv.org/abs/1203.4802.
    1. Chacon S. Github flow. 2011 http://scottchacon.com/2011/08/31/github-flow.html.
    1. Crusoe MR. Criteria-based assessment of the khmer suite. 2013 figshare. DOI: https://dx.doi.org/10.6084/m9.figshare.1558321.v1. - DOI
    1. Crusoe MR. Criteria-based assessment of the khmer suite v1.0. 2014 figshare. DOI: https://dx.doi.org/10.6084/m9.figshare.1558322.v2. - DOI

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